Starting phenix.real_space_refine on Mon Mar 11 02:20:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/03_2024/7xmr_33302.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/03_2024/7xmr_33302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/03_2024/7xmr_33302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/03_2024/7xmr_33302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/03_2024/7xmr_33302.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/03_2024/7xmr_33302.pdb" } resolution = 3.1 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4250 2.51 5 N 1091 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R ARG 116": "NH1" <-> "NH2" Residue "R ASP 122": "OD1" <-> "OD2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 247": "NH1" <-> "NH2" Residue "R ARG 256": "NH1" <-> "NH2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6611 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2165 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 273} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1728 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2351 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 308} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 253 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 114 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 3.85, per 1000 atoms: 0.58 Number of scatterers: 6611 At special positions: 0 Unit cell: (111.815, 114.95, 80.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1218 8.00 N 1091 7.00 C 4250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 14 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 43.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'R' and resid 39 through 70 removed outlier: 3.507A pdb=" N ASN R 43 " --> pdb=" O ASP R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 105 removed outlier: 3.539A pdb=" N LEU R 105 " --> pdb=" O MET R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 146 Processing helix chain 'R' and resid 149 through 154 Processing helix chain 'R' and resid 155 through 173 Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 203 through 217 removed outlier: 3.625A pdb=" N LEU R 215 " --> pdb=" O TYR R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 243 Processing helix chain 'R' and resid 246 through 282 removed outlier: 3.796A pdb=" N SER R 250 " --> pdb=" O LYS R 246 " (cutoff:3.500A) Proline residue: R 271 - end of helix removed outlier: 3.560A pdb=" N MET R 282 " --> pdb=" O SER R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 315 Proline residue: R 309 - end of helix removed outlier: 3.590A pdb=" N LEU R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 323 removed outlier: 3.531A pdb=" N LYS R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 33 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.856A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.593A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.650A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.765A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.980A pdb=" N LEU C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.507A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.182A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.306A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.118A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.891A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.723A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.934A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2095 1.34 - 1.46: 1549 1.46 - 1.58: 3039 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 6754 Sorted by residual: bond pdb=" C ILE B 270 " pdb=" O ILE B 270 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.74e-01 bond pdb=" C LEU R 270 " pdb=" N PRO R 271 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.65e-01 bond pdb=" C GLY B 144 " pdb=" O GLY B 144 " ideal model delta sigma weight residual 1.230 1.237 -0.007 1.37e-02 5.33e+03 2.99e-01 bond pdb=" C ASP C 48 " pdb=" N PRO C 49 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.19e-02 7.06e+03 2.95e-01 bond pdb=" C LEU R 96 " pdb=" O LEU R 96 " ideal model delta sigma weight residual 1.238 1.244 -0.007 1.28e-02 6.10e+03 2.67e-01 ... (remaining 6749 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 175 107.38 - 114.03: 3925 114.03 - 120.68: 2734 120.68 - 127.33: 2289 127.33 - 133.98: 70 Bond angle restraints: 9193 Sorted by residual: angle pdb=" CA LEU R 96 " pdb=" C LEU R 96 " pdb=" N PRO R 97 " ideal model delta sigma weight residual 118.44 121.60 -3.16 1.59e+00 3.96e-01 3.95e+00 angle pdb=" CA ILE B 270 " pdb=" C ILE B 270 " pdb=" N CYS B 271 " ideal model delta sigma weight residual 116.60 119.46 -2.86 1.45e+00 4.76e-01 3.90e+00 angle pdb=" N ILE R 210 " pdb=" CA ILE R 210 " pdb=" C ILE R 210 " ideal model delta sigma weight residual 113.16 110.44 2.72 1.49e+00 4.50e-01 3.33e+00 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 109.34 113.08 -3.74 2.08e+00 2.31e-01 3.23e+00 angle pdb=" N LEU R 96 " pdb=" CA LEU R 96 " pdb=" C LEU R 96 " ideal model delta sigma weight residual 109.81 113.55 -3.74 2.21e+00 2.05e-01 2.87e+00 ... (remaining 9188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 3697 17.17 - 34.35: 212 34.35 - 51.52: 35 51.52 - 68.69: 3 68.69 - 85.87: 3 Dihedral angle restraints: 3950 sinusoidal: 1418 harmonic: 2532 Sorted by residual: dihedral pdb=" CB CYS L 3 " pdb=" SG CYS L 3 " pdb=" SG CYS L 14 " pdb=" CB CYS L 14 " ideal model delta sinusoidal sigma weight residual -86.00 -130.68 44.68 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " pdb=" CD GLU B 215 " pdb=" OE1 GLU B 215 " ideal model delta sinusoidal sigma weight residual 0.00 85.87 -85.87 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " pdb=" OE1 GLU C 42 " ideal model delta sinusoidal sigma weight residual 0.00 -85.81 85.81 1 3.00e+01 1.11e-03 9.89e+00 ... (remaining 3947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 685 0.026 - 0.051: 257 0.051 - 0.077: 81 0.077 - 0.102: 38 0.102 - 0.128: 24 Chirality restraints: 1085 Sorted by residual: chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-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 3.91e-01 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 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1082 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 194 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 96 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.15e-01 pdb=" N PRO R 97 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 97 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 97 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 155 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.00e-01 pdb=" N PRO R 156 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO R 156 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 156 " 0.013 5.00e-02 4.00e+02 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1492 2.78 - 3.31: 6170 3.31 - 3.84: 10874 3.84 - 4.37: 12706 4.37 - 4.90: 22023 Nonbonded interactions: 53265 Sorted by model distance: nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.287 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR R 205 " pdb=" O ALA L 1 " model vdw 2.317 2.440 nonbonded pdb=" O ARG B 52 " pdb=" NZ LYS B 89 " model vdw 2.318 2.520 ... (remaining 53260 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.760 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 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 : 0.001 0.017 6754 Z= 0.084 Angle : 0.400 5.729 9193 Z= 0.231 Chirality : 0.036 0.128 1085 Planarity : 0.002 0.028 1148 Dihedral : 10.864 85.867 2304 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -3.39 (0.23), residues: 859 helix: -2.56 (0.19), residues: 349 sheet: -1.24 (0.38), residues: 155 loop : -2.21 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 63 HIS 0.006 0.001 HIS A 188 PHE 0.006 0.000 PHE R 51 TYR 0.004 0.000 TYR B 289 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 180 TYR cc_start: 0.7393 (m-80) cc_final: 0.6501 (m-10) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2477 time to fit residues: 51.6933 Evaluate side-chains 119 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 43 ASN R 146 HIS R 186 ASN R 276 ASN R 304 ASN A 22 ASN A 188 HIS A 331 ASN A 333 GLN B 62 HIS B 110 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6754 Z= 0.312 Angle : 0.634 7.008 9193 Z= 0.333 Chirality : 0.043 0.146 1085 Planarity : 0.005 0.046 1148 Dihedral : 3.579 23.252 921 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.72 % Allowed : 13.77 % Favored : 84.51 % 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: -1.26 (0.27), residues: 859 helix: 0.07 (0.26), residues: 350 sheet: -1.13 (0.36), residues: 167 loop : -1.53 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.010 0.002 HIS B 311 PHE 0.016 0.002 PHE R 272 TYR 0.014 0.002 TYR R 228 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 0.798 Fit side-chains REVERT: R 161 MET cc_start: 0.5400 (tmm) cc_final: 0.5182 (tmm) REVERT: R 241 ARG cc_start: 0.7324 (ttp-170) cc_final: 0.7082 (ttp-170) REVERT: A 349 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7336 (mttm) REVERT: B 76 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7388 (p0) outliers start: 12 outliers final: 9 residues processed: 138 average time/residue: 0.2028 time to fit residues: 36.6941 Evaluate side-chains 123 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6754 Z= 0.209 Angle : 0.543 7.260 9193 Z= 0.282 Chirality : 0.041 0.164 1085 Planarity : 0.003 0.034 1148 Dihedral : 3.497 20.712 921 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.01 % Allowed : 16.50 % Favored : 81.49 % 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: -0.41 (0.28), residues: 859 helix: 1.04 (0.28), residues: 349 sheet: -0.90 (0.37), residues: 169 loop : -1.25 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.011 0.001 PHE R 272 TYR 0.014 0.001 TYR B 289 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.733 Fit side-chains REVERT: R 241 ARG cc_start: 0.7241 (ttp-170) cc_final: 0.7034 (ttp-170) REVERT: A 349 LYS cc_start: 0.7592 (mtpp) cc_final: 0.7347 (mttt) REVERT: B 220 GLN cc_start: 0.7536 (mt0) cc_final: 0.7141 (mm-40) REVERT: B 329 THR cc_start: 0.8620 (m) cc_final: 0.7917 (p) outliers start: 14 outliers final: 9 residues processed: 126 average time/residue: 0.1885 time to fit residues: 31.5262 Evaluate side-chains 118 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 269 ASN A 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6754 Z= 0.202 Angle : 0.544 7.568 9193 Z= 0.280 Chirality : 0.041 0.167 1085 Planarity : 0.003 0.041 1148 Dihedral : 3.575 17.864 921 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.15 % Allowed : 17.93 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 859 helix: 1.51 (0.28), residues: 348 sheet: -0.82 (0.36), residues: 169 loop : -1.11 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.009 0.001 PHE A 334 TYR 0.012 0.001 TYR B 289 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.759 Fit side-chains REVERT: R 101 MET cc_start: 0.5938 (mmt) cc_final: 0.5660 (mmm) REVERT: A 308 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7251 (mt-10) REVERT: A 349 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7376 (mttt) REVERT: B 101 MET cc_start: 0.7857 (mtp) cc_final: 0.7559 (mtp) REVERT: B 220 GLN cc_start: 0.7577 (mt0) cc_final: 0.7207 (mm-40) REVERT: B 329 THR cc_start: 0.8730 (m) cc_final: 0.8100 (p) outliers start: 15 outliers final: 13 residues processed: 123 average time/residue: 0.2082 time to fit residues: 33.4439 Evaluate side-chains 122 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6754 Z= 0.201 Angle : 0.538 7.956 9193 Z= 0.278 Chirality : 0.041 0.145 1085 Planarity : 0.004 0.050 1148 Dihedral : 3.596 16.956 921 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.30 % Allowed : 18.65 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.29), residues: 859 helix: 1.67 (0.28), residues: 349 sheet: -0.72 (0.36), residues: 169 loop : -1.09 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.009 0.001 PHE A 334 TYR 0.015 0.001 TYR B 59 ARG 0.013 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.891 Fit side-chains REVERT: R 101 MET cc_start: 0.5911 (mmt) cc_final: 0.5647 (mmm) REVERT: R 209 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5684 (mm) REVERT: A 304 GLN cc_start: 0.7023 (tt0) cc_final: 0.6746 (tt0) REVERT: A 349 LYS cc_start: 0.7661 (mtpp) cc_final: 0.7390 (mttt) REVERT: B 101 MET cc_start: 0.7933 (mtp) cc_final: 0.7703 (mtp) REVERT: B 220 GLN cc_start: 0.7630 (mt0) cc_final: 0.7401 (mm-40) REVERT: B 329 THR cc_start: 0.8726 (m) cc_final: 0.8120 (p) outliers start: 16 outliers final: 15 residues processed: 127 average time/residue: 0.1888 time to fit residues: 31.6987 Evaluate side-chains 127 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.0470 chunk 38 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 79 optimal weight: 0.0170 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6754 Z= 0.170 Angle : 0.527 7.882 9193 Z= 0.271 Chirality : 0.041 0.147 1085 Planarity : 0.003 0.050 1148 Dihedral : 3.569 16.378 921 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.16 % Allowed : 18.22 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 859 helix: 1.82 (0.28), residues: 348 sheet: -0.65 (0.36), residues: 171 loop : -0.96 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.009 0.001 PHE A 334 TYR 0.013 0.001 TYR B 59 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.794 Fit side-chains REVERT: R 101 MET cc_start: 0.5849 (mmt) cc_final: 0.5614 (mmm) REVERT: A 349 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7370 (mttt) REVERT: B 101 MET cc_start: 0.7954 (mtp) cc_final: 0.7638 (mtp) REVERT: B 220 GLN cc_start: 0.7615 (mt0) cc_final: 0.7330 (mm-40) REVERT: B 329 THR cc_start: 0.8728 (m) cc_final: 0.8139 (p) outliers start: 22 outliers final: 18 residues processed: 134 average time/residue: 0.1786 time to fit residues: 32.2503 Evaluate side-chains 130 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 32 optimal weight: 0.0370 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN A 331 ASN L 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6754 Z= 0.278 Angle : 0.622 8.159 9193 Z= 0.321 Chirality : 0.043 0.146 1085 Planarity : 0.004 0.055 1148 Dihedral : 3.924 16.166 921 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.44 % Allowed : 19.51 % Favored : 77.04 % 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: 0.13 (0.29), residues: 859 helix: 1.56 (0.28), residues: 349 sheet: -0.80 (0.36), residues: 171 loop : -0.95 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS B 54 PHE 0.034 0.002 PHE A 189 TYR 0.028 0.002 TYR B 59 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.764 Fit side-chains REVERT: A 198 MET cc_start: 0.7808 (mpp) cc_final: 0.7466 (mpp) REVERT: A 349 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7328 (mttm) REVERT: B 220 GLN cc_start: 0.7743 (mt0) cc_final: 0.7462 (mt0) REVERT: B 329 THR cc_start: 0.8768 (m) cc_final: 0.8220 (p) outliers start: 24 outliers final: 18 residues processed: 128 average time/residue: 0.1821 time to fit residues: 31.2209 Evaluate side-chains 123 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 52 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6754 Z= 0.186 Angle : 0.575 8.316 9193 Z= 0.292 Chirality : 0.042 0.156 1085 Planarity : 0.004 0.054 1148 Dihedral : 3.818 17.780 921 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.73 % Allowed : 21.23 % Favored : 76.04 % 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: 0.22 (0.29), residues: 859 helix: 1.70 (0.29), residues: 349 sheet: -0.86 (0.35), residues: 176 loop : -0.90 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.009 0.001 HIS B 183 PHE 0.019 0.001 PHE A 189 TYR 0.013 0.001 TYR B 59 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.790 Fit side-chains REVERT: R 101 MET cc_start: 0.5882 (mmt) cc_final: 0.5630 (mmm) REVERT: R 190 ARG cc_start: 0.5988 (mtm-85) cc_final: 0.5743 (mtm-85) REVERT: A 198 MET cc_start: 0.7842 (mpp) cc_final: 0.7603 (mpp) REVERT: A 308 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 349 LYS cc_start: 0.7746 (mtpp) cc_final: 0.7499 (mttm) REVERT: B 101 MET cc_start: 0.7871 (mtp) cc_final: 0.7649 (mtp) REVERT: B 329 THR cc_start: 0.8756 (m) cc_final: 0.8219 (p) outliers start: 19 outliers final: 18 residues processed: 125 average time/residue: 0.2053 time to fit residues: 33.7673 Evaluate side-chains 128 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.0170 chunk 80 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6754 Z= 0.194 Angle : 0.578 8.435 9193 Z= 0.294 Chirality : 0.042 0.141 1085 Planarity : 0.004 0.055 1148 Dihedral : 3.819 17.199 921 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.01 % Allowed : 21.09 % Favored : 75.90 % 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: 0.24 (0.29), residues: 859 helix: 1.70 (0.28), residues: 349 sheet: -0.86 (0.35), residues: 173 loop : -0.85 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.008 0.001 HIS B 183 PHE 0.018 0.001 PHE A 189 TYR 0.015 0.001 TYR B 59 ARG 0.012 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.780 Fit side-chains REVERT: R 190 ARG cc_start: 0.6104 (mtm-85) cc_final: 0.5853 (mtm-85) REVERT: A 198 MET cc_start: 0.7825 (mpp) cc_final: 0.7485 (mpp) REVERT: A 349 LYS cc_start: 0.7737 (mtpp) cc_final: 0.7490 (mttm) REVERT: B 101 MET cc_start: 0.7943 (mtp) cc_final: 0.7716 (mtp) REVERT: B 220 GLN cc_start: 0.7733 (mt0) cc_final: 0.7509 (mt0) REVERT: B 329 THR cc_start: 0.8760 (m) cc_final: 0.8198 (p) REVERT: L 5 ASN cc_start: 0.6887 (t0) cc_final: 0.6558 (t0) outliers start: 21 outliers final: 18 residues processed: 127 average time/residue: 0.1829 time to fit residues: 31.0278 Evaluate side-chains 126 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 77 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6754 Z= 0.190 Angle : 0.583 8.639 9193 Z= 0.295 Chirality : 0.042 0.149 1085 Planarity : 0.004 0.052 1148 Dihedral : 3.844 17.315 921 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.73 % Allowed : 21.52 % Favored : 75.75 % 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: 0.21 (0.29), residues: 859 helix: 1.66 (0.28), residues: 350 sheet: -0.83 (0.35), residues: 171 loop : -0.90 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.007 0.001 HIS B 183 PHE 0.020 0.001 PHE A 189 TYR 0.015 0.001 TYR B 59 ARG 0.010 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.742 Fit side-chains REVERT: R 190 ARG cc_start: 0.6254 (mtm-85) cc_final: 0.6043 (mtm-85) REVERT: A 349 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7490 (mttm) REVERT: B 52 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7688 (mpt90) REVERT: B 101 MET cc_start: 0.7989 (mtp) cc_final: 0.7753 (mtm) REVERT: B 220 GLN cc_start: 0.7759 (mt0) cc_final: 0.7464 (mt0) REVERT: B 329 THR cc_start: 0.8763 (m) cc_final: 0.8196 (p) outliers start: 19 outliers final: 18 residues processed: 127 average time/residue: 0.2006 time to fit residues: 34.0491 Evaluate side-chains 129 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.0060 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.199378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.165605 restraints weight = 6878.704| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.07 r_work: 0.4083 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6754 Z= 0.187 Angle : 0.583 8.672 9193 Z= 0.295 Chirality : 0.042 0.152 1085 Planarity : 0.004 0.049 1148 Dihedral : 3.827 17.895 921 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.73 % Allowed : 21.38 % Favored : 75.90 % 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: 0.22 (0.29), residues: 859 helix: 1.65 (0.28), residues: 350 sheet: -0.86 (0.35), residues: 173 loop : -0.84 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS B 183 PHE 0.017 0.001 PHE A 189 TYR 0.015 0.001 TYR B 59 ARG 0.010 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.08 seconds wall clock time: 37 minutes 27.92 seconds (2247.92 seconds total)