Starting phenix.real_space_refine on Sat Feb 17 10:48:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/02_2024/7una_26618_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/02_2024/7una_26618.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/02_2024/7una_26618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/02_2024/7una_26618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/02_2024/7una_26618_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/02_2024/7una_26618_trim_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.83, per 1000 atoms: 0.43 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: 15.48 Conformation dependent library (CDL) restraints added in 1.9 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: 19.31 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: 6.20 Time building geometry restraints manager: 15.67 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=" CBI 4BW A 401 " pdb=" CBM 4BW A 401 " ideal model delta sigma weight residual 1.538 1.289 0.249 2.00e-02 2.50e+03 1.54e+02 bond pdb=" CBI 4BW H 401 " pdb=" CBM 4BW H 401 " ideal model delta sigma weight residual 1.538 1.290 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" CBI 4BW F 401 " pdb=" CBM 4BW F 401 " ideal model delta sigma weight residual 1.538 1.291 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" CBI 4BW C 401 " pdb=" CBM 4BW C 401 " ideal model delta sigma weight residual 1.538 1.293 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C4' 4BW C 401 " pdb=" O4' 4BW C 401 " ideal model delta sigma weight residual 1.445 1.656 -0.211 2.00e-02 2.50e+03 1.11e+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=" OAD 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAH 4BW C 401 " ideal model delta sigma weight residual 122.13 104.77 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" OAD 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAH 4BW A 401 " ideal model delta sigma weight residual 122.13 104.79 17.34 3.00e+00 1.11e-01 3.34e+01 angle pdb=" OAD 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAH 4BW F 401 " ideal model delta sigma weight residual 122.13 104.87 17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" OAD 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" OAH 4BW H 401 " ideal model delta sigma weight residual 122.13 104.88 17.25 3.00e+00 1.11e-01 3.31e+01 ... (remaining 33584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 8525 32.68 - 65.36: 268 65.36 - 98.03: 16 98.03 - 130.71: 15 130.71 - 163.39: 13 Dihedral angle restraints: 8837 sinusoidal: 4926 harmonic: 3911 Sorted by residual: dihedral pdb=" CAN 4BW A 401 " pdb=" OAV 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAH 4BW A 401 " ideal model delta sinusoidal sigma weight residual 330.18 166.79 163.39 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CAN 4BW H 401 " pdb=" OAV 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" OAH 4BW H 401 " ideal model delta sinusoidal sigma weight residual 330.18 167.73 162.45 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CAN 4BW F 401 " pdb=" OAV 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAH 4BW F 401 " ideal model delta sinusoidal sigma weight residual 330.18 170.25 159.93 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 8834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1185 0.045 - 0.089: 187 0.089 - 0.134: 93 0.134 - 0.178: 15 0.178 - 0.223: 7 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CBI 4BW C 401 " pdb=" CBM 4BW C 401 " pdb=" CBO 4BW C 401 " pdb=" OAG 4BW C 401 " both_signs ideal model delta sigma weight residual False 2.67 2.45 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CBI 4BW H 401 " pdb=" CBM 4BW H 401 " pdb=" CBO 4BW H 401 " pdb=" OAG 4BW H 401 " both_signs ideal model delta sigma weight residual False 2.67 2.47 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CBI 4BW F 401 " pdb=" CBM 4BW F 401 " pdb=" CBO 4BW F 401 " pdb=" OAG 4BW F 401 " both_signs ideal model delta sigma weight residual False 2.67 2.47 0.21 2.00e-01 2.50e+01 1.07e+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 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: 1.360 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: 0.280 Extract box with map and model: 5.360 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 60.740 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 0.013 0.249 9381 Z= 0.847 Angle : 1.018 17.363 12670 Z= 0.444 Chirality : 0.044 0.223 1487 Planarity : 0.006 0.111 1516 Dihedral : 18.090 163.389 3627 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 174 PHE 0.019 0.001 PHE C 191 TYR 0.018 0.001 TYR F 162 ARG 0.008 0.001 ARG D 292 *********************** 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 : 1.619 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 REVERT: A 194 ASP cc_start: 0.7626 (m-30) cc_final: 0.7347 (m-30) REVERT: A 221 LYS cc_start: 0.6088 (pptt) cc_final: 0.5159 (pptt) REVERT: A 269 GLU cc_start: 0.7889 (mp0) cc_final: 0.7598 (mp0) REVERT: B 273 LEU cc_start: 0.8277 (mm) cc_final: 0.8064 (mm) REVERT: B 320 ASN cc_start: 0.7335 (t0) cc_final: 0.7036 (t0) REVERT: C 171 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8351 (mt-10) REVERT: C 172 GLU cc_start: 0.8089 (tt0) cc_final: 0.7822 (tt0) REVERT: D 172 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7712 (mp0) REVERT: D 292 ARG cc_start: 0.8432 (tpp80) cc_final: 0.8214 (ttm-80) REVERT: F 159 ILE cc_start: 0.8183 (mt) cc_final: 0.7980 (mt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.4445 time to fit residues: 143.8496 Evaluate side-chains 180 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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: 0.5980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9381 Z= 0.165 Angle : 0.515 5.003 12670 Z= 0.276 Chirality : 0.040 0.173 1487 Planarity : 0.004 0.050 1516 Dihedral : 20.805 170.549 1449 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.28 % Allowed : 8.64 % Favored : 90.09 % 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: -0.69 (0.26), residues: 1054 helix: 1.16 (0.22), residues: 515 sheet: -2.19 (0.35), residues: 201 loop : -1.79 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 174 PHE 0.015 0.001 PHE C 191 TYR 0.022 0.001 TYR F 303 ARG 0.004 0.000 ARG B 307 *********************** 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 204 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6048 (pptt) cc_final: 0.5071 (pptt) REVERT: A 269 GLU cc_start: 0.7924 (mp0) cc_final: 0.7561 (mp0) REVERT: B 290 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8354 (mm-30) REVERT: B 292 ARG cc_start: 0.7497 (mmt90) cc_final: 0.7292 (mmt90) REVERT: B 320 ASN cc_start: 0.7329 (t0) cc_final: 0.6988 (t0) REVERT: C 171 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8241 (mt-10) REVERT: C 292 ARG cc_start: 0.7690 (mtp85) cc_final: 0.6791 (mmt-90) REVERT: D 172 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7774 (mp0) REVERT: F 159 ILE cc_start: 0.8223 (mt) cc_final: 0.8022 (mt) REVERT: F 177 GLU cc_start: 0.8404 (mp0) cc_final: 0.8118 (mm-30) REVERT: F 194 ASP cc_start: 0.7627 (m-30) cc_final: 0.7392 (t0) REVERT: G 286 MET cc_start: 0.7519 (mmp) cc_final: 0.7145 (mmp) outliers start: 13 outliers final: 9 residues processed: 199 average time/residue: 0.4560 time to fit residues: 125.8673 Evaluate side-chains 187 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain H residue 202 ASP 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: 1.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 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: 0.7394 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9381 Z= 0.268 Angle : 0.564 5.456 12670 Z= 0.308 Chirality : 0.041 0.195 1487 Planarity : 0.005 0.051 1516 Dihedral : 20.722 173.048 1449 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.45 % Allowed : 11.48 % Favored : 86.06 % 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: -0.67 (0.26), residues: 1054 helix: 1.21 (0.22), residues: 515 sheet: -1.96 (0.33), residues: 233 loop : -1.95 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 174 PHE 0.025 0.002 PHE A 191 TYR 0.032 0.002 TYR F 303 ARG 0.009 0.001 ARG D 292 *********************** 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 207 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6627 (pptt) cc_final: 0.5667 (pptt) REVERT: B 320 ASN cc_start: 0.7521 (t0) cc_final: 0.7208 (t0) REVERT: C 168 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: C 292 ARG cc_start: 0.7307 (mtp85) cc_final: 0.6949 (mmt-90) REVERT: D 192 ARG cc_start: 0.8195 (pmt170) cc_final: 0.7961 (pmt-80) REVERT: D 290 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: E 291 MET cc_start: 0.7780 (tpt) cc_final: 0.7210 (tpp) REVERT: F 159 ILE cc_start: 0.8545 (mt) cc_final: 0.8298 (mt) outliers start: 25 outliers final: 19 residues processed: 197 average time/residue: 0.4163 time to fit residues: 116.9130 Evaluate side-chains 188 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 202 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9381 Z= 0.204 Angle : 0.525 5.998 12670 Z= 0.285 Chirality : 0.040 0.185 1487 Planarity : 0.004 0.034 1516 Dihedral : 20.734 172.872 1449 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.96 % Allowed : 13.35 % Favored : 84.69 % 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 (0.26), residues: 1054 helix: 1.28 (0.22), residues: 515 sheet: -1.95 (0.34), residues: 225 loop : -1.90 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 174 PHE 0.016 0.001 PHE A 191 TYR 0.024 0.001 TYR F 303 ARG 0.009 0.001 ARG D 292 *********************** 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 201 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6637 (pptt) cc_final: 0.5718 (pptt) REVERT: A 269 GLU cc_start: 0.7901 (mp0) cc_final: 0.7603 (mp0) REVERT: B 320 ASN cc_start: 0.7568 (t0) cc_final: 0.7253 (t0) REVERT: D 192 ARG cc_start: 0.8150 (pmt170) cc_final: 0.7910 (pmt-80) REVERT: D 290 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: E 291 MET cc_start: 0.7750 (tpt) cc_final: 0.7183 (tpp) REVERT: G 191 PHE cc_start: 0.8083 (t80) cc_final: 0.7538 (t80) outliers start: 20 outliers final: 16 residues processed: 193 average time/residue: 0.4051 time to fit residues: 113.4110 Evaluate side-chains 187 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain H residue 202 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9381 Z= 0.196 Angle : 0.519 6.138 12670 Z= 0.280 Chirality : 0.040 0.185 1487 Planarity : 0.004 0.032 1516 Dihedral : 20.763 176.484 1449 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.45 % Allowed : 13.64 % Favored : 83.91 % 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: -0.48 (0.26), residues: 1054 helix: 1.32 (0.22), residues: 516 sheet: -1.81 (0.35), residues: 223 loop : -1.84 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 174 PHE 0.014 0.001 PHE A 191 TYR 0.022 0.001 TYR F 303 ARG 0.005 0.000 ARG G 292 *********************** 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 210 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6621 (pptt) cc_final: 0.5742 (pptt) REVERT: B 307 ARG cc_start: 0.7282 (ttp80) cc_final: 0.6900 (ttm-80) REVERT: B 320 ASN cc_start: 0.7558 (t0) cc_final: 0.7243 (t0) REVERT: C 291 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7710 (ptm) REVERT: C 293 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5884 (mp0) REVERT: D 290 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: G 191 PHE cc_start: 0.8096 (t80) cc_final: 0.7609 (t80) REVERT: G 286 MET cc_start: 0.7589 (mmp) cc_final: 0.7336 (mmp) outliers start: 25 outliers final: 17 residues processed: 196 average time/residue: 0.4294 time to fit residues: 120.2198 Evaluate side-chains 193 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 177 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9381 Z= 0.257 Angle : 0.555 6.410 12670 Z= 0.302 Chirality : 0.041 0.211 1487 Planarity : 0.004 0.051 1516 Dihedral : 20.802 176.389 1449 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.94 % Allowed : 15.60 % Favored : 81.45 % 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: -0.53 (0.26), residues: 1054 helix: 1.25 (0.22), residues: 517 sheet: -1.73 (0.35), residues: 234 loop : -1.91 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 174 PHE 0.017 0.002 PHE A 191 TYR 0.020 0.001 TYR F 303 ARG 0.009 0.001 ARG D 292 *********************** 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 209 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6566 (pptt) cc_final: 0.5743 (pptt) REVERT: B 194 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7104 (p0) REVERT: B 307 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6877 (ttm-80) REVERT: B 320 ASN cc_start: 0.7647 (t0) cc_final: 0.7330 (t0) REVERT: C 291 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7682 (ptt) REVERT: D 192 ARG cc_start: 0.8063 (pmt170) cc_final: 0.7686 (pmt-80) REVERT: D 290 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: E 291 MET cc_start: 0.7762 (tpt) cc_final: 0.7163 (tpp) REVERT: F 307 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8172 (ttm110) REVERT: G 191 PHE cc_start: 0.8148 (t80) cc_final: 0.7770 (t80) outliers start: 30 outliers final: 23 residues processed: 194 average time/residue: 0.4562 time to fit residues: 126.4135 Evaluate side-chains 196 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 260 ILE 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: 1.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7405 moved from start: 0.2536 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= 0.173 Angle : 0.514 6.380 12670 Z= 0.276 Chirality : 0.040 0.184 1487 Planarity : 0.004 0.040 1516 Dihedral : 20.769 177.210 1449 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.94 % Allowed : 16.19 % Favored : 80.86 % 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: -0.35 (0.26), residues: 1054 helix: 1.43 (0.22), residues: 514 sheet: -1.76 (0.35), residues: 221 loop : -1.75 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 174 PHE 0.012 0.001 PHE A 191 TYR 0.019 0.001 TYR F 303 ARG 0.006 0.000 ARG G 292 *********************** 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 207 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.545 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: A 221 LYS cc_start: 0.6497 (pptt) cc_final: 0.5694 (pptt) REVERT: B 194 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7126 (p0) REVERT: B 307 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6846 (ttm-80) REVERT: B 320 ASN cc_start: 0.7457 (t0) cc_final: 0.7143 (t0) REVERT: C 291 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7728 (ptt) REVERT: C 292 ARG cc_start: 0.7349 (mmt-90) cc_final: 0.6823 (ttm-80) REVERT: D 194 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: D 290 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: G 191 PHE cc_start: 0.8140 (t80) cc_final: 0.7741 (t80) REVERT: G 286 MET cc_start: 0.7620 (mmp) cc_final: 0.7309 (mmp) outliers start: 30 outliers final: 21 residues processed: 192 average time/residue: 0.4287 time to fit residues: 116.9986 Evaluate side-chains 197 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 177 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7426 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9381 Z= 0.211 Angle : 0.535 6.562 12670 Z= 0.289 Chirality : 0.040 0.195 1487 Planarity : 0.004 0.041 1516 Dihedral : 20.760 176.804 1449 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.75 % Allowed : 16.58 % Favored : 80.67 % 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: -0.34 (0.26), residues: 1054 helix: 1.42 (0.22), residues: 515 sheet: -1.72 (0.36), residues: 224 loop : -1.76 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 174 PHE 0.013 0.001 PHE A 191 TYR 0.041 0.001 TYR F 303 ARG 0.007 0.001 ARG F 307 *********************** 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 203 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 1.647 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: A 221 LYS cc_start: 0.6597 (pptt) cc_final: 0.5798 (pptt) REVERT: B 307 ARG cc_start: 0.7283 (ttp80) cc_final: 0.6864 (ttm-80) REVERT: B 320 ASN cc_start: 0.7527 (t0) cc_final: 0.7203 (t0) REVERT: C 291 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7820 (ptt) REVERT: D 194 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: D 290 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: F 274 TYR cc_start: 0.6197 (t80) cc_final: 0.5799 (t80) REVERT: G 191 PHE cc_start: 0.8138 (t80) cc_final: 0.7730 (t80) REVERT: G 286 MET cc_start: 0.7623 (mmp) cc_final: 0.7312 (mmp) outliers start: 28 outliers final: 22 residues processed: 188 average time/residue: 0.4250 time to fit residues: 114.0584 Evaluate side-chains 197 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain H residue 260 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7431 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9381 Z= 0.203 Angle : 0.531 6.326 12670 Z= 0.286 Chirality : 0.040 0.194 1487 Planarity : 0.004 0.045 1516 Dihedral : 20.756 178.733 1449 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.75 % Allowed : 16.78 % Favored : 80.47 % 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: -0.31 (0.26), residues: 1054 helix: 1.45 (0.22), residues: 515 sheet: -1.78 (0.36), residues: 218 loop : -1.69 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 174 PHE 0.013 0.001 PHE A 238 TYR 0.031 0.001 TYR F 303 ARG 0.006 0.000 ARG G 292 *********************** 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 199 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.480 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 REVERT: A 221 LYS cc_start: 0.6530 (pptt) cc_final: 0.5785 (pptt) REVERT: B 307 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6868 (ttm-80) REVERT: B 320 ASN cc_start: 0.7534 (t0) cc_final: 0.7205 (t0) REVERT: C 291 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7767 (ptt) REVERT: C 292 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.7325 (mmt-90) REVERT: D 194 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: G 191 PHE cc_start: 0.8119 (t80) cc_final: 0.7709 (t80) REVERT: G 286 MET cc_start: 0.7618 (mmp) cc_final: 0.7309 (mmp) outliers start: 28 outliers final: 24 residues processed: 185 average time/residue: 0.4601 time to fit residues: 118.2706 Evaluate side-chains 192 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 307 ARG Chi-restraints excluded: chain H residue 260 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9381 Z= 0.234 Angle : 0.552 6.536 12670 Z= 0.298 Chirality : 0.041 0.206 1487 Planarity : 0.004 0.041 1516 Dihedral : 20.764 178.022 1449 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.85 % Allowed : 16.78 % Favored : 80.37 % 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 (0.26), residues: 1054 helix: 1.43 (0.22), residues: 514 sheet: -1.81 (0.35), residues: 222 loop : -1.74 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 174 PHE 0.014 0.001 PHE A 238 TYR 0.030 0.001 TYR F 303 ARG 0.014 0.001 ARG F 307 ********************** 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 202 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.479 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 revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6569 (pptt) cc_final: 0.5811 (pptt) REVERT: B 307 ARG cc_start: 0.7258 (ttp80) cc_final: 0.6901 (ttm-80) REVERT: B 320 ASN cc_start: 0.7571 (t0) cc_final: 0.7254 (t0) REVERT: C 194 ASP cc_start: 0.8199 (t0) cc_final: 0.7965 (t0) REVERT: C 291 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7772 (ptt) REVERT: D 172 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7703 (mp0) REVERT: D 192 ARG cc_start: 0.8045 (pmt170) cc_final: 0.7563 (pmt-80) REVERT: G 191 PHE cc_start: 0.8143 (t80) cc_final: 0.7812 (t80) outliers start: 29 outliers final: 24 residues processed: 187 average time/residue: 0.4368 time to fit residues: 115.6604 Evaluate side-chains 194 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 307 ARG Chi-restraints excluded: chain H residue 260 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.112105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099180 restraints weight = 69342.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.102299 restraints weight = 34396.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.104441 restraints weight = 20733.628| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9381 Z= 0.179 Angle : 0.536 6.819 12670 Z= 0.287 Chirality : 0.040 0.186 1487 Planarity : 0.004 0.030 1516 Dihedral : 20.754 179.786 1449 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.55 % Allowed : 17.27 % Favored : 80.18 % 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: -0.27 (0.26), residues: 1054 helix: 1.50 (0.22), residues: 514 sheet: -1.80 (0.36), residues: 218 loop : -1.67 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 174 PHE 0.012 0.001 PHE A 238 TYR 0.031 0.001 TYR F 303 ARG 0.008 0.001 ARG F 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4022.75 seconds wall clock time: 73 minutes 57.96 seconds (4437.96 seconds total)