Starting phenix.real_space_refine on Tue Feb 13 18:35:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/02_2024/6mi7_9125_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/02_2024/6mi7_9125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/02_2024/6mi7_9125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/02_2024/6mi7_9125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/02_2024/6mi7_9125_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mi7_9125/02_2024/6mi7_9125_updated.pdb" } resolution = 4.2 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= 0.016 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 P 1 5.49 5 S 43 5.16 5 C 4713 2.51 5 N 1240 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 5": "NH1" <-> "NH2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ARG 33": "NH1" <-> "NH2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 6": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7285 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "G" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1778 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain breaks: 3 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 187 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.53, per 1000 atoms: 0.62 Number of scatterers: 7285 At special positions: 0 Unit cell: (81.18, 102.09, 109.47, 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 43 16.00 P 1 15.00 O 1288 8.00 N 1240 7.00 C 4713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 7 sheets defined 43.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.553A pdb=" N LEU F 7 " --> pdb=" O ILE F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 removed outlier: 3.709A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 51 No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 64 through 81 removed outlier: 3.569A pdb=" N PHE F 69 " --> pdb=" O PRO F 65 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 95 through 118 removed outlier: 3.747A pdb=" N LYS F 100 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET F 103 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU F 105 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE F 111 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA F 113 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN F 116 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET F 118 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 125 No H-bonds generated for 'chain 'F' and resid 122 through 125' Processing helix chain 'F' and resid 270 through 273 No H-bonds generated for 'chain 'F' and resid 270 through 273' Processing helix chain 'F' and resid 276 through 283 removed outlier: 3.999A pdb=" N ALA F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 298 No H-bonds generated for 'chain 'F' and resid 295 through 298' Processing helix chain 'F' and resid 300 through 318 removed outlier: 3.896A pdb=" N LEU F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR F 314 " --> pdb=" O PHE F 310 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 344 removed outlier: 3.723A pdb=" N THR F 333 " --> pdb=" O TRP F 330 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 337 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR F 338 " --> pdb=" O ASN F 335 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 341 " --> pdb=" O TYR F 338 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL F 344 " --> pdb=" O LEU F 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 34 removed outlier: 3.869A pdb=" N GLY G 12 " --> pdb=" O ASP G 8 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU G 23 " --> pdb=" O ILE G 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 58 No H-bonds generated for 'chain 'G' and resid 55 through 58' Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.811A pdb=" N VAL G 64 " --> pdb=" O VAL G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 60 through 64' Processing helix chain 'G' and resid 78 through 81 No H-bonds generated for 'chain 'G' and resid 78 through 81' Processing helix chain 'G' and resid 89 through 95 removed outlier: 3.883A pdb=" N ALA G 94 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.720A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.898A pdb=" N LEU G 115 " --> pdb=" O ILE G 111 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 130 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 270 through 279 removed outlier: 3.657A pdb=" N LYS G 278 " --> pdb=" O ASN G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 292 removed outlier: 3.565A pdb=" N LEU G 290 " --> pdb=" O ALA G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 323 removed outlier: 4.420A pdb=" N GLY G 316 " --> pdb=" O GLY G 312 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 318 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE G 319 " --> pdb=" O PHE G 315 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR G 320 " --> pdb=" O GLY G 316 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL G 321 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 332 removed outlier: 3.651A pdb=" N THR G 330 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 355 removed outlier: 3.851A pdb=" N PHE G 348 " --> pdb=" O PRO G 344 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER G 352 " --> pdb=" O PHE G 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.635A pdb=" N MET A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 removed outlier: 5.850A pdb=" N ALA A 76 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 113 through 122 removed outlier: 4.082A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 4.068A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.716A pdb=" N ARG A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.587A pdb=" N MET B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 4.171A pdb=" N ALA B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.773A pdb=" N ILE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 183 removed outlier: 3.981A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.589A pdb=" N LEU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 202' Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'C' and resid 5 through 22 removed outlier: 3.876A pdb=" N ILE C 9 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 11 " --> pdb=" O TRP C 7 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.551A pdb=" N LEU A 24 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 26 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 4 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.512A pdb=" N VAL A 190 " --> pdb=" O VAL A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 34 through 36 removed outlier: 7.191A pdb=" N TYR A 208 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 217 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 211 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 80 through 82 removed outlier: 6.927A pdb=" N PHE A 158 " --> pdb=" O GLY A 81 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.565A pdb=" N ILE B 61 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.563A pdb=" N VAL B 190 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 191 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR B 193 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 162 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.590A pdb=" N LYS B 11 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 19 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B 13 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 165 hydrogen bonds defined for protein. 420 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: 1.66 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2100 1.33 - 1.45: 1009 1.45 - 1.57: 4213 1.57 - 1.69: 2 1.69 - 1.81: 82 Bond restraints: 7406 Sorted by residual: bond pdb=" C11 PGT F 401 " pdb=" O3 PGT F 401 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C31 PGT F 401 " pdb=" O2 PGT F 401 " ideal model delta sigma weight residual 1.331 1.450 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C LEU F 300 " pdb=" N PRO F 301 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.65e+00 bond pdb=" O3P PGT F 401 " pdb=" P PGT F 401 " ideal model delta sigma weight residual 1.640 1.603 0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" O4P PGT F 401 " pdb=" P PGT F 401 " ideal model delta sigma weight residual 1.641 1.606 0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 7401 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.35: 217 106.35 - 113.26: 4070 113.26 - 120.17: 2817 120.17 - 127.08: 2842 127.08 - 133.98: 77 Bond angle restraints: 10023 Sorted by residual: angle pdb=" N VAL B 230 " pdb=" CA VAL B 230 " pdb=" C VAL B 230 " ideal model delta sigma weight residual 113.71 106.45 7.26 9.50e-01 1.11e+00 5.84e+01 angle pdb=" N ILE A 171 " pdb=" CA ILE A 171 " pdb=" C ILE A 171 " ideal model delta sigma weight residual 111.91 105.59 6.32 8.90e-01 1.26e+00 5.04e+01 angle pdb=" N ILE B 216 " pdb=" CA ILE B 216 " pdb=" C ILE B 216 " ideal model delta sigma weight residual 112.43 107.05 5.38 9.20e-01 1.18e+00 3.42e+01 angle pdb=" N VAL A 230 " pdb=" CA VAL A 230 " pdb=" C VAL A 230 " ideal model delta sigma weight residual 112.80 106.98 5.82 1.15e+00 7.56e-01 2.56e+01 angle pdb=" C LEU F 266 " pdb=" N ASN F 267 " pdb=" CA ASN F 267 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 ... (remaining 10018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 4316 25.94 - 51.88: 164 51.88 - 77.82: 11 77.82 - 103.76: 0 103.76 - 129.70: 1 Dihedral angle restraints: 4492 sinusoidal: 1817 harmonic: 2675 Sorted by residual: dihedral pdb=" CA ASN F 290 " pdb=" C ASN F 290 " pdb=" N PRO F 291 " pdb=" CA PRO F 291 " ideal model delta harmonic sigma weight residual -180.00 -147.24 -32.76 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA PHE B 90 " pdb=" C PHE B 90 " pdb=" N ARG B 91 " pdb=" CA ARG B 91 " ideal model delta harmonic sigma weight residual -180.00 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA PHE G 280 " pdb=" C PHE G 280 " pdb=" N GLN G 281 " pdb=" CA GLN G 281 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 4489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1074 0.090 - 0.179: 116 0.179 - 0.269: 11 0.269 - 0.358: 3 0.358 - 0.448: 1 Chirality restraints: 1205 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CB ILE A 62 " pdb=" CA ILE A 62 " pdb=" CG1 ILE A 62 " pdb=" CG2 ILE A 62 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB VAL G 258 " pdb=" CA VAL G 258 " pdb=" CG1 VAL G 258 " pdb=" CG2 VAL G 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 1202 not shown) Planarity restraints: 1246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 284 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO F 285 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 285 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 285 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 327 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO G 328 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 328 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 328 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 335 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO G 336 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO G 336 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 336 " 0.036 5.00e-02 4.00e+02 ... (remaining 1243 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 67 2.62 - 3.19: 6103 3.19 - 3.76: 10784 3.76 - 4.33: 14416 4.33 - 4.90: 22472 Nonbonded interactions: 53842 Sorted by model distance: nonbonded pdb=" O1P PGT F 401 " pdb=" O5 PGT F 401 " model vdw 2.053 2.440 nonbonded pdb=" OG1 THR A 220 " pdb=" OE1 GLU A 223 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR A 96 " pdb=" OE1 GLU A 115 " model vdw 2.342 2.440 nonbonded pdb=" O SER A 88 " pdb=" NH2 ARG A 150 " model vdw 2.352 2.520 nonbonded pdb=" OE2 GLU F 82 " pdb=" NH1 ARG B 91 " model vdw 2.353 2.520 ... (remaining 53837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.290 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: 1.950 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.560 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.006 0.125 7406 Z= 0.381 Angle : 1.187 13.614 10023 Z= 0.592 Chirality : 0.062 0.448 1205 Planarity : 0.008 0.067 1246 Dihedral : 12.825 129.702 2760 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.38 % Allowed : 9.29 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -5.97 (0.19), residues: 911 helix: -4.39 (0.11), residues: 436 sheet: -3.55 (0.43), residues: 78 loop : -3.37 (0.25), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 276 HIS 0.009 0.001 HIS F 89 PHE 0.039 0.003 PHE G 67 TYR 0.039 0.002 TYR F 80 ARG 0.005 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 373 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 TYR cc_start: 0.9254 (t80) cc_final: 0.8526 (t80) REVERT: F 59 MET cc_start: 0.5990 (tpp) cc_final: 0.5546 (ptt) REVERT: F 78 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7678 (ttmt) REVERT: F 281 LEU cc_start: 0.9068 (tt) cc_final: 0.8754 (tt) REVERT: F 297 LEU cc_start: 0.9472 (tp) cc_final: 0.9220 (tp) REVERT: F 314 THR cc_start: 0.9276 (p) cc_final: 0.8947 (m) REVERT: G 90 VAL cc_start: 0.9491 (m) cc_final: 0.9179 (t) REVERT: G 100 MET cc_start: 0.7296 (tpp) cc_final: 0.6867 (tpp) REVERT: G 108 LYS cc_start: 0.7410 (tmtt) cc_final: 0.6751 (tttt) REVERT: G 254 LEU cc_start: 0.9044 (tp) cc_final: 0.8819 (mm) REVERT: G 278 LYS cc_start: 0.9115 (ttmp) cc_final: 0.8823 (mtpt) REVERT: G 351 ILE cc_start: 0.9169 (mt) cc_final: 0.8927 (mt) REVERT: G 356 LEU cc_start: 0.7557 (pp) cc_final: 0.7350 (pp) REVERT: A 8 ASN cc_start: 0.8481 (m110) cc_final: 0.8088 (m110) REVERT: A 11 LYS cc_start: 0.8850 (tptp) cc_final: 0.8181 (tptm) REVERT: A 21 ASP cc_start: 0.7834 (t0) cc_final: 0.7451 (p0) REVERT: A 98 ASN cc_start: 0.8835 (t0) cc_final: 0.8404 (t0) REVERT: A 104 GLN cc_start: 0.8545 (mt0) cc_final: 0.8336 (mm110) REVERT: A 108 ASP cc_start: 0.9002 (p0) cc_final: 0.8694 (p0) REVERT: A 116 ASP cc_start: 0.7986 (m-30) cc_final: 0.7681 (t0) REVERT: A 123 GLU cc_start: 0.8180 (pt0) cc_final: 0.6570 (tm-30) REVERT: A 128 GLU cc_start: 0.7529 (pm20) cc_final: 0.6903 (pm20) REVERT: A 137 SER cc_start: 0.8660 (p) cc_final: 0.8417 (p) REVERT: A 155 ASN cc_start: 0.7942 (t0) cc_final: 0.7655 (t0) REVERT: A 162 ASP cc_start: 0.9049 (t0) cc_final: 0.8802 (t0) REVERT: A 185 ASP cc_start: 0.8635 (t70) cc_final: 0.8208 (t0) REVERT: A 220 THR cc_start: 0.7163 (p) cc_final: 0.6934 (m) REVERT: B 8 ASN cc_start: 0.8517 (m110) cc_final: 0.7338 (m110) REVERT: B 19 VAL cc_start: 0.9139 (t) cc_final: 0.8882 (t) REVERT: B 44 THR cc_start: 0.8961 (m) cc_final: 0.8630 (m) REVERT: B 82 TYR cc_start: 0.9066 (t80) cc_final: 0.8640 (t80) REVERT: B 95 VAL cc_start: 0.9148 (t) cc_final: 0.8932 (p) REVERT: B 100 MET cc_start: 0.8361 (mmm) cc_final: 0.7934 (mmm) REVERT: B 113 GLN cc_start: 0.7647 (pm20) cc_final: 0.7362 (pm20) REVERT: B 121 LEU cc_start: 0.9155 (tp) cc_final: 0.8821 (tt) REVERT: B 126 HIS cc_start: 0.8155 (m-70) cc_final: 0.7483 (m170) REVERT: B 145 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8545 (mtm180) REVERT: B 169 ASP cc_start: 0.8616 (p0) cc_final: 0.8408 (p0) REVERT: C 6 ARG cc_start: 0.7707 (mtp180) cc_final: 0.6003 (ptt180) outliers start: 3 outliers final: 0 residues processed: 374 average time/residue: 0.2112 time to fit residues: 101.7408 Evaluate side-chains 264 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.0270 overall best weight: 0.4252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN B 73 HIS B 85 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7406 Z= 0.161 Angle : 0.696 11.617 10023 Z= 0.343 Chirality : 0.043 0.230 1205 Planarity : 0.005 0.048 1246 Dihedral : 9.094 116.785 1050 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.25 % Allowed : 4.45 % Favored : 95.29 % 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: -4.71 (0.22), residues: 911 helix: -3.18 (0.19), residues: 436 sheet: -3.10 (0.49), residues: 68 loop : -2.94 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 354 HIS 0.002 0.001 HIS B 129 PHE 0.036 0.002 PHE G 67 TYR 0.021 0.001 TYR G 257 ARG 0.004 0.000 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 343 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.5977 (tpp) cc_final: 0.5355 (ptt) REVERT: F 88 MET cc_start: 0.8655 (tmm) cc_final: 0.8405 (tmm) REVERT: F 282 MET cc_start: 0.8667 (ptm) cc_final: 0.8404 (tmm) REVERT: F 297 LEU cc_start: 0.9460 (tp) cc_final: 0.9206 (tp) REVERT: G 20 MET cc_start: 0.6820 (tmm) cc_final: 0.6382 (tmm) REVERT: G 85 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8537 (pp30) REVERT: G 100 MET cc_start: 0.7116 (tpp) cc_final: 0.6774 (tpp) REVERT: G 108 LYS cc_start: 0.7473 (tmtt) cc_final: 0.6877 (tttt) REVERT: G 118 MET cc_start: 0.8048 (mmm) cc_final: 0.7819 (mmm) REVERT: G 254 LEU cc_start: 0.9024 (tp) cc_final: 0.8800 (mm) REVERT: G 256 ASN cc_start: 0.7925 (t0) cc_final: 0.7723 (t0) REVERT: G 288 MET cc_start: 0.8590 (mmp) cc_final: 0.8387 (mmt) REVERT: G 356 LEU cc_start: 0.7722 (pp) cc_final: 0.7515 (pp) REVERT: G 357 MET cc_start: 0.7677 (mmt) cc_final: 0.7430 (mmt) REVERT: A 21 ASP cc_start: 0.8090 (t0) cc_final: 0.7733 (t0) REVERT: A 49 VAL cc_start: 0.8882 (t) cc_final: 0.8131 (m) REVERT: A 70 LEU cc_start: 0.8477 (tp) cc_final: 0.8182 (mt) REVERT: A 89 ILE cc_start: 0.8631 (mm) cc_final: 0.8390 (mm) REVERT: A 98 ASN cc_start: 0.8837 (t0) cc_final: 0.8525 (t0) REVERT: A 100 MET cc_start: 0.8364 (ptp) cc_final: 0.8147 (ptp) REVERT: A 116 ASP cc_start: 0.7964 (m-30) cc_final: 0.7749 (t0) REVERT: A 123 GLU cc_start: 0.8178 (pt0) cc_final: 0.6963 (tm-30) REVERT: A 128 GLU cc_start: 0.7575 (pm20) cc_final: 0.6659 (pm20) REVERT: A 155 ASN cc_start: 0.8044 (t0) cc_final: 0.7762 (t0) REVERT: A 185 ASP cc_start: 0.8576 (t70) cc_final: 0.8350 (t0) REVERT: B 67 ILE cc_start: 0.9186 (pt) cc_final: 0.8978 (pt) REVERT: B 126 HIS cc_start: 0.8280 (m-70) cc_final: 0.7205 (m170) REVERT: B 145 ARG cc_start: 0.9172 (mtm-85) cc_final: 0.8462 (mtp85) REVERT: B 169 ASP cc_start: 0.8803 (p0) cc_final: 0.8503 (p0) REVERT: B 212 GLN cc_start: 0.9016 (mp10) cc_final: 0.8195 (mp10) REVERT: B 231 LYS cc_start: 0.6781 (mmpt) cc_final: 0.6109 (pttm) REVERT: C 6 ARG cc_start: 0.7571 (mtp180) cc_final: 0.6201 (ptt180) REVERT: C 19 MET cc_start: 0.8151 (tpp) cc_final: 0.7786 (tmm) outliers start: 2 outliers final: 0 residues processed: 345 average time/residue: 0.1771 time to fit residues: 81.5879 Evaluate side-chains 262 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 0.1980 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.0050 chunk 67 optimal weight: 4.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7406 Z= 0.178 Angle : 0.674 10.206 10023 Z= 0.330 Chirality : 0.043 0.230 1205 Planarity : 0.005 0.047 1246 Dihedral : 8.577 109.605 1050 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: -3.98 (0.25), residues: 911 helix: -2.48 (0.21), residues: 453 sheet: -2.81 (0.50), residues: 68 loop : -2.67 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 354 HIS 0.003 0.001 HIS F 89 PHE 0.026 0.001 PHE G 67 TYR 0.018 0.001 TYR B 13 ARG 0.003 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 5 ARG cc_start: 0.8544 (ttt180) cc_final: 0.8083 (ttp80) REVERT: F 59 MET cc_start: 0.6206 (tpp) cc_final: 0.5446 (ptt) REVERT: F 278 MET cc_start: 0.9063 (tpp) cc_final: 0.8784 (tpt) REVERT: F 279 MET cc_start: 0.8919 (mmp) cc_final: 0.8703 (mmm) REVERT: F 297 LEU cc_start: 0.9454 (tp) cc_final: 0.9109 (tp) REVERT: F 331 MET cc_start: 0.8541 (ppp) cc_final: 0.7572 (ppp) REVERT: G 20 MET cc_start: 0.6868 (tmm) cc_final: 0.6408 (tmm) REVERT: G 100 MET cc_start: 0.7389 (tpp) cc_final: 0.6811 (tpp) REVERT: G 108 LYS cc_start: 0.7450 (tmtt) cc_final: 0.6906 (tttt) REVERT: G 120 ILE cc_start: 0.8876 (pt) cc_final: 0.8517 (mm) REVERT: G 249 LEU cc_start: 0.7744 (mt) cc_final: 0.7466 (pt) REVERT: G 256 ASN cc_start: 0.7985 (t0) cc_final: 0.7781 (t0) REVERT: G 278 LYS cc_start: 0.9256 (mttt) cc_final: 0.8920 (mtpt) REVERT: G 357 MET cc_start: 0.7727 (mmt) cc_final: 0.7427 (mmt) REVERT: A 8 ASN cc_start: 0.8049 (m110) cc_final: 0.7749 (m-40) REVERT: A 21 ASP cc_start: 0.8016 (t0) cc_final: 0.7537 (p0) REVERT: A 42 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8285 (mtmm) REVERT: A 70 LEU cc_start: 0.8600 (tp) cc_final: 0.8316 (mt) REVERT: A 98 ASN cc_start: 0.8897 (t0) cc_final: 0.8465 (t0) REVERT: A 116 ASP cc_start: 0.8226 (m-30) cc_final: 0.7969 (t0) REVERT: A 123 GLU cc_start: 0.8203 (pt0) cc_final: 0.6969 (tm-30) REVERT: A 128 GLU cc_start: 0.7425 (pm20) cc_final: 0.6739 (pm20) REVERT: A 155 ASN cc_start: 0.8165 (t0) cc_final: 0.7852 (t0) REVERT: B 8 ASN cc_start: 0.8240 (m110) cc_final: 0.7375 (m110) REVERT: B 122 MET cc_start: 0.8984 (mtt) cc_final: 0.8678 (mtm) REVERT: B 126 HIS cc_start: 0.8343 (m-70) cc_final: 0.7434 (m170) REVERT: B 145 ARG cc_start: 0.9200 (mtm-85) cc_final: 0.8684 (mtm180) REVERT: B 169 ASP cc_start: 0.8856 (p0) cc_final: 0.8586 (p0) REVERT: C 6 ARG cc_start: 0.7395 (mtp180) cc_final: 0.6072 (ptt180) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1834 time to fit residues: 78.8795 Evaluate side-chains 258 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 0.0010 chunk 88 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7406 Z= 0.154 Angle : 0.656 10.614 10023 Z= 0.317 Chirality : 0.043 0.222 1205 Planarity : 0.004 0.045 1246 Dihedral : 8.182 107.267 1050 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % 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: -3.54 (0.26), residues: 911 helix: -2.09 (0.23), residues: 457 sheet: -2.34 (0.54), residues: 68 loop : -2.54 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 354 HIS 0.002 0.000 HIS B 73 PHE 0.021 0.001 PHE A 165 TYR 0.022 0.001 TYR F 80 ARG 0.003 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 5 ARG cc_start: 0.8611 (ttt180) cc_final: 0.8363 (ttp80) REVERT: F 59 MET cc_start: 0.6031 (tpp) cc_final: 0.5311 (ptt) REVERT: F 297 LEU cc_start: 0.9399 (tp) cc_final: 0.9099 (tp) REVERT: F 331 MET cc_start: 0.8487 (ppp) cc_final: 0.7557 (ppp) REVERT: G 8 ASP cc_start: 0.8011 (p0) cc_final: 0.7655 (p0) REVERT: G 9 ARG cc_start: 0.6393 (mpt180) cc_final: 0.5891 (ttm110) REVERT: G 20 MET cc_start: 0.6699 (tmm) cc_final: 0.6291 (tmm) REVERT: G 28 SER cc_start: 0.8720 (m) cc_final: 0.8060 (t) REVERT: G 100 MET cc_start: 0.7450 (tpp) cc_final: 0.6790 (tpp) REVERT: G 108 LYS cc_start: 0.7554 (tmtt) cc_final: 0.7104 (tttt) REVERT: G 249 LEU cc_start: 0.7609 (mt) cc_final: 0.7360 (pt) REVERT: G 256 ASN cc_start: 0.8008 (t0) cc_final: 0.7804 (t0) REVERT: G 288 MET cc_start: 0.8676 (mmp) cc_final: 0.8437 (mmp) REVERT: G 356 LEU cc_start: 0.7644 (pp) cc_final: 0.7278 (pp) REVERT: A 8 ASN cc_start: 0.7921 (m110) cc_final: 0.7613 (m-40) REVERT: A 21 ASP cc_start: 0.8019 (t0) cc_final: 0.7623 (p0) REVERT: A 70 LEU cc_start: 0.8596 (tp) cc_final: 0.8266 (mt) REVERT: A 98 ASN cc_start: 0.8816 (t0) cc_final: 0.8408 (t0) REVERT: A 116 ASP cc_start: 0.8356 (m-30) cc_final: 0.7933 (t0) REVERT: A 123 GLU cc_start: 0.8218 (pt0) cc_final: 0.6982 (tm-30) REVERT: A 128 GLU cc_start: 0.7392 (pm20) cc_final: 0.6723 (pm20) REVERT: A 155 ASN cc_start: 0.8125 (t0) cc_final: 0.7873 (t0) REVERT: A 162 ASP cc_start: 0.8933 (t70) cc_final: 0.8657 (t0) REVERT: B 8 ASN cc_start: 0.8335 (m110) cc_final: 0.7742 (m110) REVERT: B 65 ASP cc_start: 0.7652 (t0) cc_final: 0.7437 (t0) REVERT: B 67 ILE cc_start: 0.8917 (pt) cc_final: 0.8655 (pt) REVERT: B 100 MET cc_start: 0.7957 (mmm) cc_final: 0.7473 (mmm) REVERT: B 122 MET cc_start: 0.8916 (mtt) cc_final: 0.8621 (mtm) REVERT: B 126 HIS cc_start: 0.8214 (m-70) cc_final: 0.7633 (m170) REVERT: B 145 ARG cc_start: 0.9224 (mtm-85) cc_final: 0.8653 (mtm180) REVERT: B 186 SER cc_start: 0.9105 (m) cc_final: 0.8630 (p) REVERT: C 6 ARG cc_start: 0.7093 (mtp180) cc_final: 0.6221 (ptt180) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.1725 time to fit residues: 75.7923 Evaluate side-chains 258 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 36 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7406 Z= 0.183 Angle : 0.675 9.681 10023 Z= 0.326 Chirality : 0.044 0.221 1205 Planarity : 0.004 0.045 1246 Dihedral : 7.910 103.454 1050 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: -3.19 (0.27), residues: 911 helix: -1.79 (0.24), residues: 452 sheet: -2.03 (0.57), residues: 68 loop : -2.43 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 268 HIS 0.002 0.001 HIS F 89 PHE 0.017 0.001 PHE A 165 TYR 0.014 0.001 TYR F 80 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 0.806 Fit side-chains REVERT: F 5 ARG cc_start: 0.8625 (ttt180) cc_final: 0.8379 (ttp80) REVERT: F 26 PHE cc_start: 0.7552 (m-10) cc_final: 0.7309 (m-10) REVERT: F 59 MET cc_start: 0.5969 (tpp) cc_final: 0.5231 (ptt) REVERT: F 282 MET cc_start: 0.8853 (tmm) cc_final: 0.8494 (tmm) REVERT: F 297 LEU cc_start: 0.9414 (tp) cc_final: 0.9085 (tp) REVERT: F 331 MET cc_start: 0.8411 (ppp) cc_final: 0.7692 (ppp) REVERT: G 9 ARG cc_start: 0.6530 (mpt180) cc_final: 0.5980 (ttm110) REVERT: G 20 MET cc_start: 0.6728 (tmm) cc_final: 0.6332 (tmm) REVERT: G 28 SER cc_start: 0.8686 (m) cc_final: 0.8128 (t) REVERT: G 100 MET cc_start: 0.7612 (tpp) cc_final: 0.6913 (tpp) REVERT: G 108 LYS cc_start: 0.7697 (tmtt) cc_final: 0.7095 (tttt) REVERT: G 249 LEU cc_start: 0.7587 (mt) cc_final: 0.7380 (pt) REVERT: G 256 ASN cc_start: 0.8081 (t0) cc_final: 0.7818 (t0) REVERT: G 356 LEU cc_start: 0.7506 (pp) cc_final: 0.7130 (pp) REVERT: A 8 ASN cc_start: 0.7978 (m110) cc_final: 0.7719 (m110) REVERT: A 21 ASP cc_start: 0.8062 (t0) cc_final: 0.7708 (p0) REVERT: A 70 LEU cc_start: 0.8672 (tp) cc_final: 0.8311 (mt) REVERT: A 98 ASN cc_start: 0.9026 (t0) cc_final: 0.8559 (t0) REVERT: A 115 GLU cc_start: 0.8454 (tp30) cc_final: 0.8186 (tp30) REVERT: A 123 GLU cc_start: 0.8242 (pt0) cc_final: 0.7006 (tm-30) REVERT: A 128 GLU cc_start: 0.7423 (pm20) cc_final: 0.6720 (pm20) REVERT: A 155 ASN cc_start: 0.8196 (t0) cc_final: 0.7982 (t0) REVERT: A 162 ASP cc_start: 0.9287 (t70) cc_final: 0.8735 (t0) REVERT: A 220 THR cc_start: 0.6856 (p) cc_final: 0.5698 (p) REVERT: B 100 MET cc_start: 0.8026 (mmm) cc_final: 0.7499 (mmm) REVERT: B 122 MET cc_start: 0.8844 (mtt) cc_final: 0.8622 (mtm) REVERT: B 126 HIS cc_start: 0.8230 (m-70) cc_final: 0.7609 (m170) REVERT: B 145 ARG cc_start: 0.9277 (mtm-85) cc_final: 0.8663 (mtm180) REVERT: B 183 LEU cc_start: 0.9220 (pp) cc_final: 0.9012 (tt) REVERT: B 186 SER cc_start: 0.9139 (m) cc_final: 0.8605 (p) REVERT: C 6 ARG cc_start: 0.6914 (mtp180) cc_final: 0.6439 (ptt180) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1763 time to fit residues: 71.2580 Evaluate side-chains 249 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7406 Z= 0.183 Angle : 0.669 8.687 10023 Z= 0.322 Chirality : 0.044 0.180 1205 Planarity : 0.004 0.045 1246 Dihedral : 7.757 100.679 1050 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.13 % Allowed : 2.29 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.27), residues: 911 helix: -1.57 (0.25), residues: 441 sheet: -1.85 (0.65), residues: 56 loop : -2.32 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 268 HIS 0.003 0.001 HIS B 73 PHE 0.017 0.001 PHE A 165 TYR 0.019 0.001 TYR B 13 ARG 0.003 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 5 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8151 (ttp80) REVERT: F 26 PHE cc_start: 0.7525 (m-10) cc_final: 0.7316 (m-10) REVERT: F 59 MET cc_start: 0.6012 (tpp) cc_final: 0.5308 (ptt) REVERT: F 86 THR cc_start: 0.9057 (m) cc_final: 0.8800 (m) REVERT: F 282 MET cc_start: 0.8856 (tmm) cc_final: 0.8463 (tmm) REVERT: F 286 LEU cc_start: 0.9313 (tp) cc_final: 0.8811 (tt) REVERT: F 297 LEU cc_start: 0.9442 (tp) cc_final: 0.9097 (tp) REVERT: G 9 ARG cc_start: 0.6473 (mpt180) cc_final: 0.6163 (ttm110) REVERT: G 20 MET cc_start: 0.6843 (tmm) cc_final: 0.6422 (tmm) REVERT: G 28 SER cc_start: 0.8649 (m) cc_final: 0.8056 (t) REVERT: G 100 MET cc_start: 0.7342 (tpp) cc_final: 0.6762 (tpp) REVERT: G 108 LYS cc_start: 0.7656 (tmtt) cc_final: 0.7103 (tttt) REVERT: A 8 ASN cc_start: 0.8053 (m110) cc_final: 0.7795 (m110) REVERT: A 9 LEU cc_start: 0.8616 (mm) cc_final: 0.8316 (mt) REVERT: A 70 LEU cc_start: 0.8724 (tp) cc_final: 0.8339 (mt) REVERT: A 98 ASN cc_start: 0.8966 (t0) cc_final: 0.8570 (t0) REVERT: A 123 GLU cc_start: 0.8287 (pt0) cc_final: 0.7030 (tm-30) REVERT: A 128 GLU cc_start: 0.7405 (pm20) cc_final: 0.6719 (pm20) REVERT: A 155 ASN cc_start: 0.8246 (t0) cc_final: 0.8020 (t0) REVERT: A 162 ASP cc_start: 0.9169 (t70) cc_final: 0.8584 (t0) REVERT: B 8 ASN cc_start: 0.8181 (m110) cc_final: 0.7417 (m110) REVERT: B 100 MET cc_start: 0.7994 (mmm) cc_final: 0.7426 (mmm) REVERT: B 122 MET cc_start: 0.8838 (mtt) cc_final: 0.8561 (mtm) REVERT: B 126 HIS cc_start: 0.8435 (m-70) cc_final: 0.7909 (m170) REVERT: B 145 ARG cc_start: 0.9260 (mtm-85) cc_final: 0.8636 (mtm180) REVERT: B 183 LEU cc_start: 0.9208 (pp) cc_final: 0.8998 (tt) REVERT: B 186 SER cc_start: 0.9151 (m) cc_final: 0.8714 (p) REVERT: C 6 ARG cc_start: 0.6907 (mtp180) cc_final: 0.6410 (ptt180) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.1781 time to fit residues: 73.6753 Evaluate side-chains 252 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7406 Z= 0.175 Angle : 0.687 11.744 10023 Z= 0.326 Chirality : 0.044 0.231 1205 Planarity : 0.004 0.045 1246 Dihedral : 7.596 98.145 1050 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.27), residues: 911 helix: -1.46 (0.25), residues: 435 sheet: -1.78 (0.67), residues: 56 loop : -2.24 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 268 HIS 0.003 0.000 HIS B 73 PHE 0.046 0.001 PHE G 67 TYR 0.018 0.001 TYR F 80 ARG 0.003 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 5 ARG cc_start: 0.8621 (ttt180) cc_final: 0.8265 (ttp80) REVERT: F 59 MET cc_start: 0.5921 (tpp) cc_final: 0.5186 (ptt) REVERT: F 68 LEU cc_start: 0.9059 (tp) cc_final: 0.8594 (tt) REVERT: F 282 MET cc_start: 0.8885 (tmm) cc_final: 0.8387 (tmm) REVERT: F 297 LEU cc_start: 0.9419 (tp) cc_final: 0.9106 (tp) REVERT: G 9 ARG cc_start: 0.6563 (mpt180) cc_final: 0.6063 (ttm110) REVERT: G 28 SER cc_start: 0.8612 (m) cc_final: 0.8042 (t) REVERT: G 100 MET cc_start: 0.7426 (tpp) cc_final: 0.6934 (tpp) REVERT: G 108 LYS cc_start: 0.7728 (tmtt) cc_final: 0.7155 (tttt) REVERT: G 270 ARG cc_start: 0.8307 (mtm180) cc_final: 0.8105 (mtp180) REVERT: G 357 MET cc_start: 0.7774 (mmt) cc_final: 0.7537 (mmt) REVERT: A 70 LEU cc_start: 0.8724 (tp) cc_final: 0.8404 (mt) REVERT: A 73 HIS cc_start: 0.8696 (p90) cc_final: 0.8016 (p90) REVERT: A 98 ASN cc_start: 0.8910 (t0) cc_final: 0.8577 (t0) REVERT: A 100 MET cc_start: 0.8303 (ptp) cc_final: 0.8083 (ptp) REVERT: A 123 GLU cc_start: 0.8301 (pt0) cc_final: 0.7022 (tm-30) REVERT: A 128 GLU cc_start: 0.7361 (pm20) cc_final: 0.6785 (pm20) REVERT: A 155 ASN cc_start: 0.8228 (t0) cc_final: 0.7975 (t0) REVERT: A 161 LEU cc_start: 0.9128 (mp) cc_final: 0.8914 (mp) REVERT: A 162 ASP cc_start: 0.9162 (t70) cc_final: 0.8559 (t0) REVERT: B 100 MET cc_start: 0.7968 (mmm) cc_final: 0.7418 (mmm) REVERT: B 122 MET cc_start: 0.8808 (mtt) cc_final: 0.8563 (mtm) REVERT: B 126 HIS cc_start: 0.8472 (m-70) cc_final: 0.7895 (m170) REVERT: B 145 ARG cc_start: 0.9276 (mtm-85) cc_final: 0.8644 (mtm180) REVERT: B 186 SER cc_start: 0.9127 (m) cc_final: 0.8701 (p) REVERT: C 6 ARG cc_start: 0.6787 (mtp180) cc_final: 0.6404 (ptt180) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1724 time to fit residues: 72.3929 Evaluate side-chains 242 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7406 Z= 0.160 Angle : 0.682 13.883 10023 Z= 0.323 Chirality : 0.044 0.219 1205 Planarity : 0.005 0.052 1246 Dihedral : 7.475 96.420 1050 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.13 % Allowed : 0.89 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.27), residues: 911 helix: -1.39 (0.25), residues: 446 sheet: -1.60 (0.69), residues: 56 loop : -2.24 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 268 HIS 0.003 0.000 HIS B 73 PHE 0.029 0.001 PHE G 67 TYR 0.018 0.001 TYR B 96 ARG 0.003 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: F 5 ARG cc_start: 0.8620 (ttt180) cc_final: 0.8252 (ttp80) REVERT: F 26 PHE cc_start: 0.7403 (m-10) cc_final: 0.7192 (m-10) REVERT: F 59 MET cc_start: 0.5958 (tpp) cc_final: 0.5230 (ptt) REVERT: F 68 LEU cc_start: 0.9010 (tp) cc_final: 0.8577 (tt) REVERT: F 78 LYS cc_start: 0.8167 (tttt) cc_final: 0.7374 (tptt) REVERT: F 282 MET cc_start: 0.8944 (tmm) cc_final: 0.8352 (tmm) REVERT: F 286 LEU cc_start: 0.9320 (tp) cc_final: 0.8850 (tt) REVERT: F 297 LEU cc_start: 0.9405 (tp) cc_final: 0.9097 (tp) REVERT: G 8 ASP cc_start: 0.7980 (p0) cc_final: 0.7634 (p0) REVERT: G 9 ARG cc_start: 0.7188 (mpt180) cc_final: 0.6509 (ttm110) REVERT: G 20 MET cc_start: 0.6588 (tmm) cc_final: 0.6330 (tmm) REVERT: G 28 SER cc_start: 0.8627 (m) cc_final: 0.8071 (t) REVERT: G 100 MET cc_start: 0.7466 (tpp) cc_final: 0.6999 (tpp) REVERT: G 108 LYS cc_start: 0.7755 (tmtt) cc_final: 0.7138 (tttt) REVERT: G 120 ILE cc_start: 0.8842 (pt) cc_final: 0.8607 (mm) REVERT: G 270 ARG cc_start: 0.8285 (mtm180) cc_final: 0.8018 (mtp180) REVERT: G 357 MET cc_start: 0.7796 (mmt) cc_final: 0.7514 (mmt) REVERT: A 70 LEU cc_start: 0.8718 (tp) cc_final: 0.8377 (mt) REVERT: A 73 HIS cc_start: 0.8709 (p90) cc_final: 0.8023 (p90) REVERT: A 98 ASN cc_start: 0.8892 (t0) cc_final: 0.8541 (t0) REVERT: A 123 GLU cc_start: 0.8306 (pt0) cc_final: 0.7012 (tm-30) REVERT: A 128 GLU cc_start: 0.7356 (pm20) cc_final: 0.6781 (pm20) REVERT: A 155 ASN cc_start: 0.8201 (t0) cc_final: 0.7986 (t0) REVERT: A 161 LEU cc_start: 0.9083 (mp) cc_final: 0.8881 (mp) REVERT: A 162 ASP cc_start: 0.9138 (t70) cc_final: 0.8496 (t0) REVERT: B 8 ASN cc_start: 0.8213 (m110) cc_final: 0.7409 (m110) REVERT: B 100 MET cc_start: 0.7893 (mmm) cc_final: 0.7356 (mmm) REVERT: B 126 HIS cc_start: 0.8453 (m-70) cc_final: 0.8163 (m170) REVERT: B 186 SER cc_start: 0.9120 (m) cc_final: 0.8711 (p) REVERT: C 6 ARG cc_start: 0.6872 (mtp180) cc_final: 0.6472 (ptt180) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.1644 time to fit residues: 67.7358 Evaluate side-chains 243 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN F 313 GLN A 27 ASN B 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7406 Z= 0.235 Angle : 0.717 11.094 10023 Z= 0.346 Chirality : 0.046 0.211 1205 Planarity : 0.005 0.052 1246 Dihedral : 7.658 91.322 1050 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.27), residues: 911 helix: -1.38 (0.25), residues: 445 sheet: -1.97 (0.63), residues: 66 loop : -2.20 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 268 HIS 0.004 0.001 HIS F 89 PHE 0.032 0.002 PHE G 67 TYR 0.018 0.001 TYR F 80 ARG 0.003 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 0.882 Fit side-chains REVERT: F 59 MET cc_start: 0.6187 (tpp) cc_final: 0.5483 (ptt) REVERT: F 282 MET cc_start: 0.8966 (tmm) cc_final: 0.8400 (tmm) REVERT: F 286 LEU cc_start: 0.9341 (tp) cc_final: 0.8922 (tt) REVERT: F 297 LEU cc_start: 0.9418 (tp) cc_final: 0.9030 (tt) REVERT: G 8 ASP cc_start: 0.7986 (p0) cc_final: 0.7638 (p0) REVERT: G 9 ARG cc_start: 0.7271 (mpt180) cc_final: 0.6514 (ttp-110) REVERT: G 20 MET cc_start: 0.6658 (tmm) cc_final: 0.6457 (tmm) REVERT: G 62 LYS cc_start: 0.8833 (tptt) cc_final: 0.8279 (tppt) REVERT: G 100 MET cc_start: 0.7599 (tpp) cc_final: 0.7035 (tpp) REVERT: G 108 LYS cc_start: 0.7673 (tmtt) cc_final: 0.7066 (tttt) REVERT: G 120 ILE cc_start: 0.8871 (pt) cc_final: 0.8559 (mm) REVERT: G 270 ARG cc_start: 0.8305 (mtm180) cc_final: 0.8015 (mtp180) REVERT: G 357 MET cc_start: 0.7926 (mmt) cc_final: 0.7647 (mmt) REVERT: A 70 LEU cc_start: 0.8832 (tp) cc_final: 0.8468 (mt) REVERT: A 73 HIS cc_start: 0.8810 (p90) cc_final: 0.8057 (p90) REVERT: A 98 ASN cc_start: 0.9003 (t0) cc_final: 0.8670 (t0) REVERT: A 100 MET cc_start: 0.8337 (ptp) cc_final: 0.8093 (ptp) REVERT: A 107 ASP cc_start: 0.8114 (p0) cc_final: 0.7173 (m-30) REVERT: A 108 ASP cc_start: 0.8981 (p0) cc_final: 0.8760 (p0) REVERT: A 123 GLU cc_start: 0.8318 (pt0) cc_final: 0.7107 (tm-30) REVERT: A 128 GLU cc_start: 0.7371 (pm20) cc_final: 0.6811 (pm20) REVERT: A 155 ASN cc_start: 0.8292 (t0) cc_final: 0.8057 (t0) REVERT: A 162 ASP cc_start: 0.9188 (t70) cc_final: 0.8648 (t0) REVERT: A 220 THR cc_start: 0.6303 (p) cc_final: 0.5776 (t) REVERT: B 8 ASN cc_start: 0.8403 (m110) cc_final: 0.7652 (m-40) REVERT: B 100 MET cc_start: 0.7982 (mmm) cc_final: 0.7762 (mmm) REVERT: B 122 MET cc_start: 0.8914 (mtm) cc_final: 0.8703 (mtm) REVERT: B 126 HIS cc_start: 0.8504 (m-70) cc_final: 0.8194 (m170) REVERT: B 186 SER cc_start: 0.9213 (m) cc_final: 0.8803 (p) REVERT: C 1 MET cc_start: 0.5058 (tpt) cc_final: 0.4846 (ttm) REVERT: C 6 ARG cc_start: 0.7230 (mtp180) cc_final: 0.6237 (ptt180) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1682 time to fit residues: 65.9643 Evaluate side-chains 234 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7406 Z= 0.219 Angle : 0.717 11.541 10023 Z= 0.344 Chirality : 0.045 0.220 1205 Planarity : 0.005 0.049 1246 Dihedral : 7.662 89.240 1050 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -2.65 (0.27), residues: 911 helix: -1.34 (0.25), residues: 449 sheet: -1.78 (0.69), residues: 56 loop : -2.17 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 268 HIS 0.004 0.001 HIS B 73 PHE 0.031 0.002 PHE G 67 TYR 0.019 0.001 TYR B 96 ARG 0.003 0.000 ARG B 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 0.847 Fit side-chains REVERT: F 59 MET cc_start: 0.6172 (tpp) cc_final: 0.5517 (ptt) REVERT: F 78 LYS cc_start: 0.8165 (tttt) cc_final: 0.7408 (tptt) REVERT: F 282 MET cc_start: 0.9016 (tmm) cc_final: 0.8117 (tmm) REVERT: F 286 LEU cc_start: 0.9346 (tp) cc_final: 0.8959 (tt) REVERT: F 297 LEU cc_start: 0.9434 (tp) cc_final: 0.9038 (tt) REVERT: G 9 ARG cc_start: 0.7359 (mpt180) cc_final: 0.6535 (ttp-110) REVERT: G 100 MET cc_start: 0.7662 (tpp) cc_final: 0.7144 (tpp) REVERT: G 108 LYS cc_start: 0.7661 (tmtt) cc_final: 0.7108 (tttt) REVERT: G 120 ILE cc_start: 0.8882 (pt) cc_final: 0.8544 (mm) REVERT: G 270 ARG cc_start: 0.8348 (mtm180) cc_final: 0.8039 (mtp180) REVERT: G 357 MET cc_start: 0.7904 (mmt) cc_final: 0.7630 (mmt) REVERT: A 70 LEU cc_start: 0.8889 (tp) cc_final: 0.8539 (mt) REVERT: A 73 HIS cc_start: 0.8830 (p90) cc_final: 0.8059 (p90) REVERT: A 98 ASN cc_start: 0.9013 (t0) cc_final: 0.8557 (t0) REVERT: A 100 MET cc_start: 0.8294 (ptp) cc_final: 0.8064 (ptp) REVERT: A 107 ASP cc_start: 0.8124 (p0) cc_final: 0.7214 (m-30) REVERT: A 123 GLU cc_start: 0.8314 (pt0) cc_final: 0.6720 (tm-30) REVERT: A 128 GLU cc_start: 0.7360 (pm20) cc_final: 0.7022 (pm20) REVERT: A 155 ASN cc_start: 0.8264 (t0) cc_final: 0.7979 (t0) REVERT: A 162 ASP cc_start: 0.9195 (t70) cc_final: 0.8633 (t0) REVERT: B 82 TYR cc_start: 0.8780 (t80) cc_final: 0.8549 (t80) REVERT: B 100 MET cc_start: 0.7990 (mmm) cc_final: 0.7648 (mmm) REVERT: B 126 HIS cc_start: 0.8484 (m-70) cc_final: 0.8150 (m170) REVERT: B 186 SER cc_start: 0.9238 (m) cc_final: 0.8737 (p) REVERT: C 6 ARG cc_start: 0.7253 (mtp180) cc_final: 0.6211 (ptt180) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1702 time to fit residues: 63.3180 Evaluate side-chains 235 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.0050 chunk 64 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN B 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115641 restraints weight = 12200.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118217 restraints weight = 7952.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120016 restraints weight = 5940.949| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7406 Z= 0.159 Angle : 0.705 12.736 10023 Z= 0.331 Chirality : 0.043 0.228 1205 Planarity : 0.004 0.047 1246 Dihedral : 7.343 89.411 1050 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -2.42 (0.27), residues: 911 helix: -1.17 (0.26), residues: 438 sheet: -1.51 (0.71), residues: 56 loop : -2.04 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 268 HIS 0.004 0.001 HIS B 129 PHE 0.026 0.001 PHE G 67 TYR 0.018 0.001 TYR F 6 ARG 0.004 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.96 seconds wall clock time: 37 minutes 19.00 seconds (2239.00 seconds total)