Starting phenix.real_space_refine on Thu Sep 18 21:57:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt3_26109/09_2025/7tt3_26109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt3_26109/09_2025/7tt3_26109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tt3_26109/09_2025/7tt3_26109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt3_26109/09_2025/7tt3_26109.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt3_26109/09_2025/7tt3_26109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt3_26109/09_2025/7tt3_26109.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.006 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 6600 2.51 5 N 1786 2.21 5 O 2046 1.98 5 H 10060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20524 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 9493 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 589} Chain breaks: 4 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 675 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "B" Number of atoms: 5199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5199 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain breaks: 2 Chain: "P" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 386 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain breaks: 1 Time building chain proxies: 3.52, per 1000 atoms: 0.17 Number of scatterers: 20524 At special positions: 0 Unit cell: (105.234, 124.563, 141.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2046 8.00 N 1786 7.00 C 6600 6.00 H 10060 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 557.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 24.1% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.777A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.558A pdb=" N ARG A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.947A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 removed outlier: 4.141A pdb=" N GLN A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.727A pdb=" N ASN A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.701A pdb=" N GLN A 753 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 83 removed outlier: 4.863A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.705A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.284A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.822A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.813A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.757A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 183 removed outlier: 3.774A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 276 removed outlier: 5.894A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.787A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 354 removed outlier: 7.852A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 354 removed outlier: 7.852A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.831A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.184A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.906A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.579A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.999A pdb=" N THR B 50 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER B 389 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL B 52 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 387 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER B 54 " --> pdb=" O GLY B 385 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.843A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.114A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.773A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.951A pdb=" N ARG B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.932A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.725A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.517A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 10060 1.03 - 1.22: 0 1.22 - 1.42: 4646 1.42 - 1.62: 5986 1.62 - 1.81: 60 Bond restraints: 20752 Sorted by residual: bond pdb=" CA TYR A 348 " pdb=" CB TYR A 348 " ideal model delta sigma weight residual 1.534 1.499 0.036 2.33e-02 1.84e+03 2.32e+00 bond pdb=" N HIS D 139 " pdb=" CA HIS D 139 " ideal model delta sigma weight residual 1.458 1.440 0.019 1.26e-02 6.30e+03 2.22e+00 bond pdb=" C LEU D 174 " pdb=" O LEU D 174 " ideal model delta sigma weight residual 1.236 1.254 -0.017 1.22e-02 6.72e+03 2.05e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.01e+00 bond pdb=" CA VAL A 364 " pdb=" C VAL A 364 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.27e-02 6.20e+03 1.80e+00 ... (remaining 20747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 36552 2.26 - 4.52: 678 4.52 - 6.78: 51 6.78 - 9.03: 4 9.03 - 11.29: 2 Bond angle restraints: 37287 Sorted by residual: angle pdb=" C GLY B 265 " pdb=" N ASN B 266 " pdb=" CA ASN B 266 " ideal model delta sigma weight residual 122.47 115.74 6.73 1.50e+00 4.44e-01 2.01e+01 angle pdb=" N ASN A 579 " pdb=" CA ASN A 579 " pdb=" C ASN A 579 " ideal model delta sigma weight residual 107.61 114.99 -7.38 1.74e+00 3.30e-01 1.80e+01 angle pdb=" N ASP A 746 " pdb=" CA ASP A 746 " pdb=" C ASP A 746 " ideal model delta sigma weight residual 107.75 115.39 -7.64 1.86e+00 2.89e-01 1.69e+01 angle pdb=" N GLY B 196 " pdb=" CA GLY B 196 " pdb=" C GLY B 196 " ideal model delta sigma weight residual 113.18 103.88 9.30 2.37e+00 1.78e-01 1.54e+01 angle pdb=" N GLY B 214 " pdb=" CA GLY B 214 " pdb=" C GLY B 214 " ideal model delta sigma weight residual 114.76 108.31 6.45 1.70e+00 3.46e-01 1.44e+01 ... (remaining 37282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 9330 17.78 - 35.56: 306 35.56 - 53.33: 156 53.33 - 71.11: 54 71.11 - 88.89: 14 Dihedral angle restraints: 9860 sinusoidal: 5293 harmonic: 4567 Sorted by residual: dihedral pdb=" CA GLU B 197 " pdb=" C GLU B 197 " pdb=" N SER B 198 " pdb=" CA SER B 198 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CB GLU A 262 " pdb=" CG GLU A 262 " pdb=" CD GLU A 262 " pdb=" OE1 GLU A 262 " ideal model delta sinusoidal sigma weight residual 0.00 80.46 -80.46 1 3.00e+01 1.11e-03 8.90e+00 dihedral pdb=" CA PRO B 330 " pdb=" C PRO B 330 " pdb=" N VAL B 331 " pdb=" CA VAL B 331 " ideal model delta harmonic sigma weight residual 180.00 165.81 14.19 0 5.00e+00 4.00e-02 8.05e+00 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 891 0.036 - 0.072: 437 0.072 - 0.108: 165 0.108 - 0.144: 69 0.144 - 0.181: 13 Chirality restraints: 1575 Sorted by residual: chirality pdb=" CA TYR A 522 " pdb=" N TYR A 522 " pdb=" C TYR A 522 " pdb=" CB TYR A 522 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA ARG D 141 " pdb=" N ARG D 141 " pdb=" C ARG D 141 " pdb=" CB ARG D 141 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR D 185 " pdb=" N TYR D 185 " pdb=" C TYR D 185 " pdb=" CB TYR D 185 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 1572 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 158 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C SER B 158 " 0.071 2.00e-02 2.50e+03 pdb=" O SER B 158 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP B 159 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 73 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C LEU D 73 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU D 73 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP D 74 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO D 86 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO D 86 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU D 87 " -0.021 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 384 2.07 - 2.71: 33662 2.71 - 3.34: 55532 3.34 - 3.97: 71843 3.97 - 4.60: 112152 Nonbonded interactions: 273573 Sorted by model distance: nonbonded pdb=" OD1 ASP B 271 " pdb=" H LEU B 272 " model vdw 1.442 2.450 nonbonded pdb=" H ILE A 352 " pdb=" OE2 GLU A 373 " model vdw 1.452 2.450 nonbonded pdb=" HG SER B 193 " pdb=" OD2 ASP B 242 " model vdw 1.508 2.450 nonbonded pdb=" HD1 HIS B 64 " pdb=" O PRO B 65 " model vdw 1.518 2.450 nonbonded pdb=" OD2 ASP A 569 " pdb="HD22 ASN A 606 " model vdw 1.527 2.450 ... (remaining 273568 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10694 Z= 0.270 Angle : 0.988 11.293 14528 Z= 0.606 Chirality : 0.052 0.181 1575 Planarity : 0.006 0.049 1911 Dihedral : 10.456 88.889 3854 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1312 helix: 0.33 (0.28), residues: 263 sheet: 1.20 (0.24), residues: 418 loop : 0.75 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG A 366 TYR 0.019 0.003 TYR D 205 PHE 0.017 0.002 PHE A 785 TRP 0.025 0.003 TRP A 739 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00552 (10692) covalent geometry : angle 0.98813 (14524) SS BOND : bond 0.00036 ( 2) SS BOND : angle 1.46499 ( 4) hydrogen bonds : bond 0.13770 ( 471) hydrogen bonds : angle 7.30458 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8791 (mt0) cc_final: 0.8549 (mp10) REVERT: A 240 ILE cc_start: 0.9170 (mt) cc_final: 0.8910 (mt) REVERT: A 254 ILE cc_start: 0.8570 (mt) cc_final: 0.8348 (tp) REVERT: A 387 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 446 GLN cc_start: 0.7139 (mt0) cc_final: 0.6890 (mt0) REVERT: A 648 PHE cc_start: 0.7885 (p90) cc_final: 0.7284 (p90) REVERT: A 673 VAL cc_start: 0.8468 (t) cc_final: 0.8230 (p) REVERT: A 711 MET cc_start: 0.8696 (ppp) cc_final: 0.8052 (ptt) REVERT: A 716 LEU cc_start: 0.8785 (tt) cc_final: 0.8450 (mp) REVERT: A 745 TRP cc_start: 0.8289 (p90) cc_final: 0.8014 (p90) REVERT: D 74 ASP cc_start: 0.8856 (m-30) cc_final: 0.8636 (m-30) REVERT: D 82 ASN cc_start: 0.7976 (t0) cc_final: 0.7513 (t0) REVERT: D 165 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8614 (mmmm) REVERT: C 42 LEU cc_start: 0.9042 (mt) cc_final: 0.8553 (tt) REVERT: C 82 ILE cc_start: 0.8965 (pt) cc_final: 0.8697 (mp) REVERT: B 95 VAL cc_start: 0.6903 (p) cc_final: 0.6653 (p) REVERT: B 154 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7603 (ttp80) REVERT: B 166 THR cc_start: 0.9057 (p) cc_final: 0.8800 (p) REVERT: B 327 LEU cc_start: 0.9067 (mt) cc_final: 0.8658 (mt) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2403 time to fit residues: 135.5798 Evaluate side-chains 255 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN E 52 GLN B 170 GLN B 172 GLN B 266 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112938 restraints weight = 61847.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117413 restraints weight = 41240.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117808 restraints weight = 31356.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120343 restraints weight = 19604.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120870 restraints weight = 16523.819| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10694 Z= 0.241 Angle : 0.663 7.220 14528 Z= 0.377 Chirality : 0.045 0.168 1575 Planarity : 0.005 0.044 1911 Dihedral : 5.171 59.664 1465 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.22), residues: 1312 helix: 1.16 (0.30), residues: 276 sheet: 0.57 (0.24), residues: 412 loop : 0.30 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 338 TYR 0.020 0.002 TYR D 184 PHE 0.019 0.002 PHE P1274 TRP 0.024 0.002 TRP D 48 HIS 0.008 0.002 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00513 (10692) covalent geometry : angle 0.66184 (14524) SS BOND : bond 0.00970 ( 2) SS BOND : angle 2.74001 ( 4) hydrogen bonds : bond 0.06072 ( 471) hydrogen bonds : angle 6.30213 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8753 (mt) cc_final: 0.8307 (mm) REVERT: A 357 ASN cc_start: 0.8658 (m-40) cc_final: 0.8353 (m-40) REVERT: A 369 MET cc_start: 0.9337 (mmp) cc_final: 0.9040 (mmm) REVERT: A 387 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8745 (mt-10) REVERT: A 408 SER cc_start: 0.8704 (t) cc_final: 0.8375 (m) REVERT: A 417 LYS cc_start: 0.8870 (mttt) cc_final: 0.8528 (mtpp) REVERT: A 445 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 446 GLN cc_start: 0.7294 (mt0) cc_final: 0.6949 (mt0) REVERT: A 540 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7787 (mm-40) REVERT: A 645 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 716 LEU cc_start: 0.8524 (tt) cc_final: 0.8135 (mp) REVERT: A 745 TRP cc_start: 0.8813 (p90) cc_final: 0.8593 (p90) REVERT: D 82 ASN cc_start: 0.8394 (t0) cc_final: 0.7766 (t0) REVERT: D 107 TYR cc_start: 0.7972 (t80) cc_final: 0.7739 (t80) REVERT: D 165 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8765 (mmmm) REVERT: C 82 ILE cc_start: 0.9199 (pt) cc_final: 0.8927 (mp) REVERT: E 84 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 95 VAL cc_start: 0.6798 (p) cc_final: 0.5769 (p) REVERT: B 154 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7561 (ttp80) REVERT: B 327 LEU cc_start: 0.9013 (mt) cc_final: 0.8790 (mt) REVERT: P 1274 PHE cc_start: 0.8543 (p90) cc_final: 0.8247 (p90) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2274 time to fit residues: 91.4550 Evaluate side-chains 238 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN B 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114589 restraints weight = 64493.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119501 restraints weight = 41555.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121022 restraints weight = 25968.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121243 restraints weight = 20708.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123125 restraints weight = 17892.853| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10694 Z= 0.128 Angle : 0.549 5.253 14528 Z= 0.306 Chirality : 0.044 0.173 1575 Planarity : 0.004 0.051 1911 Dihedral : 4.901 55.623 1465 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.22), residues: 1312 helix: 1.38 (0.30), residues: 276 sheet: 0.49 (0.23), residues: 415 loop : 0.07 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 273 TYR 0.020 0.001 TYR A 550 PHE 0.020 0.002 PHE A 738 TRP 0.016 0.001 TRP D 48 HIS 0.006 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00263 (10692) covalent geometry : angle 0.54761 (14524) SS BOND : bond 0.00981 ( 2) SS BOND : angle 2.05670 ( 4) hydrogen bonds : bond 0.05180 ( 471) hydrogen bonds : angle 5.79467 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8707 (mt) cc_final: 0.8237 (tp) REVERT: A 325 MET cc_start: 0.8744 (pmm) cc_final: 0.8229 (pmm) REVERT: A 357 ASN cc_start: 0.8637 (m-40) cc_final: 0.8408 (m-40) REVERT: A 408 SER cc_start: 0.8643 (t) cc_final: 0.8375 (m) REVERT: A 417 LYS cc_start: 0.8851 (mttt) cc_final: 0.8485 (mtpp) REVERT: A 445 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 645 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 651 ASN cc_start: 0.8789 (m-40) cc_final: 0.8410 (m-40) REVERT: A 716 LEU cc_start: 0.8444 (tt) cc_final: 0.8153 (mp) REVERT: A 745 TRP cc_start: 0.8679 (p90) cc_final: 0.8441 (p90) REVERT: A 801 GLN cc_start: 0.8441 (mp10) cc_final: 0.8235 (mp10) REVERT: D 82 ASN cc_start: 0.8366 (t0) cc_final: 0.7758 (t0) REVERT: C 82 ILE cc_start: 0.9140 (pt) cc_final: 0.8909 (mp) REVERT: B 154 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7591 (ttp80) REVERT: B 192 LEU cc_start: 0.7669 (tp) cc_final: 0.7457 (tp) REVERT: B 388 TYR cc_start: 0.7409 (m-80) cc_final: 0.6970 (m-80) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2317 time to fit residues: 93.7655 Evaluate side-chains 230 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.0060 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.151509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113420 restraints weight = 64368.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117388 restraints weight = 45062.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118702 restraints weight = 28530.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119937 restraints weight = 19764.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121355 restraints weight = 17936.062| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10694 Z= 0.143 Angle : 0.528 5.932 14528 Z= 0.293 Chirality : 0.043 0.158 1575 Planarity : 0.004 0.047 1911 Dihedral : 4.753 51.457 1465 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.22), residues: 1312 helix: 1.35 (0.30), residues: 277 sheet: 0.33 (0.24), residues: 403 loop : -0.13 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.016 0.001 TYR D 184 PHE 0.017 0.001 PHE P1274 TRP 0.012 0.001 TRP D 48 HIS 0.009 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00303 (10692) covalent geometry : angle 0.52719 (14524) SS BOND : bond 0.00501 ( 2) SS BOND : angle 1.99882 ( 4) hydrogen bonds : bond 0.04653 ( 471) hydrogen bonds : angle 5.59060 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8688 (pmm) cc_final: 0.8190 (pmm) REVERT: A 357 ASN cc_start: 0.8678 (m-40) cc_final: 0.8477 (m-40) REVERT: A 369 MET cc_start: 0.9312 (mmp) cc_final: 0.8889 (mmm) REVERT: A 408 SER cc_start: 0.8692 (t) cc_final: 0.8358 (m) REVERT: A 417 LYS cc_start: 0.8871 (mttt) cc_final: 0.8528 (mtpp) REVERT: A 445 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 458 ILE cc_start: 0.9466 (mp) cc_final: 0.9190 (mp) REVERT: A 569 ASP cc_start: 0.8332 (m-30) cc_final: 0.8085 (m-30) REVERT: A 609 TYR cc_start: 0.8890 (p90) cc_final: 0.8319 (p90) REVERT: A 641 LEU cc_start: 0.8684 (mm) cc_final: 0.8454 (mm) REVERT: A 645 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 648 PHE cc_start: 0.8464 (p90) cc_final: 0.7484 (p90) REVERT: A 651 ASN cc_start: 0.8762 (m-40) cc_final: 0.8390 (m-40) REVERT: A 716 LEU cc_start: 0.8440 (tt) cc_final: 0.8147 (mp) REVERT: A 745 TRP cc_start: 0.8748 (p90) cc_final: 0.8501 (p90) REVERT: D 82 ASN cc_start: 0.8387 (t0) cc_final: 0.7730 (t0) REVERT: C 81 ASP cc_start: 0.8191 (t70) cc_final: 0.7818 (t0) REVERT: B 35 LEU cc_start: 0.9244 (mt) cc_final: 0.8922 (mp) REVERT: B 154 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7624 (ttp80) REVERT: B 324 HIS cc_start: 0.7704 (m-70) cc_final: 0.7458 (m-70) REVERT: B 381 GLN cc_start: 0.8924 (tt0) cc_final: 0.8290 (tm-30) REVERT: P 1298 TYR cc_start: 0.8580 (t80) cc_final: 0.8377 (t80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2317 time to fit residues: 86.1460 Evaluate side-chains 230 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 68 optimal weight: 0.0030 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 181 ASN D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112407 restraints weight = 64543.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116857 restraints weight = 45724.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118407 restraints weight = 29082.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118474 restraints weight = 21839.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122167 restraints weight = 19245.390| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10694 Z= 0.156 Angle : 0.516 4.264 14528 Z= 0.288 Chirality : 0.042 0.152 1575 Planarity : 0.004 0.054 1911 Dihedral : 4.712 47.008 1465 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1312 helix: 1.29 (0.30), residues: 276 sheet: 0.09 (0.24), residues: 416 loop : -0.23 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P1269 TYR 0.022 0.001 TYR A 550 PHE 0.017 0.001 PHE P1300 TRP 0.016 0.001 TRP B 317 HIS 0.010 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00333 (10692) covalent geometry : angle 0.51566 (14524) SS BOND : bond 0.00521 ( 2) SS BOND : angle 1.39855 ( 4) hydrogen bonds : bond 0.04469 ( 471) hydrogen bonds : angle 5.48237 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8714 (mt) cc_final: 0.8301 (mm) REVERT: A 325 MET cc_start: 0.8689 (pmm) cc_final: 0.8169 (pmm) REVERT: A 369 MET cc_start: 0.9209 (mmp) cc_final: 0.8914 (tpp) REVERT: A 408 SER cc_start: 0.8756 (t) cc_final: 0.8419 (m) REVERT: A 417 LYS cc_start: 0.8912 (mttt) cc_final: 0.8563 (mtpp) REVERT: A 569 ASP cc_start: 0.8363 (m-30) cc_final: 0.8093 (m-30) REVERT: A 645 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 651 ASN cc_start: 0.8733 (m-40) cc_final: 0.8338 (m-40) REVERT: A 716 LEU cc_start: 0.8443 (tt) cc_final: 0.8123 (mp) REVERT: A 745 TRP cc_start: 0.8810 (p90) cc_final: 0.8548 (p90) REVERT: D 49 ARG cc_start: 0.8867 (mtp180) cc_final: 0.8535 (mmm-85) REVERT: D 82 ASN cc_start: 0.8412 (t0) cc_final: 0.7670 (t0) REVERT: C 81 ASP cc_start: 0.8077 (t70) cc_final: 0.7731 (t70) REVERT: E 103 ASN cc_start: 0.7902 (t0) cc_final: 0.7620 (t0) REVERT: B 35 LEU cc_start: 0.9237 (mt) cc_final: 0.8952 (mp) REVERT: B 154 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7543 (ttp80) REVERT: B 192 LEU cc_start: 0.7636 (tp) cc_final: 0.7429 (tp) REVERT: B 226 MET cc_start: 0.8743 (tmm) cc_final: 0.8519 (tmm) REVERT: B 324 HIS cc_start: 0.7671 (m-70) cc_final: 0.7433 (m-70) REVERT: B 381 GLN cc_start: 0.8947 (tt0) cc_final: 0.8356 (tm-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2224 time to fit residues: 83.0371 Evaluate side-chains 224 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 85 optimal weight: 0.0470 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN B 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099298 restraints weight = 64878.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102337 restraints weight = 34233.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104204 restraints weight = 23138.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105849 restraints weight = 19778.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105934 restraints weight = 18369.361| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10694 Z= 0.223 Angle : 0.553 4.766 14528 Z= 0.310 Chirality : 0.043 0.158 1575 Planarity : 0.004 0.048 1911 Dihedral : 4.791 43.389 1465 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.22), residues: 1312 helix: 1.09 (0.30), residues: 275 sheet: -0.08 (0.23), residues: 414 loop : -0.39 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 366 TYR 0.019 0.002 TYR D 184 PHE 0.023 0.002 PHE A 804 TRP 0.013 0.001 TRP A 576 HIS 0.011 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00479 (10692) covalent geometry : angle 0.55287 (14524) SS BOND : bond 0.00527 ( 2) SS BOND : angle 1.49019 ( 4) hydrogen bonds : bond 0.04546 ( 471) hydrogen bonds : angle 5.61757 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8648 (mt) cc_final: 0.8193 (mm) REVERT: A 325 MET cc_start: 0.8642 (pmm) cc_final: 0.8093 (pmm) REVERT: A 338 ARG cc_start: 0.8392 (mtp-110) cc_final: 0.8137 (mtp-110) REVERT: A 364 VAL cc_start: 0.9150 (t) cc_final: 0.8855 (t) REVERT: A 408 SER cc_start: 0.8917 (t) cc_final: 0.8480 (m) REVERT: A 645 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7951 (mm-30) REVERT: A 651 ASN cc_start: 0.8756 (m-40) cc_final: 0.8364 (m-40) REVERT: A 716 LEU cc_start: 0.8360 (tt) cc_final: 0.8031 (mp) REVERT: A 745 TRP cc_start: 0.8899 (p90) cc_final: 0.8584 (p90) REVERT: D 49 ARG cc_start: 0.8918 (mtp180) cc_final: 0.8602 (mmm-85) REVERT: D 82 ASN cc_start: 0.8579 (t0) cc_final: 0.7778 (t0) REVERT: C 81 ASP cc_start: 0.8050 (t70) cc_final: 0.7752 (t70) REVERT: E 103 ASN cc_start: 0.8013 (t0) cc_final: 0.7614 (t0) REVERT: B 35 LEU cc_start: 0.9401 (mt) cc_final: 0.9085 (mp) REVERT: B 73 TYR cc_start: 0.8404 (m-80) cc_final: 0.8192 (m-80) REVERT: B 154 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7500 (ttp80) REVERT: B 192 LEU cc_start: 0.7597 (tp) cc_final: 0.7360 (tp) REVERT: B 226 MET cc_start: 0.8801 (tmm) cc_final: 0.8583 (tmm) REVERT: B 324 HIS cc_start: 0.8149 (m-70) cc_final: 0.7842 (m-70) REVERT: B 381 GLN cc_start: 0.9284 (tt0) cc_final: 0.8548 (tm-30) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2411 time to fit residues: 83.3800 Evaluate side-chains 216 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN B 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.147673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.097801 restraints weight = 61792.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102650 restraints weight = 30080.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105855 restraints weight = 19862.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107669 restraints weight = 15615.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108847 restraints weight = 13696.513| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10694 Z= 0.209 Angle : 0.553 5.893 14528 Z= 0.309 Chirality : 0.042 0.142 1575 Planarity : 0.004 0.046 1911 Dihedral : 4.828 38.194 1465 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.22), residues: 1312 helix: 0.96 (0.30), residues: 275 sheet: -0.20 (0.24), residues: 412 loop : -0.51 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 366 TYR 0.024 0.002 TYR A 550 PHE 0.011 0.002 PHE A 347 TRP 0.014 0.001 TRP A 739 HIS 0.014 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00448 (10692) covalent geometry : angle 0.55181 (14524) SS BOND : bond 0.00293 ( 2) SS BOND : angle 2.04445 ( 4) hydrogen bonds : bond 0.04498 ( 471) hydrogen bonds : angle 5.55722 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8714 (mt) cc_final: 0.8220 (mm) REVERT: A 325 MET cc_start: 0.8667 (pmm) cc_final: 0.8123 (pmm) REVERT: A 338 ARG cc_start: 0.8467 (mtp-110) cc_final: 0.8168 (mtp-110) REVERT: A 369 MET cc_start: 0.9154 (mmp) cc_final: 0.8695 (mmm) REVERT: A 408 SER cc_start: 0.8908 (t) cc_final: 0.8478 (m) REVERT: A 645 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 651 ASN cc_start: 0.8742 (m-40) cc_final: 0.8330 (m-40) REVERT: A 716 LEU cc_start: 0.8429 (tt) cc_final: 0.8112 (mp) REVERT: A 745 TRP cc_start: 0.8921 (p90) cc_final: 0.8602 (p90) REVERT: D 49 ARG cc_start: 0.8848 (mtp180) cc_final: 0.8529 (mmm-85) REVERT: D 82 ASN cc_start: 0.8551 (t0) cc_final: 0.7766 (t0) REVERT: C 57 ILE cc_start: 0.9450 (tt) cc_final: 0.9223 (tt) REVERT: C 81 ASP cc_start: 0.8071 (t70) cc_final: 0.7836 (t70) REVERT: E 103 ASN cc_start: 0.7994 (t0) cc_final: 0.7621 (t0) REVERT: B 154 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7531 (ttp80) REVERT: B 192 LEU cc_start: 0.7560 (tp) cc_final: 0.7324 (tp) REVERT: B 226 MET cc_start: 0.8815 (tmm) cc_final: 0.8585 (tmm) REVERT: B 381 GLN cc_start: 0.9219 (tt0) cc_final: 0.8504 (tm-30) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2327 time to fit residues: 78.1678 Evaluate side-chains 210 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.150459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100833 restraints weight = 62091.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106063 restraints weight = 29296.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109455 restraints weight = 19026.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111401 restraints weight = 14798.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112649 restraints weight = 12868.912| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10694 Z= 0.105 Angle : 0.497 5.133 14528 Z= 0.273 Chirality : 0.043 0.157 1575 Planarity : 0.004 0.042 1911 Dihedral : 4.578 37.867 1465 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.22), residues: 1312 helix: 1.40 (0.31), residues: 274 sheet: -0.10 (0.23), residues: 411 loop : -0.44 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.023 0.001 TYR B 263 PHE 0.013 0.001 PHE A 804 TRP 0.010 0.001 TRP D 48 HIS 0.013 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00225 (10692) covalent geometry : angle 0.49581 (14524) SS BOND : bond 0.00483 ( 2) SS BOND : angle 1.70406 ( 4) hydrogen bonds : bond 0.04046 ( 471) hydrogen bonds : angle 5.21119 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8727 (mt) cc_final: 0.8229 (mm) REVERT: A 325 MET cc_start: 0.8549 (pmm) cc_final: 0.8323 (pmm) REVERT: A 338 ARG cc_start: 0.8426 (mtp-110) cc_final: 0.8121 (mtp-110) REVERT: A 369 MET cc_start: 0.9093 (mmp) cc_final: 0.8755 (tpp) REVERT: A 408 SER cc_start: 0.8914 (t) cc_final: 0.8558 (m) REVERT: A 609 TYR cc_start: 0.8906 (p90) cc_final: 0.8349 (p90) REVERT: A 641 LEU cc_start: 0.8613 (mm) cc_final: 0.8389 (mm) REVERT: A 645 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 648 PHE cc_start: 0.8542 (p90) cc_final: 0.7580 (p90) REVERT: A 651 ASN cc_start: 0.8715 (m-40) cc_final: 0.8379 (m-40) REVERT: A 716 LEU cc_start: 0.8415 (tt) cc_final: 0.8064 (mp) REVERT: A 745 TRP cc_start: 0.8739 (p90) cc_final: 0.8432 (p90) REVERT: A 783 LEU cc_start: 0.7865 (mm) cc_final: 0.7489 (mt) REVERT: D 49 ARG cc_start: 0.8834 (mtp180) cc_final: 0.8515 (mmm-85) REVERT: D 82 ASN cc_start: 0.8525 (t0) cc_final: 0.7749 (t0) REVERT: C 81 ASP cc_start: 0.8050 (t70) cc_final: 0.7729 (t70) REVERT: E 103 ASN cc_start: 0.7941 (t0) cc_final: 0.7590 (t0) REVERT: B 154 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7358 (ttp80) REVERT: B 192 LEU cc_start: 0.7531 (tp) cc_final: 0.7319 (tp) REVERT: B 226 MET cc_start: 0.8895 (tmm) cc_final: 0.8679 (tmm) REVERT: B 324 HIS cc_start: 0.7879 (m-70) cc_final: 0.7613 (m-70) REVERT: B 388 TYR cc_start: 0.7375 (m-80) cc_final: 0.6750 (m-80) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2144 time to fit residues: 76.7560 Evaluate side-chains 221 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.151185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112710 restraints weight = 61761.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118736 restraints weight = 41017.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119065 restraints weight = 26034.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119921 restraints weight = 19153.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121685 restraints weight = 17112.713| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10694 Z= 0.099 Angle : 0.474 4.629 14528 Z= 0.261 Chirality : 0.042 0.141 1575 Planarity : 0.004 0.042 1911 Dihedral : 4.429 37.362 1465 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.23), residues: 1312 helix: 1.58 (0.31), residues: 275 sheet: -0.04 (0.24), residues: 412 loop : -0.44 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.018 0.001 TYR B 263 PHE 0.011 0.001 PHE A 428 TRP 0.023 0.001 TRP B 317 HIS 0.014 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00213 (10692) covalent geometry : angle 0.47344 (14524) SS BOND : bond 0.00999 ( 2) SS BOND : angle 1.81016 ( 4) hydrogen bonds : bond 0.03726 ( 471) hydrogen bonds : angle 5.06259 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8783 (mt) cc_final: 0.8281 (mm) REVERT: A 325 MET cc_start: 0.8458 (pmm) cc_final: 0.8237 (pmm) REVERT: A 338 ARG cc_start: 0.8381 (mtp-110) cc_final: 0.8081 (mtp-110) REVERT: A 369 MET cc_start: 0.9007 (mmp) cc_final: 0.8741 (tpp) REVERT: A 408 SER cc_start: 0.8698 (t) cc_final: 0.8425 (m) REVERT: A 609 TYR cc_start: 0.8815 (p90) cc_final: 0.8229 (p90) REVERT: A 645 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8024 (mm-30) REVERT: A 648 PHE cc_start: 0.8537 (p90) cc_final: 0.7551 (p90) REVERT: A 651 ASN cc_start: 0.8625 (m-40) cc_final: 0.8348 (m-40) REVERT: A 716 LEU cc_start: 0.8473 (tt) cc_final: 0.8112 (mp) REVERT: A 745 TRP cc_start: 0.8747 (p90) cc_final: 0.8538 (p90) REVERT: A 783 LEU cc_start: 0.7968 (mm) cc_final: 0.7587 (mt) REVERT: D 49 ARG cc_start: 0.8800 (mtp180) cc_final: 0.8514 (mmm-85) REVERT: D 82 ASN cc_start: 0.8475 (t0) cc_final: 0.7726 (t0) REVERT: C 81 ASP cc_start: 0.8058 (t70) cc_final: 0.7762 (t70) REVERT: E 103 ASN cc_start: 0.8201 (t0) cc_final: 0.7872 (t0) REVERT: B 154 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7503 (ttp80) REVERT: B 170 GLN cc_start: 0.8408 (pt0) cc_final: 0.8183 (pt0) REVERT: B 226 MET cc_start: 0.8846 (tmm) cc_final: 0.8623 (tmm) REVERT: B 388 TYR cc_start: 0.7250 (m-80) cc_final: 0.6678 (m-80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2215 time to fit residues: 78.5720 Evaluate side-chains 223 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 88 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 0.0000 chunk 26 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.151781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113577 restraints weight = 61701.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117548 restraints weight = 41822.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118197 restraints weight = 32567.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119728 restraints weight = 20659.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120872 restraints weight = 18067.978| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10694 Z= 0.095 Angle : 0.477 6.156 14528 Z= 0.260 Chirality : 0.042 0.140 1575 Planarity : 0.003 0.042 1911 Dihedral : 4.353 36.439 1465 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.23), residues: 1312 helix: 1.72 (0.31), residues: 274 sheet: 0.05 (0.24), residues: 405 loop : -0.41 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.025 0.001 TYR A 550 PHE 0.012 0.001 PHE A 652 TRP 0.013 0.001 TRP B 317 HIS 0.013 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00207 (10692) covalent geometry : angle 0.47640 (14524) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.43354 ( 4) hydrogen bonds : bond 0.03601 ( 471) hydrogen bonds : angle 4.99449 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8797 (mt) cc_final: 0.8304 (mm) REVERT: A 325 MET cc_start: 0.8483 (pmm) cc_final: 0.8177 (pmm) REVERT: A 338 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.8046 (mtp-110) REVERT: A 369 MET cc_start: 0.8983 (mmp) cc_final: 0.8742 (tpp) REVERT: A 408 SER cc_start: 0.8651 (t) cc_final: 0.8388 (m) REVERT: A 582 ASP cc_start: 0.8666 (m-30) cc_final: 0.8214 (t0) REVERT: A 609 TYR cc_start: 0.8798 (p90) cc_final: 0.8202 (p90) REVERT: A 641 LEU cc_start: 0.8604 (mm) cc_final: 0.8326 (mm) REVERT: A 645 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 648 PHE cc_start: 0.8424 (p90) cc_final: 0.8025 (p90) REVERT: A 716 LEU cc_start: 0.8483 (tt) cc_final: 0.8112 (mp) REVERT: A 745 TRP cc_start: 0.8776 (p90) cc_final: 0.8544 (p90) REVERT: A 783 LEU cc_start: 0.7966 (mm) cc_final: 0.7588 (mt) REVERT: D 49 ARG cc_start: 0.8803 (mtp180) cc_final: 0.8520 (mmm-85) REVERT: D 82 ASN cc_start: 0.8502 (t0) cc_final: 0.7758 (t0) REVERT: C 81 ASP cc_start: 0.8056 (t70) cc_final: 0.7788 (t0) REVERT: E 103 ASN cc_start: 0.8237 (t0) cc_final: 0.7910 (t0) REVERT: B 154 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7493 (ttp80) REVERT: B 170 GLN cc_start: 0.8422 (pt0) cc_final: 0.8214 (pt0) REVERT: B 226 MET cc_start: 0.8864 (tmm) cc_final: 0.8639 (tmm) REVERT: B 388 TYR cc_start: 0.7208 (m-80) cc_final: 0.6584 (m-80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2190 time to fit residues: 76.4351 Evaluate side-chains 218 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 85 optimal weight: 0.0470 chunk 127 optimal weight: 4.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.151233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113215 restraints weight = 61550.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117251 restraints weight = 43918.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118657 restraints weight = 29859.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119349 restraints weight = 20654.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122412 restraints weight = 18282.908| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10694 Z= 0.106 Angle : 0.476 4.946 14528 Z= 0.259 Chirality : 0.042 0.150 1575 Planarity : 0.003 0.041 1911 Dihedral : 4.302 36.137 1465 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.23), residues: 1312 helix: 1.76 (0.31), residues: 275 sheet: 0.06 (0.24), residues: 405 loop : -0.43 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.017 0.001 TYR D 205 PHE 0.011 0.001 PHE A 428 TRP 0.013 0.001 TRP B 317 HIS 0.013 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00234 (10692) covalent geometry : angle 0.47528 (14524) SS BOND : bond 0.00338 ( 2) SS BOND : angle 1.51261 ( 4) hydrogen bonds : bond 0.03545 ( 471) hydrogen bonds : angle 4.95659 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3379.21 seconds wall clock time: 58 minutes 5.83 seconds (3485.83 seconds total)