Starting phenix.real_space_refine (version: dev) on Thu Jun 2 03:19:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9c_33071/06_2022/7x9c_33071_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "R ASP 36": "OD1" <-> "OD2" Residue "R ARG 139": "NH1" <-> "NH2" Residue "R PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 211": "NH1" <-> "NH2" Residue "R PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 236": "NH1" <-> "NH2" Residue "R ARG 239": "NH1" <-> "NH2" Residue "R ARG 243": "NH1" <-> "NH2" Residue "R PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 33": "NH1" <-> "NH2" Residue "P ARG 35": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4617/modules/chem_data/mon_lib" Total number of atoms: 7219 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2358 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1691 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2503 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 383 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 284 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 30} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 4.65, per 1000 atoms: 0.64 Number of scatterers: 7219 At special positions: 0 Unit cell: (123.31, 119.13, 84.645, 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 62 16.00 O 1302 8.00 N 1240 7.00 C 4615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 983.1 milliseconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 42.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'R' and resid 39 through 67 Processing helix chain 'R' and resid 75 through 102 Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 111 through 143 Processing helix chain 'R' and resid 153 through 176 Proline residue: R 173 - end of helix removed outlier: 3.612A pdb=" N ALA R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 222 removed outlier: 3.898A pdb=" N ILE R 213 " --> pdb=" O HIS R 209 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR R 214 " --> pdb=" O HIS R 210 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 247 removed outlier: 3.580A pdb=" N VAL R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 290 removed outlier: 4.099A pdb=" N TRP R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU R 279 " --> pdb=" O ALA R 275 " (cutoff:3.500A) Proline residue: R 280 - end of helix Processing helix chain 'R' and resid 300 through 322 removed outlier: 4.492A pdb=" N SER R 314 " --> pdb=" O LEU R 310 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THR R 315 " --> pdb=" O ALA R 311 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS R 316 " --> pdb=" O MET R 312 " (cutoff:3.500A) Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 327 through 340 removed outlier: 3.671A pdb=" N LYS R 330 " --> pdb=" O THR R 327 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LYS R 331 " --> pdb=" O ASN R 328 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS R 340 " --> pdb=" O VAL R 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.209A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.592A pdb=" N ILE A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.515A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.583A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.653A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.812A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'P' and resid 14 through 31 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.865A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.458A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.890A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.824A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 191 removed outlier: 7.105A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 232 removed outlier: 7.096A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 308 Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.008A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 3.03 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: 1161 1.31 - 1.43: 1987 1.43 - 1.56: 4130 1.56 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 7366 Sorted by residual: bond pdb=" CA LYS R 190 " pdb=" C LYS R 190 " ideal model delta sigma weight residual 1.522 1.583 -0.060 1.20e-02 6.94e+03 2.54e+01 bond pdb=" N LEU R 192 " pdb=" CA LEU R 192 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.26e-02 6.30e+03 7.20e+00 bond pdb=" N GLN R 121 " pdb=" CA GLN R 121 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.28e+00 bond pdb=" C ALA P 1 " pdb=" N PRO P 2 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.11e-02 8.12e+03 3.74e+00 bond pdb=" N LYS R 190 " pdb=" CA LYS R 190 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.95e-02 2.63e+03 1.27e+00 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.05: 169 107.05 - 113.78: 4226 113.78 - 120.51: 2875 120.51 - 127.24: 2663 127.24 - 133.97: 82 Bond angle restraints: 10015 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 109.46 4.01 1.01e+00 9.80e-01 1.58e+01 angle pdb=" C GLN R 121 " pdb=" CA GLN R 121 " pdb=" CB GLN R 121 " ideal model delta sigma weight residual 110.85 115.85 -5.00 1.70e+00 3.46e-01 8.65e+00 angle pdb=" C ILE R 144 " pdb=" N ASN R 145 " pdb=" CA ASN R 145 " ideal model delta sigma weight residual 121.80 128.47 -6.67 2.44e+00 1.68e-01 7.48e+00 angle pdb=" CA LEU R 172 " pdb=" CB LEU R 172 " pdb=" CG LEU R 172 " ideal model delta sigma weight residual 116.30 124.69 -8.39 3.50e+00 8.16e-02 5.75e+00 angle pdb=" CA GLN R 121 " pdb=" C GLN R 121 " pdb=" O GLN R 121 " ideal model delta sigma weight residual 120.42 117.91 2.51 1.06e+00 8.90e-01 5.61e+00 ... (remaining 10010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 4096 15.95 - 31.89: 211 31.89 - 47.84: 46 47.84 - 63.78: 4 63.78 - 79.73: 1 Dihedral angle restraints: 4358 sinusoidal: 1596 harmonic: 2762 Sorted by residual: dihedral pdb=" CA TYR B 85 " pdb=" C TYR B 85 " pdb=" N THR B 86 " pdb=" CA THR B 86 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 dihedral pdb=" C GLN R 121 " pdb=" N GLN R 121 " pdb=" CA GLN R 121 " pdb=" CB GLN R 121 " ideal model delta harmonic sigma weight residual -122.60 -130.21 7.61 0 2.50e+00 1.60e-01 9.27e+00 dihedral pdb=" CB GLU R 181 " pdb=" CG GLU R 181 " pdb=" CD GLU R 181 " pdb=" OE1 GLU R 181 " ideal model delta sinusoidal sigma weight residual 0.00 79.73 -79.73 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 4355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 848 0.037 - 0.073: 257 0.073 - 0.110: 61 0.110 - 0.147: 15 0.147 - 0.183: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA GLN R 121 " pdb=" N GLN R 121 " pdb=" C GLN R 121 " pdb=" CB GLN R 121 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA HIS R 188 " pdb=" N HIS R 188 " pdb=" C HIS R 188 " pdb=" CB HIS R 188 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1179 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 225 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO R 226 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 226 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 226 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 172 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO R 173 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 173 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO B 194 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.015 5.00e-02 4.00e+02 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 736 2.75 - 3.28: 7412 3.28 - 3.82: 12400 3.82 - 4.36: 14491 4.36 - 4.90: 24912 Nonbonded interactions: 59951 Sorted by model distance: nonbonded pdb=" OH TYR R 48 " pdb=" O LEU R 305 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.210 2.440 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.272 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" OE1 GLU A 298 " model vdw 2.298 2.440 nonbonded pdb=" OG1 THR R 52 " pdb=" OE1 GLN R 95 " model vdw 2.329 2.440 ... (remaining 59946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 4615 2.51 5 N 1240 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 4.190 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 22.900 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 7366 Z= 0.135 Angle : 0.506 8.390 10015 Z= 0.286 Chirality : 0.038 0.183 1182 Planarity : 0.003 0.031 1260 Dihedral : 10.162 79.725 2557 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.24), residues: 928 helix: -1.03 (0.24), residues: 392 sheet: -1.64 (0.36), residues: 183 loop : -2.20 (0.28), residues: 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.822 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.8142 time to fit residues: 140.5040 Evaluate side-chains 111 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.0020 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 306 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7366 Z= 0.162 Angle : 0.540 8.659 10015 Z= 0.271 Chirality : 0.039 0.135 1182 Planarity : 0.003 0.028 1260 Dihedral : 3.455 15.224 1007 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.66 % 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: -1.36 (0.26), residues: 928 helix: 0.13 (0.26), residues: 404 sheet: -1.41 (0.38), residues: 163 loop : -1.76 (0.29), residues: 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.979 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 139 average time/residue: 0.8265 time to fit residues: 124.1186 Evaluate side-chains 129 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.0908 time to fit residues: 1.4422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 7366 Z= 0.177 Angle : 0.527 9.032 10015 Z= 0.266 Chirality : 0.040 0.130 1182 Planarity : 0.003 0.030 1260 Dihedral : 3.549 16.299 1007 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.27), residues: 928 helix: 0.67 (0.26), residues: 404 sheet: -1.34 (0.37), residues: 168 loop : -1.48 (0.30), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.784 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 136 average time/residue: 0.8679 time to fit residues: 127.2736 Evaluate side-chains 126 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.3226 time to fit residues: 2.7495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 88 optimal weight: 0.0070 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 185 HIS R 222 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7366 Z= 0.172 Angle : 0.543 9.472 10015 Z= 0.270 Chirality : 0.040 0.126 1182 Planarity : 0.003 0.032 1260 Dihedral : 3.605 14.059 1007 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 928 helix: 0.84 (0.26), residues: 406 sheet: -1.11 (0.37), residues: 165 loop : -1.40 (0.31), residues: 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.824 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 129 average time/residue: 0.8584 time to fit residues: 119.2793 Evaluate side-chains 123 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.3034 time to fit residues: 3.0075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 185 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 7366 Z= 0.219 Angle : 0.576 10.054 10015 Z= 0.288 Chirality : 0.040 0.126 1182 Planarity : 0.004 0.078 1260 Dihedral : 3.781 14.363 1007 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.27), residues: 928 helix: 0.95 (0.26), residues: 408 sheet: -1.04 (0.37), residues: 157 loop : -1.46 (0.30), residues: 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.802 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 131 average time/residue: 0.8823 time to fit residues: 124.2113 Evaluate side-chains 120 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0698 time to fit residues: 1.2726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 222 GLN R 264 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 7366 Z= 0.218 Angle : 0.571 10.329 10015 Z= 0.288 Chirality : 0.040 0.126 1182 Planarity : 0.004 0.072 1260 Dihedral : 3.812 15.011 1007 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 3.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.27), residues: 928 helix: 1.05 (0.27), residues: 403 sheet: -1.15 (0.38), residues: 152 loop : -1.37 (0.30), residues: 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 0.849 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 140 average time/residue: 0.8592 time to fit residues: 129.3657 Evaluate side-chains 129 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.0989 time to fit residues: 1.7839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 55 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 7366 Z= 0.187 Angle : 0.575 10.621 10015 Z= 0.287 Chirality : 0.040 0.141 1182 Planarity : 0.004 0.074 1260 Dihedral : 3.758 14.809 1007 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 3.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.27), residues: 928 helix: 1.18 (0.27), residues: 405 sheet: -1.10 (0.38), residues: 152 loop : -1.38 (0.30), residues: 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 0.822 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 139 average time/residue: 0.8241 time to fit residues: 123.4747 Evaluate side-chains 125 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0646 time to fit residues: 1.3261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 222 GLN R 264 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.116 7366 Z= 0.230 Angle : 0.598 10.829 10015 Z= 0.299 Chirality : 0.041 0.153 1182 Planarity : 0.004 0.074 1260 Dihedral : 3.897 14.777 1007 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 928 helix: 1.15 (0.27), residues: 400 sheet: -1.28 (0.38), residues: 156 loop : -1.33 (0.30), residues: 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.807 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.9158 time to fit residues: 131.0124 Evaluate side-chains 128 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 2 average time/residue: 0.6269 time to fit residues: 2.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS R 210 HIS R 222 GLN R 264 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 7366 Z= 0.234 Angle : 0.611 13.111 10015 Z= 0.304 Chirality : 0.041 0.163 1182 Planarity : 0.004 0.056 1260 Dihedral : 3.985 15.133 1007 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 928 helix: 1.08 (0.26), residues: 405 sheet: -1.19 (0.37), residues: 154 loop : -1.30 (0.30), residues: 369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.724 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 134 average time/residue: 0.8823 time to fit residues: 127.0059 Evaluate side-chains 127 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 4 average time/residue: 0.3325 time to fit residues: 2.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 GLN R 145 ASN R 210 HIS R 222 GLN R 264 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 7366 Z= 0.240 Angle : 0.639 13.595 10015 Z= 0.316 Chirality : 0.041 0.152 1182 Planarity : 0.004 0.050 1260 Dihedral : 4.106 15.734 1007 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.27), residues: 928 helix: 1.02 (0.26), residues: 399 sheet: -1.13 (0.37), residues: 161 loop : -1.28 (0.30), residues: 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.849 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 0.9164 time to fit residues: 128.6549 Evaluate side-chains 124 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 1 average time/residue: 0.1073 time to fit residues: 1.3197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS R 210 HIS R 222 GLN R 264 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126566 restraints weight = 8107.310| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.45 r_work: 0.3524 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work: 0.3486 rms_B_bonded: 2.29 restraints_weight: 0.1250 r_work: 0.3465 rms_B_bonded: 2.45 restraints_weight: 0.0625 r_work: 0.3442 rms_B_bonded: 2.67 restraints_weight: 0.0312 r_work: 0.3417 rms_B_bonded: 2.96 restraints_weight: 0.0156 r_work: 0.3389 rms_B_bonded: 3.33 restraints_weight: 0.0078 r_work: 0.3358 rms_B_bonded: 3.78 restraints_weight: 0.0039 r_work: 0.3323 rms_B_bonded: 4.34 restraints_weight: 0.0020 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 7366 Z= 0.236 Angle : 0.659 12.420 10015 Z= 0.325 Chirality : 0.041 0.155 1182 Planarity : 0.004 0.046 1260 Dihedral : 4.133 17.697 1007 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.26 % 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: -0.36 (0.27), residues: 928 helix: 1.05 (0.26), residues: 400 sheet: -1.11 (0.37), residues: 158 loop : -1.22 (0.30), residues: 370 =============================================================================== Job complete usr+sys time: 2624.13 seconds wall clock time: 47 minutes 25.88 seconds (2845.88 seconds total)