Starting phenix.real_space_refine (version: dev) on Wed Dec 14 01:56:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2022/7una_26618_trim_updated.pdb" } resolution = 4.0 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= 0.002 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 "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ASP 203": "OD1" <-> "OD2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H GLU 180": "OE1" <-> "OE2" Residue "H ASP 194": "OD1" <-> "OD2" Residue "H PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 295": "OE1" <-> "OE2" Residue "H TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18414 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2286 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain breaks: 4 Chain: "B" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2266 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "C" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2306 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 4 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2298 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 3 Chain: "E" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2249 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 4 Chain: "F" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2277 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "G" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2271 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain breaks: 4 Chain: "H" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2281 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1' 4BW A 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW A 401 " occ=0.47 residue: pdb=" C1' 4BW C 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW C 401 " occ=0.47 residue: pdb=" C1' 4BW F 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW F 401 " occ=0.47 residue: pdb=" C1' 4BW H 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW H 401 " occ=0.47 Time building chain proxies: 10.80, per 1000 atoms: 0.59 Number of scatterers: 18414 At special positions: 0 Unit cell: (134.2, 126.5, 171.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 8 15.00 O 1724 8.00 N 1521 7.00 C 5918 6.00 H 9203 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 16 sheets defined 48.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 155 through 176 Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 286 through 307 Processing helix chain 'B' and resid 154 through 176 Processing helix chain 'B' and resid 207 through 217 Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.740A pdb=" N TYR B 274 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 307 Processing helix chain 'C' and resid 155 through 176 Processing helix chain 'C' and resid 207 through 217 Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 285 through 307 Processing helix chain 'D' and resid 154 through 176 Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 286 through 307 Processing helix chain 'E' and resid 153 through 176 Processing helix chain 'E' and resid 207 through 217 Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 286 through 307 Processing helix chain 'F' and resid 154 through 176 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 262 through 273 Processing helix chain 'F' and resid 285 through 307 Processing helix chain 'G' and resid 153 through 176 Processing helix chain 'G' and resid 207 through 217 Processing helix chain 'G' and resid 262 through 273 Processing helix chain 'G' and resid 286 through 307 removed outlier: 3.861A pdb=" N ARG G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 176 Processing helix chain 'H' and resid 207 through 217 removed outlier: 3.593A pdb=" N TYR H 217 " --> pdb=" O TYR H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 274 Processing helix chain 'H' and resid 286 through 306 Processing sheet with id= A, first strand: chain 'A' and resid 257 through 260 Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 Processing sheet with id= C, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= D, first strand: chain 'B' and resid 220 through 222 Processing sheet with id= E, first strand: chain 'C' and resid 255 through 260 Processing sheet with id= F, first strand: chain 'C' and resid 220 through 222 Processing sheet with id= G, first strand: chain 'D' and resid 257 through 259 Processing sheet with id= H, first strand: chain 'D' and resid 220 through 222 Processing sheet with id= I, first strand: chain 'E' and resid 257 through 260 removed outlier: 3.703A pdb=" N ASP E 259 " --> pdb=" O ASP E 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 220 through 222 Processing sheet with id= K, first strand: chain 'F' and resid 315 through 318 removed outlier: 6.082A pdb=" N VAL F 193 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 318 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL F 195 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 220 through 222 Processing sheet with id= M, first strand: chain 'G' and resid 220 through 222 Processing sheet with id= N, first strand: chain 'G' and resid 193 through 198 Processing sheet with id= O, first strand: chain 'H' and resid 257 through 259 Processing sheet with id= P, first strand: chain 'H' and resid 220 through 222 497 hydrogen bonds defined for protein. 1221 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: 12.75 Time building geometry restraints manager: 18.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9179 1.03 - 1.23: 27 1.23 - 1.42: 3844 1.42 - 1.61: 5454 1.61 - 1.81: 80 Bond restraints: 18584 Sorted by residual: bond pdb=" C4' 4BW C 401 " pdb=" O4' 4BW C 401 " ideal model delta sigma weight residual 1.299 1.656 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CBI 4BW F 401 " pdb=" CBO 4BW F 401 " ideal model delta sigma weight residual 1.297 1.653 -0.356 2.00e-02 2.50e+03 3.17e+02 bond pdb=" CBI 4BW C 401 " pdb=" CBO 4BW C 401 " ideal model delta sigma weight residual 1.297 1.653 -0.356 2.00e-02 2.50e+03 3.17e+02 bond pdb=" CBI 4BW H 401 " pdb=" CBO 4BW H 401 " ideal model delta sigma weight residual 1.297 1.652 -0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" CBI 4BW A 401 " pdb=" CBO 4BW A 401 " ideal model delta sigma weight residual 1.297 1.651 -0.354 2.00e-02 2.50e+03 3.13e+02 ... (remaining 18579 not shown) Histogram of bond angle deviations from ideal: 100.13 - 107.17: 470 107.17 - 114.21: 22829 114.21 - 121.25: 6900 121.25 - 128.29: 3339 128.29 - 135.34: 51 Bond angle restraints: 33589 Sorted by residual: angle pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" CD PRO A 237 " ideal model delta sigma weight residual 112.00 103.69 8.31 1.40e+00 5.10e-01 3.52e+01 angle pdb=" O3' 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAV 4BW F 401 " ideal model delta sigma weight residual 99.67 113.57 -13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O3' 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" OAV 4BW H 401 " ideal model delta sigma weight residual 99.67 113.38 -13.71 3.00e+00 1.11e-01 2.09e+01 angle pdb=" O3' 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAV 4BW C 401 " ideal model delta sigma weight residual 99.67 113.33 -13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" O3' 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAV 4BW A 401 " ideal model delta sigma weight residual 99.67 113.23 -13.56 3.00e+00 1.11e-01 2.04e+01 ... (remaining 33584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.79: 7098 25.79 - 51.59: 269 51.59 - 77.38: 17 77.38 - 103.17: 6 103.17 - 128.97: 4 Dihedral angle restraints: 7394 sinusoidal: 3483 harmonic: 3911 Sorted by residual: dihedral pdb=" CA SER C 190 " pdb=" C SER C 190 " pdb=" N PHE C 191 " pdb=" CA PHE C 191 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CAN 4BW A 401 " pdb=" OAV 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" O3' 4BW A 401 " ideal model delta sinusoidal sigma weight residual 163.79 34.82 128.97 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" CAN 4BW H 401 " pdb=" OAV 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" O3' 4BW H 401 " ideal model delta sinusoidal sigma weight residual 163.79 35.89 127.90 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 7391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1218 0.047 - 0.095: 171 0.095 - 0.142: 82 0.142 - 0.190: 12 0.190 - 0.237: 4 Chirality restraints: 1487 Sorted by residual: chirality pdb=" C2' 4BW C 401 " pdb=" C1' 4BW C 401 " pdb=" C3' 4BW C 401 " pdb=" O2' 4BW C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2' 4BW H 401 " pdb=" C1' 4BW H 401 " pdb=" C3' 4BW H 401 " pdb=" O2' 4BW H 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' 4BW A 401 " pdb=" C1' 4BW A 401 " pdb=" C3' 4BW A 401 " pdb=" O2' 4BW A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1484 not shown) Planarity restraints: 2581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 236 " 0.077 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A 237 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 163 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C ASN A 163 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 163 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 164 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 163 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ASN C 163 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN C 163 " 0.017 2.00e-02 2.50e+03 pdb=" N SER C 164 " 0.015 2.00e-02 2.50e+03 ... (remaining 2578 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1128 2.19 - 2.79: 37776 2.79 - 3.40: 49819 3.40 - 4.00: 62060 4.00 - 4.60: 96007 Nonbonded interactions: 246790 Sorted by model distance: nonbonded pdb=" O SER F 270 " pdb=" H TYR F 274 " model vdw 1.591 1.850 nonbonded pdb=" HG1 THR H 263 " pdb=" O3' 4BW H 401 " model vdw 1.594 1.850 nonbonded pdb=" O GLU F 172 " pdb=" HG SER F 176 " model vdw 1.596 1.850 nonbonded pdb=" OD1 ASN D 308 " pdb=" H ALA D 310 " model vdw 1.599 1.850 nonbonded pdb=" O GLU H 172 " pdb=" HG SER H 176 " model vdw 1.601 1.850 ... (remaining 246785 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' and (resid 153 through 225 or (resid 235 and (name N or name CA or na \ me C or name O or name HA2 or name HA3)) or resid 236 through 241 or (resid 253 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name \ HG22 or name HG23)) or resid 254 through 274 or resid 285 through 321)) selection = (chain 'B' and (resid 153 through 184 or resid 186 through 225 or resid 235 thro \ ugh 241 or (resid 253 and (name N or name CA or name C or name O or name CB or n \ ame CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 \ or name HG21 or name HG22 or name HG23)) or resid 254 through 274 or resid 285 \ through 321)) selection = (chain 'C' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 241 or (resid 253 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 throu \ gh 274 or (resid 285 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 286 \ through 321)) selection = (chain 'D' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 321)) selection = (chain 'E' and (resid 153 through 225 or resid 235 through 241 or (resid 253 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 254 through 255 or (resid 256 and (name N or name CA o \ r name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or \ name HE2)) or resid 257 through 274 or resid 285 through 321)) selection = (chain 'F' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 241 \ or (resid 253 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name \ HG21 or name HG22 or name HG23)) or resid 254 through 274 or (resid 285 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name OD \ 2 or name HA or name HB2 or name HB3)) or resid 286 through 321)) selection = (chain 'G' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or resid 235 through 241 or (resid 253 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 through \ 255 or (resid 256 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 257 through 321)) \ selection = (chain 'H' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 241 or (resid 253 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 throu \ gh 274 or resid 285 through 321)) } 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 40 5.16 5 C 5918 2.51 5 N 1521 2.21 5 O 1724 1.98 5 H 9203 0.53 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=0.47 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.380 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.160 Process input model: 74.680 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.820 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.020 0.357 9381 Z= 1.388 Angle : 0.827 13.902 12670 Z= 0.397 Chirality : 0.044 0.237 1487 Planarity : 0.006 0.111 1516 Dihedral : 14.248 128.968 3391 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % 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: -0.95 (0.26), residues: 1054 helix: 0.94 (0.22), residues: 519 sheet: -2.23 (0.33), residues: 211 loop : -1.96 (0.33), residues: 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.4488 time to fit residues: 146.7542 Evaluate side-chains 178 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN D 316 ASN G 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9381 Z= 0.217 Angle : 0.557 5.110 12670 Z= 0.296 Chirality : 0.041 0.173 1487 Planarity : 0.004 0.053 1516 Dihedral : 5.961 88.331 1213 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % 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: -0.76 (0.26), residues: 1054 helix: 1.12 (0.22), residues: 516 sheet: -2.17 (0.35), residues: 201 loop : -1.89 (0.32), residues: 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 202 average time/residue: 0.4139 time to fit residues: 118.1434 Evaluate side-chains 191 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1887 time to fit residues: 8.2442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN D 316 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 9381 Z= 0.324 Angle : 0.623 6.176 12670 Z= 0.337 Chirality : 0.042 0.177 1487 Planarity : 0.005 0.039 1516 Dihedral : 4.950 59.378 1213 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 1.96 % 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: -0.95 (0.25), residues: 1054 helix: 0.98 (0.22), residues: 518 sheet: -2.03 (0.33), residues: 233 loop : -2.17 (0.32), residues: 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 192 average time/residue: 0.4060 time to fit residues: 113.2905 Evaluate side-chains 176 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2144 time to fit residues: 5.3397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN C 204 ASN D 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9381 Z= 0.169 Angle : 0.530 6.010 12670 Z= 0.283 Chirality : 0.040 0.184 1487 Planarity : 0.004 0.033 1516 Dihedral : 4.557 51.468 1213 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1054 helix: 1.23 (0.22), residues: 515 sheet: -1.99 (0.34), residues: 225 loop : -1.96 (0.32), residues: 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 189 average time/residue: 0.4332 time to fit residues: 116.2889 Evaluate side-chains 182 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3870 time to fit residues: 8.1828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.005 0.052 9381 Z= 0.296 Angle : 0.591 6.252 12670 Z= 0.319 Chirality : 0.041 0.178 1487 Planarity : 0.004 0.039 1516 Dihedral : 4.563 45.341 1213 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1054 helix: 1.05 (0.22), residues: 518 sheet: -1.94 (0.33), residues: 234 loop : -2.11 (0.31), residues: 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 183 average time/residue: 0.4209 time to fit residues: 111.7390 Evaluate side-chains 181 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.459 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2062 time to fit residues: 7.3326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 9381 Z= 0.330 Angle : 0.621 6.396 12670 Z= 0.337 Chirality : 0.042 0.176 1487 Planarity : 0.005 0.054 1516 Dihedral : 4.686 42.856 1213 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 1.77 % 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: -0.99 (0.25), residues: 1054 helix: 0.92 (0.22), residues: 520 sheet: -2.03 (0.33), residues: 241 loop : -2.15 (0.32), residues: 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 183 average time/residue: 0.4082 time to fit residues: 107.0257 Evaluate side-chains 175 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3031 time to fit residues: 7.5527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS C 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9381 Z= 0.167 Angle : 0.547 6.271 12670 Z= 0.291 Chirality : 0.040 0.186 1487 Planarity : 0.004 0.043 1516 Dihedral : 4.337 37.200 1213 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1054 helix: 1.22 (0.22), residues: 518 sheet: -1.96 (0.34), residues: 230 loop : -1.98 (0.32), residues: 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 185 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 191 average time/residue: 0.3991 time to fit residues: 109.2654 Evaluate side-chains 176 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1987 time to fit residues: 3.7258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.0470 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN C 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9381 Z= 0.174 Angle : 0.543 6.181 12670 Z= 0.286 Chirality : 0.040 0.177 1487 Planarity : 0.004 0.052 1516 Dihedral : 4.185 31.602 1213 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.26), residues: 1054 helix: 1.36 (0.22), residues: 514 sheet: -1.92 (0.35), residues: 220 loop : -1.89 (0.32), residues: 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 181 average time/residue: 0.4103 time to fit residues: 106.2692 Evaluate side-chains 182 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2072 time to fit residues: 5.3213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9381 Z= 0.198 Angle : 0.560 6.444 12670 Z= 0.296 Chirality : 0.040 0.180 1487 Planarity : 0.004 0.043 1516 Dihedral : 4.208 30.526 1213 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.59 % 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: -0.49 (0.26), residues: 1054 helix: 1.34 (0.22), residues: 515 sheet: -1.88 (0.35), residues: 220 loop : -1.84 (0.32), residues: 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 176 average time/residue: 0.4405 time to fit residues: 110.8321 Evaluate side-chains 176 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3493 time to fit residues: 4.0838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN C 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9381 Z= 0.175 Angle : 0.544 6.736 12670 Z= 0.285 Chirality : 0.040 0.176 1487 Planarity : 0.004 0.049 1516 Dihedral : 4.081 29.172 1213 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.39 % 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 (0.26), residues: 1054 helix: 1.43 (0.22), residues: 514 sheet: -1.78 (0.36), residues: 220 loop : -1.71 (0.32), residues: 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 176 average time/residue: 0.4337 time to fit residues: 107.9610 Evaluate side-chains 170 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2026 time to fit residues: 2.7454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.112318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099444 restraints weight = 69731.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.102564 restraints weight = 34814.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104673 restraints weight = 21061.505| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9381 Z= 0.182 Angle : 0.553 6.805 12670 Z= 0.292 Chirality : 0.040 0.169 1487 Planarity : 0.004 0.048 1516 Dihedral : 4.116 28.959 1213 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.49 % 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: -0.31 (0.26), residues: 1054 helix: 1.44 (0.22), residues: 514 sheet: -1.78 (0.36), residues: 220 loop : -1.66 (0.32), residues: 320 =============================================================================== Job complete usr+sys time: 3865.60 seconds wall clock time: 70 minutes 45.93 seconds (4245.93 seconds total)