Starting phenix.real_space_refine on Thu Jan 16 09:25:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rik_19188/01_2025/8rik_19188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rik_19188/01_2025/8rik_19188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rik_19188/01_2025/8rik_19188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rik_19188/01_2025/8rik_19188.map" model { file = "/net/cci-nas-00/data/ceres_data/8rik_19188/01_2025/8rik_19188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rik_19188/01_2025/8rik_19188.cif" } resolution = 3.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 5873 2.51 5 N 1591 2.21 5 O 1821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9353 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3358 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "K" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2448 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 3, 24 Classifications: {'peptide': 3} Link IDs: {'PTRANS': 1, 'TRANS': 1} Chain: "t" Number of atoms: 22 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 22 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ALYS T 922 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS T 922 " occ=0.50 residue: pdb=" N APRO T 923 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO T 923 " occ=0.50 residue: pdb=" N AILE T 924 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE T 924 " occ=0.50 residue: pdb=" N BILE t 920 " occ=0.50 ... (6 atoms not shown) pdb=" CD1BILE t 920 " occ=0.50 residue: pdb=" N BALA t 921 " occ=0.50 ... (3 atoms not shown) pdb=" CB BALA t 921 " occ=0.50 residue: pdb=" N BLYS t 922 " occ=0.50 ... (7 atoms not shown) pdb=" NZ BLYS t 922 " occ=0.50 Time building chain proxies: 6.13, per 1000 atoms: 0.66 Number of scatterers: 9353 At special positions: 0 Unit cell: (70.395, 109.383, 115.881, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 7 15.00 Mg 1 11.99 O 1821 8.00 N 1591 7.00 C 5873 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 46.2% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.300A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.639A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.642A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.819A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 removed outlier: 3.701A pdb=" N ARG B 243 " --> pdb=" O THR B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.532A pdb=" N VAL B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 removed outlier: 3.572A pdb=" N PHE B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.862A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.980A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.613A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.627A pdb=" N GLU A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.630A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.739A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.606A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.714A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.837A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.505A pdb=" N HIS A 309 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.676A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.086A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.434A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 24 removed outlier: 4.254A pdb=" N ASN K 24 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 66 removed outlier: 3.627A pdb=" N VAL K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 74 removed outlier: 3.549A pdb=" N LEU K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 96 Processing helix chain 'K' and resid 106 through 118 removed outlier: 4.002A pdb=" N ARG K 110 " --> pdb=" O GLY K 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR K 118 " --> pdb=" O ASP K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 237 through 241 Processing helix chain 'K' and resid 245 through 271 Processing helix chain 'K' and resid 280 through 286 Processing helix chain 'K' and resid 305 through 307 No H-bonds generated for 'chain 'K' and resid 305 through 307' Processing helix chain 'K' and resid 308 through 323 removed outlier: 3.961A pdb=" N ALA K 322 " --> pdb=" O PHE K 318 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS K 323 " --> pdb=" O GLY K 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.447A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU B 3 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLN B 136 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ALA B 9 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 168 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.690A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 272 through 273 removed outlier: 3.664A pdb=" N THR B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.168A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 273 removed outlier: 4.237A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.705A pdb=" N ARG K 50 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN K 78 " --> pdb=" O ARG K 295 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR K 297 " --> pdb=" O ASN K 78 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR K 80 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL K 299 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY K 79 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL K 230 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 81 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 127 " --> pdb=" O GLU K 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 84 through 85 removed outlier: 6.890A pdb=" N ASN K 78 " --> pdb=" O ARG K 295 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR K 297 " --> pdb=" O ASN K 78 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR K 80 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL K 299 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY K 79 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL K 230 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 81 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 127 " --> pdb=" O GLU K 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.737A pdb=" N THR K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 154 through 157 removed outlier: 4.283A pdb=" N SER K 154 " --> pdb=" O LYS K 166 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1308 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: 3.12 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1589 1.32 - 1.44: 2544 1.44 - 1.56: 5309 1.56 - 1.69: 17 1.69 - 1.81: 94 Bond restraints: 9553 Sorted by residual: bond pdb=" N ASP K 231 " pdb=" CA ASP K 231 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.38e-02 5.25e+03 5.64e+00 bond pdb=" N HIS K 191 " pdb=" CA HIS K 191 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.25e-02 6.40e+03 4.63e+00 bond pdb=" N ARG K 190 " pdb=" CA ARG K 190 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.31e-02 5.83e+03 4.03e+00 bond pdb=" CG HIS K 191 " pdb=" CD2 HIS K 191 " ideal model delta sigma weight residual 1.354 1.335 0.019 1.10e-02 8.26e+03 3.13e+00 bond pdb=" C ASP K 231 " pdb=" N LEU K 232 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.41e-02 5.03e+03 1.43e+00 ... (remaining 9548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 12812 2.31 - 4.61: 125 4.61 - 6.92: 16 6.92 - 9.23: 4 9.23 - 11.53: 3 Bond angle restraints: 12960 Sorted by residual: angle pdb=" CA HIS K 191 " pdb=" CB HIS K 191 " pdb=" CG HIS K 191 " ideal model delta sigma weight residual 113.80 118.36 -4.56 1.00e+00 1.00e+00 2.08e+01 angle pdb=" C10 TA1 B 502 " pdb=" C18 TA1 B 502 " pdb=" C20 TA1 B 502 " ideal model delta sigma weight residual 104.78 116.31 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CA ASP K 231 " pdb=" CB ASP K 231 " pdb=" CG ASP K 231 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" C14 TA1 B 502 " pdb=" C11 TA1 B 502 " pdb=" O04 TA1 B 502 " ideal model delta sigma weight residual 119.42 109.44 9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C10 TA1 B 502 " pdb=" C18 TA1 B 502 " pdb=" C17 TA1 B 502 " ideal model delta sigma weight residual 114.79 105.44 9.35 3.00e+00 1.11e-01 9.71e+00 ... (remaining 12955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 5652 33.86 - 67.72: 108 67.72 - 101.57: 7 101.57 - 135.43: 17 135.43 - 169.29: 5 Dihedral angle restraints: 5789 sinusoidal: 2398 harmonic: 3391 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.44 -169.29 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -52.74 157.33 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 135.38 138.74 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 5786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 996 0.039 - 0.079: 313 0.079 - 0.118: 103 0.118 - 0.158: 12 0.158 - 0.197: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C3' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C4' GTP A 501 " pdb=" O3' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.67 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" C21 TA1 B 502 " pdb=" C20 TA1 B 502 " pdb=" C24 TA1 B 502 " pdb=" O09 TA1 B 502 " both_signs ideal model delta sigma weight residual False -2.30 -2.49 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" C3' GDP B 501 " pdb=" C4' GDP B 501 " pdb=" O3' GDP B 501 " pdb=" C2' GDP B 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1423 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO B 32 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 325 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 189 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C ASN K 189 " -0.028 2.00e-02 2.50e+03 pdb=" O ASN K 189 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG K 190 " 0.009 2.00e-02 2.50e+03 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 60 2.56 - 3.14: 7172 3.14 - 3.73: 13658 3.73 - 4.31: 19037 4.31 - 4.90: 33313 Nonbonded interactions: 73240 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 1.971 2.170 nonbonded pdb=" OD2 ASP B 427 " pdb=" NH1 ARG K 278 " model vdw 2.270 3.120 nonbonded pdb=" NH1 ARG A 264 " pdb=" OD2 ASP A 431 " model vdw 2.277 3.120 nonbonded pdb=" NH2 ARG A 215 " pdb=" O ALA A 299 " model vdw 2.277 3.120 nonbonded pdb=" O GLY A 142 " pdb=" ND2 ASN A 186 " model vdw 2.293 3.120 ... (remaining 73235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9553 Z= 0.206 Angle : 0.587 11.535 12960 Z= 0.285 Chirality : 0.043 0.197 1426 Planarity : 0.004 0.061 1673 Dihedral : 16.280 169.290 3611 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1158 helix: 1.68 (0.25), residues: 468 sheet: 0.98 (0.36), residues: 210 loop : -1.24 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 21 HIS 0.008 0.001 HIS K 191 PHE 0.008 0.001 PHE A 255 TYR 0.008 0.001 TYR A 312 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.8824 (tttm) cc_final: 0.8473 (ttpt) REVERT: B 75 MET cc_start: 0.9010 (mmt) cc_final: 0.8664 (mmt) REVERT: B 116 ASP cc_start: 0.8735 (m-30) cc_final: 0.8438 (m-30) REVERT: B 215 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7728 (ttp-110) REVERT: B 282 GLN cc_start: 0.8815 (mp10) cc_final: 0.8124 (mp10) REVERT: A 211 ASP cc_start: 0.8743 (t0) cc_final: 0.8386 (t0) REVERT: A 239 THR cc_start: 0.9362 (m) cc_final: 0.9162 (p) REVERT: A 280 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8084 (mmtt) REVERT: A 425 MET cc_start: 0.9028 (mmm) cc_final: 0.8579 (tpp) REVERT: A 429 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8045 (mt-10) REVERT: K 72 ASP cc_start: 0.8633 (m-30) cc_final: 0.8429 (m-30) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2703 time to fit residues: 85.8432 Evaluate side-chains 142 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.0470 chunk 29 optimal weight: 0.0470 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN B 434 GLN A 226 ASN A 249 ASN K 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.083737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.069152 restraints weight = 18537.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.071789 restraints weight = 8919.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.073566 restraints weight = 5501.647| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9553 Z= 0.247 Angle : 0.622 11.831 12960 Z= 0.303 Chirality : 0.045 0.268 1426 Planarity : 0.004 0.062 1673 Dihedral : 14.369 168.290 1413 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.98 % Allowed : 12.48 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1158 helix: 1.70 (0.25), residues: 480 sheet: 1.18 (0.36), residues: 205 loop : -1.11 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS A 139 PHE 0.009 0.001 PHE K 128 TYR 0.015 0.001 TYR K 118 ARG 0.008 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8962 (mmt) cc_final: 0.8590 (mmt) REVERT: B 308 ARG cc_start: 0.7533 (mtt-85) cc_final: 0.7220 (mtt-85) REVERT: A 26 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9017 (mm) REVERT: A 128 GLN cc_start: 0.8323 (tt0) cc_final: 0.8054 (tm-30) REVERT: A 211 ASP cc_start: 0.8602 (t0) cc_final: 0.8175 (t0) REVERT: A 239 THR cc_start: 0.9217 (m) cc_final: 0.8914 (p) REVERT: A 280 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8114 (mmtt) REVERT: A 425 MET cc_start: 0.8857 (mmm) cc_final: 0.8363 (tpp) REVERT: A 432 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.6581 (t80) REVERT: K 72 ASP cc_start: 0.8430 (m-30) cc_final: 0.8119 (m-30) REVERT: K 136 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8329 (pt0) outliers start: 20 outliers final: 10 residues processed: 166 average time/residue: 0.2457 time to fit residues: 55.2152 Evaluate side-chains 142 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 219 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 16 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN K 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.080291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.065772 restraints weight = 19000.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.068330 restraints weight = 9207.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.070067 restraints weight = 5693.935| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9553 Z= 0.340 Angle : 0.621 7.876 12960 Z= 0.310 Chirality : 0.046 0.382 1426 Planarity : 0.004 0.062 1673 Dihedral : 10.855 163.551 1413 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.27 % Allowed : 12.38 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.63 (0.25), residues: 1158 helix: 1.53 (0.24), residues: 486 sheet: 1.10 (0.36), residues: 204 loop : -1.11 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.005 0.001 HIS B 192 PHE 0.010 0.001 PHE K 128 TYR 0.009 0.001 TYR A 161 ARG 0.006 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9062 (mm) REVERT: A 211 ASP cc_start: 0.8647 (t0) cc_final: 0.8148 (t0) REVERT: A 280 LYS cc_start: 0.9282 (mtpt) cc_final: 0.8253 (mmtt) REVERT: A 425 MET cc_start: 0.8913 (mmm) cc_final: 0.8359 (tpp) REVERT: A 432 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.6606 (t80) REVERT: K 136 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: K 220 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: K 311 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8116 (pm20) outliers start: 33 outliers final: 20 residues processed: 146 average time/residue: 0.2328 time to fit residues: 47.3744 Evaluate side-chains 132 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 220 GLU Chi-restraints excluded: chain K residue 311 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.082591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.068052 restraints weight = 18636.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.070642 restraints weight = 9032.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.072409 restraints weight = 5589.923| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9553 Z= 0.190 Angle : 0.559 9.732 12960 Z= 0.274 Chirality : 0.045 0.298 1426 Planarity : 0.004 0.062 1673 Dihedral : 10.040 157.342 1413 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.67 % Allowed : 14.46 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.82 (0.25), residues: 1158 helix: 1.69 (0.25), residues: 482 sheet: 1.37 (0.37), residues: 199 loop : -1.07 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.002 0.001 HIS A 88 PHE 0.009 0.001 PHE B 377 TYR 0.008 0.001 TYR K 62 ARG 0.004 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8902 (mmt) cc_final: 0.8526 (mmt) REVERT: A 26 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8967 (mm) REVERT: A 168 GLU cc_start: 0.6809 (mp0) cc_final: 0.6592 (mp0) REVERT: A 211 ASP cc_start: 0.8646 (t0) cc_final: 0.7711 (t0) REVERT: A 215 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7239 (ttm110) REVERT: A 280 LYS cc_start: 0.9270 (mtpt) cc_final: 0.8401 (mmtt) REVERT: A 286 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9017 (mt) REVERT: A 425 MET cc_start: 0.8909 (mmm) cc_final: 0.8494 (tpp) REVERT: A 432 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.6767 (t80) REVERT: K 136 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: K 220 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8046 (tp30) outliers start: 27 outliers final: 16 residues processed: 143 average time/residue: 0.2345 time to fit residues: 46.5836 Evaluate side-chains 138 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 220 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.081574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.067096 restraints weight = 18661.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.069687 restraints weight = 9053.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.071423 restraints weight = 5591.245| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9553 Z= 0.228 Angle : 0.571 8.352 12960 Z= 0.283 Chirality : 0.045 0.262 1426 Planarity : 0.004 0.060 1673 Dihedral : 9.790 151.672 1413 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.07 % Allowed : 14.26 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.87 (0.25), residues: 1158 helix: 1.68 (0.25), residues: 486 sheet: 1.41 (0.36), residues: 199 loop : -1.00 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS B 266 PHE 0.012 0.001 PHE B 377 TYR 0.012 0.001 TYR K 118 ARG 0.004 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8910 (mmt) cc_final: 0.8551 (mmt) REVERT: A 26 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8982 (mm) REVERT: A 168 GLU cc_start: 0.6891 (mp0) cc_final: 0.6625 (mp0) REVERT: A 211 ASP cc_start: 0.8645 (t0) cc_final: 0.7863 (t0) REVERT: A 215 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7298 (ttm110) REVERT: A 280 LYS cc_start: 0.9366 (mtpt) cc_final: 0.8407 (mmtt) REVERT: A 425 MET cc_start: 0.8919 (mmm) cc_final: 0.8277 (tpp) REVERT: A 432 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6703 (t80) REVERT: K 136 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8136 (pt0) REVERT: K 311 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8140 (pm20) outliers start: 31 outliers final: 20 residues processed: 137 average time/residue: 0.2367 time to fit residues: 45.0040 Evaluate side-chains 132 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 311 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.081182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.066697 restraints weight = 18750.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.069275 restraints weight = 9071.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.071037 restraints weight = 5595.146| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9553 Z= 0.244 Angle : 0.564 7.856 12960 Z= 0.279 Chirality : 0.045 0.240 1426 Planarity : 0.004 0.067 1673 Dihedral : 9.584 147.978 1413 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.47 % Allowed : 14.95 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.85 (0.25), residues: 1158 helix: 1.72 (0.25), residues: 482 sheet: 1.39 (0.37), residues: 199 loop : -1.04 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS B 266 PHE 0.011 0.001 PHE B 377 TYR 0.009 0.001 TYR K 277 ARG 0.003 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8987 (mm) REVERT: A 168 GLU cc_start: 0.6827 (mp0) cc_final: 0.6513 (mp0) REVERT: A 211 ASP cc_start: 0.8682 (t0) cc_final: 0.8161 (t0) REVERT: A 280 LYS cc_start: 0.9386 (mtpt) cc_final: 0.8444 (mmtt) REVERT: A 425 MET cc_start: 0.8923 (mmm) cc_final: 0.8311 (tpp) REVERT: A 432 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.6726 (t80) REVERT: K 136 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8145 (pt0) REVERT: K 311 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8148 (pm20) outliers start: 35 outliers final: 24 residues processed: 134 average time/residue: 0.2342 time to fit residues: 43.3430 Evaluate side-chains 138 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 311 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.080387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.065867 restraints weight = 19088.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.068427 restraints weight = 9236.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.070138 restraints weight = 5700.816| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9553 Z= 0.272 Angle : 0.574 7.959 12960 Z= 0.285 Chirality : 0.045 0.235 1426 Planarity : 0.004 0.066 1673 Dihedral : 9.493 145.525 1413 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.56 % Allowed : 14.75 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.82 (0.25), residues: 1158 helix: 1.69 (0.24), residues: 482 sheet: 1.31 (0.36), residues: 207 loop : -1.08 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS B 266 PHE 0.012 0.001 PHE B 377 TYR 0.015 0.001 TYR K 118 ARG 0.003 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 369 ARG cc_start: 0.8351 (ttm170) cc_final: 0.8090 (mmm160) REVERT: A 26 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9030 (mm) REVERT: A 168 GLU cc_start: 0.6764 (mp0) cc_final: 0.6473 (mp0) REVERT: A 211 ASP cc_start: 0.8669 (t0) cc_final: 0.8131 (t0) REVERT: A 280 LYS cc_start: 0.9400 (mtpt) cc_final: 0.8393 (mmtt) REVERT: A 425 MET cc_start: 0.8962 (mmm) cc_final: 0.8504 (tpp) REVERT: A 432 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.6729 (t80) REVERT: K 136 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: K 311 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7891 (pm20) outliers start: 36 outliers final: 27 residues processed: 141 average time/residue: 0.2262 time to fit residues: 44.4317 Evaluate side-chains 138 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 311 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.079868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.065468 restraints weight = 19195.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.068008 restraints weight = 9242.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.069746 restraints weight = 5697.326| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9553 Z= 0.311 Angle : 0.600 8.264 12960 Z= 0.298 Chirality : 0.046 0.232 1426 Planarity : 0.004 0.065 1673 Dihedral : 9.485 144.444 1413 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.47 % Allowed : 15.74 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.75 (0.25), residues: 1158 helix: 1.63 (0.24), residues: 482 sheet: 1.25 (0.36), residues: 207 loop : -1.09 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS B 266 PHE 0.012 0.001 PHE B 377 TYR 0.015 0.001 TYR K 118 ARG 0.003 0.000 ARG K 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 369 ARG cc_start: 0.8355 (ttm170) cc_final: 0.8090 (mmm160) REVERT: A 26 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9037 (mm) REVERT: A 168 GLU cc_start: 0.6823 (mp0) cc_final: 0.6490 (mp0) REVERT: A 211 ASP cc_start: 0.8671 (t0) cc_final: 0.8122 (t0) REVERT: A 280 LYS cc_start: 0.9412 (mtpt) cc_final: 0.8405 (mmtt) REVERT: A 425 MET cc_start: 0.8963 (mmm) cc_final: 0.8511 (tpp) REVERT: A 432 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6719 (t80) REVERT: K 136 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: K 311 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8166 (pm20) outliers start: 35 outliers final: 27 residues processed: 137 average time/residue: 0.2393 time to fit residues: 45.4091 Evaluate side-chains 139 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 311 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.082485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.068067 restraints weight = 18564.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.070668 restraints weight = 8943.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.072411 restraints weight = 5512.097| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9553 Z= 0.164 Angle : 0.555 8.755 12960 Z= 0.272 Chirality : 0.044 0.203 1426 Planarity : 0.004 0.065 1673 Dihedral : 9.148 143.464 1413 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.77 % Allowed : 16.34 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1158 helix: 1.82 (0.25), residues: 483 sheet: 1.29 (0.35), residues: 213 loop : -1.01 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 21 HIS 0.002 0.001 HIS B 229 PHE 0.010 0.001 PHE B 377 TYR 0.009 0.001 TYR K 277 ARG 0.005 0.000 ARG K 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8943 (mm) REVERT: A 168 GLU cc_start: 0.6788 (mp0) cc_final: 0.6525 (mp0) REVERT: A 211 ASP cc_start: 0.8675 (t0) cc_final: 0.7760 (t0) REVERT: A 215 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7048 (ttm110) REVERT: A 280 LYS cc_start: 0.9380 (mtpt) cc_final: 0.8379 (mmtt) REVERT: A 425 MET cc_start: 0.8893 (mmm) cc_final: 0.8463 (tpp) REVERT: A 432 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.6832 (t80) REVERT: K 114 ASP cc_start: 0.8233 (m-30) cc_final: 0.7978 (m-30) REVERT: K 136 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: K 311 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7965 (pm20) outliers start: 28 outliers final: 20 residues processed: 136 average time/residue: 0.2369 time to fit residues: 44.8085 Evaluate side-chains 133 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 311 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 78 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.083430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.068985 restraints weight = 18685.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.071567 restraints weight = 9006.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.073372 restraints weight = 5583.021| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9553 Z= 0.157 Angle : 0.557 8.947 12960 Z= 0.271 Chirality : 0.043 0.206 1426 Planarity : 0.004 0.063 1673 Dihedral : 8.882 140.731 1413 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.18 % Allowed : 17.13 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.11 (0.25), residues: 1158 helix: 1.88 (0.25), residues: 487 sheet: 1.50 (0.36), residues: 208 loop : -0.91 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.002 0.000 HIS B 266 PHE 0.009 0.001 PHE B 377 TYR 0.008 0.001 TYR K 277 ARG 0.004 0.000 ARG K 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8929 (mm) REVERT: A 168 GLU cc_start: 0.6789 (mp0) cc_final: 0.6521 (mp0) REVERT: A 211 ASP cc_start: 0.8675 (t0) cc_final: 0.8109 (t0) REVERT: A 280 LYS cc_start: 0.9375 (mtpt) cc_final: 0.8385 (mmtt) REVERT: A 425 MET cc_start: 0.8857 (mmm) cc_final: 0.8261 (tpp) REVERT: A 432 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7033 (t80) REVERT: K 114 ASP cc_start: 0.8253 (m-30) cc_final: 0.8023 (m-30) REVERT: K 136 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: K 185 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7908 (tm-30) REVERT: K 311 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8141 (pm20) outliers start: 22 outliers final: 17 residues processed: 129 average time/residue: 0.2455 time to fit residues: 43.5904 Evaluate side-chains 136 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 311 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 17 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.081421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.067038 restraints weight = 18830.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.069571 restraints weight = 9096.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.071329 restraints weight = 5652.080| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9553 Z= 0.235 Angle : 0.581 9.813 12960 Z= 0.285 Chirality : 0.044 0.209 1426 Planarity : 0.004 0.063 1673 Dihedral : 8.928 141.705 1413 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.28 % Allowed : 17.33 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.04 (0.25), residues: 1158 helix: 1.89 (0.25), residues: 483 sheet: 1.32 (0.35), residues: 213 loop : -0.96 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS B 266 PHE 0.010 0.001 PHE B 377 TYR 0.010 0.001 TYR K 277 ARG 0.005 0.000 ARG K 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.93 seconds wall clock time: 49 minutes 7.91 seconds (2947.91 seconds total)