Starting phenix.real_space_refine on Sat Jan 20 05:49:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0g_24790/01_2024/7s0g_24790_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0g_24790/01_2024/7s0g_24790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0g_24790/01_2024/7s0g_24790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0g_24790/01_2024/7s0g_24790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0g_24790/01_2024/7s0g_24790_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0g_24790/01_2024/7s0g_24790_trim_updated.pdb" } resolution = 3.86 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= 0.968 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: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 4451 2.51 5 N 1198 2.21 5 O 1292 1.98 5 H 6854 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 185": "OE1" <-> "OE2" Residue "R ASP 186": "OD1" <-> "OD2" Residue "R GLU 236": "OE1" <-> "OE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13846 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4248 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5098 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3526 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 959 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.70, per 1000 atoms: 0.48 Number of scatterers: 13846 At special positions: 0 Unit cell: (84.8065, 98.762, 130.967, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1292 8.00 N 1198 7.00 C 4451 6.00 H 6854 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 199 " distance=2.03 Simple disulfide: pdb=" SG CYS R 192 " - pdb=" SG CYS R 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.32 Conformation dependent library (CDL) restraints added in 1.5 seconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 9 sheets defined 42.9% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'R' and resid 41 through 68 removed outlier: 3.915A pdb=" N LEU R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 104 removed outlier: 3.809A pdb=" N PHE R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 111 through 144 Processing helix chain 'R' and resid 146 through 152 Processing helix chain 'R' and resid 155 through 178 removed outlier: 4.186A pdb=" N LEU R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 187 through 194 Processing helix chain 'R' and resid 205 through 215 Processing helix chain 'R' and resid 217 through 240 Processing helix chain 'R' and resid 287 through 315 removed outlier: 3.672A pdb=" N ILE R 295 " --> pdb=" O THR R 291 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 305 - end of helix removed outlier: 3.584A pdb=" N VAL R 314 " --> pdb=" O ASN R 310 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE R 315 " --> pdb=" O ILE R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 319 No H-bonds generated for 'chain 'R' and resid 317 through 319' Processing helix chain 'R' and resid 322 through 343 removed outlier: 3.674A pdb=" N ASN R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER R 336 " --> pdb=" O GLY R 332 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA R 337 " --> pdb=" O TYR R 333 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 347 through 355 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.177A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.196A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.659A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 150 removed outlier: 7.013A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.807A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.611A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.566A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 48 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 34 through 37 Processing sheet with id= I, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.448A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 975 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: 4.42 Time building geometry restraints manager: 11.55 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: 6828 1.03 - 1.23: 36 1.23 - 1.43: 2999 1.43 - 1.62: 4051 1.62 - 1.82: 72 Bond restraints: 13986 Sorted by residual: bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.438 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.417 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 1.457 1.493 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" CAE 5FW R 401 " pdb=" CAH 5FW R 401 " ideal model delta sigma weight residual 1.515 1.546 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" CAG 5FW R 401 " pdb=" CAJ 5FW R 401 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 13981 not shown) Histogram of bond angle deviations from ideal: 0.06 - 26.85: 1 26.85 - 53.64: 0 53.64 - 80.44: 0 80.44 - 107.23: 235 107.23 - 134.03: 24945 Bond angle restraints: 25181 Sorted by residual: angle pdb=" HB2 GLU A 352 " pdb=" CB GLU A 352 " pdb=" HB3 GLU A 352 " ideal model delta sigma weight residual 110.00 0.06 109.94 3.00e+00 1.11e-01 1.34e+03 angle pdb=" C VAL R 95 " pdb=" CA VAL R 95 " pdb=" CB VAL R 95 " ideal model delta sigma weight residual 114.00 110.72 3.28 1.31e+00 5.83e-01 6.28e+00 angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 111.88 109.50 2.38 1.06e+00 8.90e-01 5.03e+00 angle pdb=" C VAL R 94 " pdb=" N VAL R 95 " pdb=" CA VAL R 95 " ideal model delta sigma weight residual 120.33 122.02 -1.69 8.00e-01 1.56e+00 4.44e+00 angle pdb=" CAJ 5FW R 401 " pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 114.52 109.00 5.52 3.00e+00 1.11e-01 3.39e+00 ... (remaining 25176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 5963 15.60 - 31.20: 430 31.20 - 46.81: 78 46.81 - 62.41: 17 62.41 - 78.01: 7 Dihedral angle restraints: 6495 sinusoidal: 3399 harmonic: 3096 Sorted by residual: dihedral pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " pdb=" CG ASP B 153 " pdb=" OD1 ASP B 153 " ideal model delta sinusoidal sigma weight residual -30.00 -82.44 52.44 1 2.00e+01 2.50e-03 9.37e+00 dihedral pdb=" CA ASP B 312 " pdb=" CB ASP B 312 " pdb=" CG ASP B 312 " pdb=" OD1 ASP B 312 " ideal model delta sinusoidal sigma weight residual -30.00 -82.17 52.17 1 2.00e+01 2.50e-03 9.28e+00 dihedral pdb=" CA ASN R 310 " pdb=" CB ASN R 310 " pdb=" CG ASN R 310 " pdb=" OD1 ASN R 310 " ideal model delta sinusoidal sigma weight residual 120.00 178.63 -58.63 2 2.00e+01 2.50e-03 8.75e+00 ... (remaining 6492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 984 0.057 - 0.114: 111 0.114 - 0.171: 11 0.171 - 0.229: 0 0.229 - 0.286: 1 Chirality restraints: 1107 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.58 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1104 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO G 49 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 218 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO R 219 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO R 219 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 219 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 320 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.13e-01 pdb=" N PRO R 321 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 321 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 321 " -0.013 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1083 2.23 - 2.82: 30249 2.82 - 3.41: 35370 3.41 - 4.01: 47276 4.01 - 4.60: 73264 Nonbonded interactions: 187242 Sorted by model distance: nonbonded pdb=" HG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 1.635 1.850 nonbonded pdb=" OE1 GLU A 289 " pdb=" H GLU A 289 " model vdw 1.641 1.850 nonbonded pdb=" OD1 ASP B 205 " pdb=" HG SER B 207 " model vdw 1.668 1.850 nonbonded pdb=" OD1 ASP R 184 " pdb=" H ASP R 186 " model vdw 1.681 1.850 nonbonded pdb="HH11 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 1.686 1.850 ... (remaining 187237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.040 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: 0.210 Extract box with map and model: 4.210 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 45.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.003 0.085 7132 Z= 0.180 Angle : 0.441 5.523 9669 Z= 0.261 Chirality : 0.037 0.286 1107 Planarity : 0.002 0.029 1224 Dihedral : 12.412 78.012 2543 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.27), residues: 881 helix: 0.26 (0.24), residues: 403 sheet: -2.74 (0.35), residues: 158 loop : -2.36 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 117 HIS 0.004 0.001 HIS A 347 PHE 0.009 0.001 PHE R 174 TYR 0.008 0.001 TYR G 40 ARG 0.001 0.000 ARG R 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.065 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 LEU cc_start: 0.8061 (tt) cc_final: 0.7857 (tt) REVERT: R 236 GLU cc_start: 0.8452 (tt0) cc_final: 0.8201 (tt0) REVERT: R 240 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8394 (mttt) REVERT: R 285 GLU cc_start: 0.7637 (pm20) cc_final: 0.7348 (mt-10) REVERT: R 323 TRP cc_start: 0.7904 (p-90) cc_final: 0.7507 (p-90) REVERT: B 68 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7888 (ttt180) REVERT: B 75 GLN cc_start: 0.7283 (mt0) cc_final: 0.6931 (mt0) REVERT: B 97 SER cc_start: 0.9234 (t) cc_final: 0.8826 (p) REVERT: B 134 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6701 (mtp-110) REVERT: B 176 GLN cc_start: 0.8763 (mt0) cc_final: 0.8447 (mt0) REVERT: B 228 ASP cc_start: 0.8307 (m-30) cc_final: 0.8064 (m-30) REVERT: B 237 ASN cc_start: 0.9048 (t0) cc_final: 0.8781 (t0) REVERT: B 247 ASP cc_start: 0.7841 (t0) cc_final: 0.7453 (t0) REVERT: B 304 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7491 (ttp80) REVERT: B 321 THR cc_start: 0.9297 (p) cc_final: 0.9062 (p) REVERT: A 16 SER cc_start: 0.8901 (p) cc_final: 0.8666 (p) REVERT: A 22 ASN cc_start: 0.8403 (m-40) cc_final: 0.8091 (m110) REVERT: A 214 CYS cc_start: 0.8533 (m) cc_final: 0.8031 (t) REVERT: A 312 LYS cc_start: 0.8307 (mttt) cc_final: 0.7964 (mmmt) REVERT: A 330 LYS cc_start: 0.8574 (mttt) cc_final: 0.8365 (mmtp) REVERT: G 27 ARG cc_start: 0.7354 (mtt-85) cc_final: 0.6339 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.4565 time to fit residues: 189.5674 Evaluate side-chains 266 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 79 optimal weight: 0.6980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 GLN R 237 GLN R 310 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7132 Z= 0.173 Angle : 0.448 5.243 9669 Z= 0.238 Chirality : 0.037 0.128 1107 Planarity : 0.003 0.032 1224 Dihedral : 3.516 34.898 970 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.08 % Allowed : 15.50 % Favored : 83.42 % 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: -0.92 (0.28), residues: 881 helix: 1.31 (0.26), residues: 404 sheet: -2.71 (0.33), residues: 156 loop : -1.96 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 117 HIS 0.001 0.000 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR G 40 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 281 time to evaluate : 1.128 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8047 (mt-10) REVERT: R 236 GLU cc_start: 0.8403 (tt0) cc_final: 0.8178 (tt0) REVERT: R 240 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8404 (mttt) REVERT: R 285 GLU cc_start: 0.7622 (pm20) cc_final: 0.7335 (mt-10) REVERT: R 323 TRP cc_start: 0.8271 (p-90) cc_final: 0.7568 (p-90) REVERT: B 75 GLN cc_start: 0.7377 (mt0) cc_final: 0.6947 (mm-40) REVERT: B 97 SER cc_start: 0.9219 (t) cc_final: 0.8809 (p) REVERT: B 134 ARG cc_start: 0.6967 (mmm-85) cc_final: 0.6694 (mtp-110) REVERT: B 176 GLN cc_start: 0.8735 (mt0) cc_final: 0.8416 (mt0) REVERT: B 225 HIS cc_start: 0.6896 (m-70) cc_final: 0.6685 (m90) REVERT: B 228 ASP cc_start: 0.8247 (m-30) cc_final: 0.8033 (m-30) REVERT: B 237 ASN cc_start: 0.9002 (t0) cc_final: 0.8790 (t0) REVERT: B 247 ASP cc_start: 0.7815 (t0) cc_final: 0.7465 (t0) REVERT: B 325 MET cc_start: 0.8076 (mmt) cc_final: 0.7192 (mmt) REVERT: A 16 SER cc_start: 0.8926 (p) cc_final: 0.8724 (p) REVERT: A 22 ASN cc_start: 0.8403 (m-40) cc_final: 0.8110 (m110) REVERT: A 25 GLU cc_start: 0.7590 (tp30) cc_final: 0.7386 (tp30) REVERT: A 214 CYS cc_start: 0.8404 (m) cc_final: 0.7960 (t) REVERT: A 289 GLU cc_start: 0.7680 (pm20) cc_final: 0.6250 (tp30) REVERT: A 312 LYS cc_start: 0.8378 (mttt) cc_final: 0.8023 (mmmt) REVERT: G 27 ARG cc_start: 0.7273 (mtt-85) cc_final: 0.6899 (mtt90) outliers start: 8 outliers final: 7 residues processed: 285 average time/residue: 0.4288 time to fit residues: 159.3909 Evaluate side-chains 273 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 266 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 347 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 GLN B 230 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7132 Z= 0.198 Angle : 0.461 6.972 9669 Z= 0.247 Chirality : 0.037 0.125 1107 Planarity : 0.003 0.051 1224 Dihedral : 3.565 31.635 970 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.56 % Allowed : 16.44 % Favored : 81.00 % 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: -0.51 (0.29), residues: 881 helix: 1.73 (0.26), residues: 401 sheet: -2.60 (0.34), residues: 161 loop : -1.78 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 117 HIS 0.002 0.001 HIS R 180 PHE 0.015 0.001 PHE A 189 TYR 0.012 0.001 TYR B 85 ARG 0.006 0.000 ARG R 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 1.055 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8084 (mt-10) REVERT: R 236 GLU cc_start: 0.8397 (tt0) cc_final: 0.8188 (tt0) REVERT: R 240 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8398 (mttt) REVERT: R 285 GLU cc_start: 0.7675 (pm20) cc_final: 0.7333 (mt-10) REVERT: R 323 TRP cc_start: 0.8283 (p-90) cc_final: 0.7563 (p-90) REVERT: B 57 LYS cc_start: 0.8454 (ptpt) cc_final: 0.8107 (ptmt) REVERT: B 75 GLN cc_start: 0.7366 (mt0) cc_final: 0.6923 (mm-40) REVERT: B 97 SER cc_start: 0.9222 (t) cc_final: 0.8791 (p) REVERT: B 134 ARG cc_start: 0.6958 (mmm-85) cc_final: 0.6699 (mtp-110) REVERT: B 176 GLN cc_start: 0.8720 (mt0) cc_final: 0.8399 (mt0) REVERT: B 247 ASP cc_start: 0.7861 (t0) cc_final: 0.7474 (t0) REVERT: A 8 GLU cc_start: 0.8450 (mp0) cc_final: 0.8157 (mp0) REVERT: A 22 ASN cc_start: 0.8433 (m-40) cc_final: 0.8137 (m110) REVERT: A 25 GLU cc_start: 0.7608 (tp30) cc_final: 0.7386 (tp30) REVERT: A 214 CYS cc_start: 0.8372 (m) cc_final: 0.7996 (t) REVERT: A 289 GLU cc_start: 0.7788 (pm20) cc_final: 0.6241 (tp30) REVERT: A 312 LYS cc_start: 0.8399 (mttt) cc_final: 0.8032 (mmmt) REVERT: G 27 ARG cc_start: 0.7276 (mtt-85) cc_final: 0.6825 (mtt-85) REVERT: G 46 LYS cc_start: 0.8707 (mttp) cc_final: 0.8487 (mmmm) outliers start: 19 outliers final: 18 residues processed: 278 average time/residue: 0.3847 time to fit residues: 142.3448 Evaluate side-chains 288 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 270 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 336 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 GLN R 237 GLN A 306 GLN A 322 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7132 Z= 0.282 Angle : 0.496 7.415 9669 Z= 0.272 Chirality : 0.038 0.149 1107 Planarity : 0.004 0.040 1224 Dihedral : 3.919 33.340 970 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.04 % Allowed : 16.31 % Favored : 79.65 % 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: -0.57 (0.28), residues: 881 helix: 1.80 (0.26), residues: 396 sheet: -2.73 (0.34), residues: 159 loop : -1.86 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.002 0.001 HIS A 213 PHE 0.016 0.001 PHE A 189 TYR 0.010 0.001 TYR G 40 ARG 0.005 0.000 ARG R 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 272 time to evaluate : 1.090 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 150 GLN cc_start: 0.8365 (tp40) cc_final: 0.8131 (tp-100) REVERT: R 236 GLU cc_start: 0.8410 (tt0) cc_final: 0.8200 (tt0) REVERT: R 240 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8432 (mttt) REVERT: R 285 GLU cc_start: 0.7734 (pm20) cc_final: 0.7353 (mt-10) REVERT: R 323 TRP cc_start: 0.8356 (p-90) cc_final: 0.7591 (p-90) REVERT: B 49 ARG cc_start: 0.8150 (mpt-90) cc_final: 0.7784 (mpt-90) REVERT: B 57 LYS cc_start: 0.8466 (ptpt) cc_final: 0.8103 (ptmt) REVERT: B 59 TYR cc_start: 0.8972 (m-10) cc_final: 0.8747 (m-80) REVERT: B 97 SER cc_start: 0.9245 (t) cc_final: 0.8551 (p) REVERT: B 118 ASP cc_start: 0.8551 (p0) cc_final: 0.8293 (p0) REVERT: B 134 ARG cc_start: 0.7035 (mmm-85) cc_final: 0.6756 (mtp-110) REVERT: B 176 GLN cc_start: 0.8750 (mt0) cc_final: 0.8425 (mt0) REVERT: B 228 ASP cc_start: 0.8230 (m-30) cc_final: 0.7769 (m-30) REVERT: B 247 ASP cc_start: 0.7920 (t0) cc_final: 0.7451 (t0) REVERT: B 325 MET cc_start: 0.7969 (mmt) cc_final: 0.7544 (mmt) REVERT: A 8 GLU cc_start: 0.8468 (mp0) cc_final: 0.8180 (mp0) REVERT: A 22 ASN cc_start: 0.8515 (m-40) cc_final: 0.8256 (m110) REVERT: A 248 LYS cc_start: 0.8850 (mttp) cc_final: 0.8445 (mtpt) REVERT: A 286 CYS cc_start: 0.8268 (p) cc_final: 0.7474 (t) REVERT: A 289 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: A 312 LYS cc_start: 0.8476 (mttt) cc_final: 0.8104 (mmmt) REVERT: G 27 ARG cc_start: 0.7358 (mtt-85) cc_final: 0.6897 (mtt-85) REVERT: G 46 LYS cc_start: 0.8735 (mttp) cc_final: 0.8523 (mmmm) outliers start: 30 outliers final: 27 residues processed: 280 average time/residue: 0.3979 time to fit residues: 147.3521 Evaluate side-chains 286 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 258 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 336 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7132 Z= 0.266 Angle : 0.501 7.064 9669 Z= 0.273 Chirality : 0.038 0.128 1107 Planarity : 0.004 0.051 1224 Dihedral : 4.057 31.211 970 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.64 % Allowed : 18.73 % Favored : 77.63 % 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 (0.29), residues: 881 helix: 1.92 (0.26), residues: 396 sheet: -2.83 (0.35), residues: 149 loop : -1.86 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 117 HIS 0.008 0.001 HIS R 180 PHE 0.016 0.001 PHE A 189 TYR 0.010 0.001 TYR G 40 ARG 0.006 0.000 ARG R 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 1.097 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7988 (mt-10) REVERT: R 150 GLN cc_start: 0.8378 (tp40) cc_final: 0.8138 (tp-100) REVERT: R 236 GLU cc_start: 0.8400 (tt0) cc_final: 0.8196 (tt0) REVERT: R 240 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8438 (mttt) REVERT: R 285 GLU cc_start: 0.7802 (pm20) cc_final: 0.7381 (mt-10) REVERT: B 57 LYS cc_start: 0.8445 (ptpt) cc_final: 0.8164 (ptmt) REVERT: B 97 SER cc_start: 0.9348 (t) cc_final: 0.8649 (p) REVERT: B 118 ASP cc_start: 0.8523 (p0) cc_final: 0.8273 (p0) REVERT: B 134 ARG cc_start: 0.7058 (mmm-85) cc_final: 0.6761 (mtp-110) REVERT: B 176 GLN cc_start: 0.8776 (mt0) cc_final: 0.8426 (mt0) REVERT: B 228 ASP cc_start: 0.8225 (m-30) cc_final: 0.7775 (m-30) REVERT: B 247 ASP cc_start: 0.7947 (t0) cc_final: 0.7525 (t0) REVERT: B 325 MET cc_start: 0.8128 (mmt) cc_final: 0.7564 (mmt) REVERT: A 8 GLU cc_start: 0.8470 (mp0) cc_final: 0.8200 (mp0) REVERT: A 22 ASN cc_start: 0.8504 (m-40) cc_final: 0.8246 (m110) REVERT: A 25 GLU cc_start: 0.7599 (tp30) cc_final: 0.7391 (tp30) REVERT: A 214 CYS cc_start: 0.8586 (m) cc_final: 0.8324 (m) REVERT: A 248 LYS cc_start: 0.8871 (mttp) cc_final: 0.8463 (mtpt) REVERT: A 286 CYS cc_start: 0.8290 (p) cc_final: 0.7505 (t) REVERT: A 289 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: A 312 LYS cc_start: 0.8478 (mttt) cc_final: 0.8160 (mmmt) REVERT: G 27 ARG cc_start: 0.7328 (mtt-85) cc_final: 0.6831 (mtt-85) REVERT: G 46 LYS cc_start: 0.8723 (mttp) cc_final: 0.8514 (mmmm) outliers start: 27 outliers final: 25 residues processed: 262 average time/residue: 0.4102 time to fit residues: 143.3922 Evaluate side-chains 282 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 256 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 336 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 0.0070 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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: 0.7334 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7132 Z= 0.276 Angle : 0.501 6.719 9669 Z= 0.274 Chirality : 0.039 0.167 1107 Planarity : 0.004 0.043 1224 Dihedral : 4.180 31.535 970 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.77 % Allowed : 18.73 % Favored : 77.49 % 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: -0.46 (0.29), residues: 881 helix: 1.94 (0.26), residues: 396 sheet: -2.83 (0.36), residues: 149 loop : -1.85 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS A 213 PHE 0.015 0.001 PHE A 189 TYR 0.011 0.001 TYR G 40 ARG 0.006 0.000 ARG R 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 254 time to evaluate : 1.012 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8000 (mt-10) REVERT: R 236 GLU cc_start: 0.8397 (tt0) cc_final: 0.8191 (tt0) REVERT: R 285 GLU cc_start: 0.7812 (pm20) cc_final: 0.7315 (mt-10) REVERT: R 343 TYR cc_start: 0.8328 (m-80) cc_final: 0.8113 (m-80) REVERT: B 57 LYS cc_start: 0.8446 (ptpt) cc_final: 0.8156 (ptmt) REVERT: B 97 SER cc_start: 0.9290 (t) cc_final: 0.8625 (p) REVERT: B 118 ASP cc_start: 0.8496 (p0) cc_final: 0.8264 (p0) REVERT: B 134 ARG cc_start: 0.6911 (mmm-85) cc_final: 0.6617 (mtp-110) REVERT: B 176 GLN cc_start: 0.8780 (mt0) cc_final: 0.8434 (mt0) REVERT: B 228 ASP cc_start: 0.8150 (m-30) cc_final: 0.7751 (m-30) REVERT: B 247 ASP cc_start: 0.7938 (t0) cc_final: 0.7552 (t0) REVERT: B 325 MET cc_start: 0.8140 (mmt) cc_final: 0.7583 (mmt) REVERT: A 8 GLU cc_start: 0.8467 (mp0) cc_final: 0.8211 (mp0) REVERT: A 22 ASN cc_start: 0.8500 (m-40) cc_final: 0.8244 (m110) REVERT: A 214 CYS cc_start: 0.8523 (m) cc_final: 0.8259 (m) REVERT: A 248 LYS cc_start: 0.8923 (mttp) cc_final: 0.8476 (mtpt) REVERT: A 283 LEU cc_start: 0.8271 (tp) cc_final: 0.7998 (tt) REVERT: A 286 CYS cc_start: 0.8316 (p) cc_final: 0.7546 (t) REVERT: A 289 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: A 312 LYS cc_start: 0.8495 (mttt) cc_final: 0.8163 (mmmt) REVERT: A 333 GLN cc_start: 0.8831 (tt0) cc_final: 0.8573 (tp40) REVERT: G 27 ARG cc_start: 0.7339 (mtt-85) cc_final: 0.7090 (mtt-85) REVERT: G 46 LYS cc_start: 0.8724 (mttp) cc_final: 0.8508 (mmmm) outliers start: 28 outliers final: 27 residues processed: 263 average time/residue: 0.3962 time to fit residues: 138.4905 Evaluate side-chains 281 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 253 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 336 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7132 Z= 0.182 Angle : 0.476 7.449 9669 Z= 0.255 Chirality : 0.038 0.129 1107 Planarity : 0.003 0.045 1224 Dihedral : 3.996 24.738 970 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.83 % Allowed : 20.22 % Favored : 76.95 % 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: -0.17 (0.29), residues: 881 helix: 2.20 (0.26), residues: 396 sheet: -2.71 (0.36), residues: 150 loop : -1.72 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.006 0.001 HIS R 180 PHE 0.013 0.001 PHE A 189 TYR 0.010 0.001 TYR G 40 ARG 0.004 0.000 ARG R 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 249 time to evaluate : 1.055 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7928 (mt-10) REVERT: R 236 GLU cc_start: 0.8403 (tt0) cc_final: 0.8175 (tt0) REVERT: R 285 GLU cc_start: 0.7866 (pm20) cc_final: 0.7321 (mt-10) REVERT: B 57 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8134 (ptmt) REVERT: B 97 SER cc_start: 0.9318 (t) cc_final: 0.8653 (p) REVERT: B 118 ASP cc_start: 0.8507 (p0) cc_final: 0.8265 (p0) REVERT: B 134 ARG cc_start: 0.6879 (mmm-85) cc_final: 0.6597 (mtp-110) REVERT: B 176 GLN cc_start: 0.8755 (mt0) cc_final: 0.8411 (mt0) REVERT: B 228 ASP cc_start: 0.8147 (m-30) cc_final: 0.7776 (m-30) REVERT: B 247 ASP cc_start: 0.7894 (t0) cc_final: 0.7495 (t0) REVERT: B 325 MET cc_start: 0.8114 (mmt) cc_final: 0.7504 (mmt) REVERT: A 8 GLU cc_start: 0.8451 (mp0) cc_final: 0.8209 (mp0) REVERT: A 22 ASN cc_start: 0.8412 (m-40) cc_final: 0.8162 (m110) REVERT: A 214 CYS cc_start: 0.8513 (m) cc_final: 0.8238 (m) REVERT: A 248 LYS cc_start: 0.8888 (mttp) cc_final: 0.8477 (mtpt) REVERT: A 283 LEU cc_start: 0.8280 (tp) cc_final: 0.8060 (tt) REVERT: A 289 GLU cc_start: 0.8032 (pm20) cc_final: 0.7295 (pm20) REVERT: A 312 LYS cc_start: 0.8223 (mttt) cc_final: 0.7806 (mmmt) REVERT: A 351 TYR cc_start: 0.7855 (m-10) cc_final: 0.7639 (m-10) REVERT: G 27 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.6844 (mtt-85) REVERT: G 46 LYS cc_start: 0.8684 (mttp) cc_final: 0.8471 (mmmm) outliers start: 21 outliers final: 18 residues processed: 258 average time/residue: 0.3991 time to fit residues: 136.5352 Evaluate side-chains 262 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 244 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 336 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7132 Z= 0.408 Angle : 0.564 5.921 9669 Z= 0.316 Chirality : 0.040 0.184 1107 Planarity : 0.004 0.046 1224 Dihedral : 4.581 35.770 970 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.37 % Allowed : 20.08 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.29), residues: 881 helix: 1.79 (0.25), residues: 395 sheet: -2.96 (0.35), residues: 161 loop : -1.83 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 117 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.002 PHE A 189 TYR 0.015 0.002 TYR B 289 ARG 0.006 0.001 ARG R 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 255 time to evaluate : 1.103 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 236 GLU cc_start: 0.8441 (tt0) cc_final: 0.8234 (tt0) REVERT: R 285 GLU cc_start: 0.7937 (pm20) cc_final: 0.7316 (mt-10) REVERT: B 57 LYS cc_start: 0.8381 (ptpt) cc_final: 0.8108 (ptmt) REVERT: B 110 ASN cc_start: 0.8978 (m-40) cc_final: 0.8740 (m-40) REVERT: B 134 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6671 (mtp-110) REVERT: B 176 GLN cc_start: 0.8828 (mt0) cc_final: 0.8518 (mt0) REVERT: B 228 ASP cc_start: 0.8165 (m-30) cc_final: 0.7734 (m-30) REVERT: A 22 ASN cc_start: 0.8580 (m-40) cc_final: 0.8335 (m110) REVERT: A 214 CYS cc_start: 0.8575 (m) cc_final: 0.8301 (m) REVERT: A 248 LYS cc_start: 0.8983 (mttp) cc_final: 0.8510 (mtpt) REVERT: A 252 SER cc_start: 0.8745 (t) cc_final: 0.8453 (p) REVERT: A 289 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: A 312 LYS cc_start: 0.8263 (mttt) cc_final: 0.7907 (mmmt) REVERT: A 333 GLN cc_start: 0.8843 (tt0) cc_final: 0.8601 (tp40) REVERT: G 27 ARG cc_start: 0.7395 (mtt-85) cc_final: 0.7061 (mtt-85) REVERT: G 46 LYS cc_start: 0.8735 (mttp) cc_final: 0.8520 (mmmm) outliers start: 25 outliers final: 23 residues processed: 264 average time/residue: 0.4091 time to fit residues: 144.6204 Evaluate side-chains 274 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 250 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 336 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7132 Z= 0.218 Angle : 0.502 5.185 9669 Z= 0.273 Chirality : 0.038 0.129 1107 Planarity : 0.004 0.045 1224 Dihedral : 4.332 31.651 970 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.56 % Allowed : 22.51 % Favored : 74.93 % 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 (0.29), residues: 881 helix: 2.08 (0.26), residues: 393 sheet: -2.87 (0.36), residues: 151 loop : -1.79 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 330 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE A 189 TYR 0.011 0.001 TYR G 40 ARG 0.006 0.000 ARG R 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 250 time to evaluate : 0.773 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 180 HIS cc_start: 0.8489 (m-70) cc_final: 0.8267 (m-70) REVERT: R 236 GLU cc_start: 0.8422 (tt0) cc_final: 0.8207 (tt0) REVERT: R 285 GLU cc_start: 0.7989 (pm20) cc_final: 0.7379 (mt-10) REVERT: B 57 LYS cc_start: 0.8397 (ptpt) cc_final: 0.8132 (ptmt) REVERT: B 110 ASN cc_start: 0.8902 (m-40) cc_final: 0.8624 (m-40) REVERT: B 134 ARG cc_start: 0.6946 (mmm-85) cc_final: 0.6634 (mtp-110) REVERT: B 163 ASP cc_start: 0.7735 (t0) cc_final: 0.7524 (t0) REVERT: B 176 GLN cc_start: 0.8778 (mt0) cc_final: 0.8463 (mt0) REVERT: B 228 ASP cc_start: 0.8192 (m-30) cc_final: 0.7805 (m-30) REVERT: B 247 ASP cc_start: 0.8080 (t0) cc_final: 0.7694 (t0) REVERT: A 22 ASN cc_start: 0.8522 (m-40) cc_final: 0.8269 (m-40) REVERT: A 214 CYS cc_start: 0.8532 (m) cc_final: 0.8240 (m) REVERT: A 248 LYS cc_start: 0.8916 (mttp) cc_final: 0.8409 (mtpt) REVERT: A 252 SER cc_start: 0.8682 (t) cc_final: 0.8406 (p) REVERT: A 289 GLU cc_start: 0.8105 (pm20) cc_final: 0.7449 (pm20) REVERT: A 312 LYS cc_start: 0.8507 (mttt) cc_final: 0.8179 (mmmt) REVERT: G 27 ARG cc_start: 0.7346 (mtt-85) cc_final: 0.6981 (mtt-85) REVERT: G 46 LYS cc_start: 0.8696 (mttp) cc_final: 0.8483 (mmmm) outliers start: 19 outliers final: 19 residues processed: 257 average time/residue: 0.3017 time to fit residues: 103.5701 Evaluate side-chains 266 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 247 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 336 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 0.0770 chunk 74 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7132 Z= 0.168 Angle : 0.477 5.283 9669 Z= 0.257 Chirality : 0.038 0.132 1107 Planarity : 0.003 0.045 1224 Dihedral : 4.008 26.513 970 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.43 % Allowed : 22.10 % Favored : 75.47 % 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: 0.02 (0.29), residues: 881 helix: 2.36 (0.26), residues: 396 sheet: -2.62 (0.37), residues: 150 loop : -1.62 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.002 0.000 HIS A 188 PHE 0.013 0.001 PHE A 189 TYR 0.009 0.001 TYR G 40 ARG 0.006 0.000 ARG R 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 1.143 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 236 GLU cc_start: 0.8394 (tt0) cc_final: 0.8172 (tt0) REVERT: R 285 GLU cc_start: 0.8005 (pm20) cc_final: 0.7362 (mt-10) REVERT: B 57 LYS cc_start: 0.8370 (ptpt) cc_final: 0.8110 (ptmt) REVERT: B 97 SER cc_start: 0.9348 (t) cc_final: 0.8906 (p) REVERT: B 134 ARG cc_start: 0.6910 (mmm-85) cc_final: 0.6617 (mtp-110) REVERT: B 176 GLN cc_start: 0.8748 (mt0) cc_final: 0.8430 (mt0) REVERT: B 228 ASP cc_start: 0.8154 (m-30) cc_final: 0.7765 (m-30) REVERT: B 247 ASP cc_start: 0.7902 (t0) cc_final: 0.7670 (t0) REVERT: A 22 ASN cc_start: 0.8485 (m-40) cc_final: 0.8220 (m110) REVERT: A 214 CYS cc_start: 0.8533 (m) cc_final: 0.8245 (m) REVERT: A 248 LYS cc_start: 0.8906 (mttp) cc_final: 0.8497 (mtpt) REVERT: A 289 GLU cc_start: 0.8037 (pm20) cc_final: 0.7363 (pm20) REVERT: A 312 LYS cc_start: 0.8486 (mttt) cc_final: 0.8170 (mmmt) REVERT: G 27 ARG cc_start: 0.7314 (mtt-85) cc_final: 0.7080 (mtt-85) REVERT: G 46 LYS cc_start: 0.8625 (mttp) cc_final: 0.8423 (mmmm) outliers start: 18 outliers final: 17 residues processed: 259 average time/residue: 0.3976 time to fit residues: 137.7480 Evaluate side-chains 265 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 248 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 336 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.145677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114569 restraints weight = 24554.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120672 restraints weight = 11532.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124772 restraints weight = 7113.891| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7132 Z= 0.178 Angle : 0.479 5.149 9669 Z= 0.261 Chirality : 0.038 0.133 1107 Planarity : 0.003 0.043 1224 Dihedral : 3.934 25.941 970 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.29 % Allowed : 22.64 % Favored : 75.07 % 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: 0.13 (0.29), residues: 881 helix: 2.41 (0.25), residues: 398 sheet: -2.52 (0.37), residues: 150 loop : -1.55 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.003 0.000 HIS B 225 PHE 0.013 0.001 PHE A 189 TYR 0.009 0.001 TYR G 40 ARG 0.006 0.000 ARG R 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4073.93 seconds wall clock time: 84 minutes 36.59 seconds (5076.59 seconds total)