Starting phenix.real_space_refine on Tue Apr 9 11:39:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp0_40672/04_2024/8sp0_40672_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp0_40672/04_2024/8sp0_40672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp0_40672/04_2024/8sp0_40672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp0_40672/04_2024/8sp0_40672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp0_40672/04_2024/8sp0_40672_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp0_40672/04_2024/8sp0_40672_neut.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 82 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 10228 2.51 5 N 2708 2.21 5 O 3206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16270 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.15, per 1000 atoms: 0.56 Number of scatterers: 16270 At special positions: 0 Unit cell: (106.4, 171.95, 124.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 82 15.00 Mg 2 11.99 O 3206 8.00 N 2708 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 2.6 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 25 sheets defined 34.6% alpha, 16.6% beta 18 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.567A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.756A pdb=" N ILE A 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 removed outlier: 4.279A pdb=" N GLY A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.598A pdb=" N LYS A 162 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A 163 " --> pdb=" O HIS A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 163' Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.729A pdb=" N LEU A 203 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 257 through 279 Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 365 removed outlier: 3.665A pdb=" N GLY A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.599A pdb=" N ASP B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.539A pdb=" N ILE B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 131 removed outlier: 4.054A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 263 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 477 through 480 Processing helix chain 'B' and resid 481 through 491 removed outlier: 3.616A pdb=" N ILE B 489 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 28 removed outlier: 3.675A pdb=" N LEU E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 147 through 158 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.878A pdb=" N LEU E 203 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 Processing helix chain 'E' and resid 300 through 304 removed outlier: 3.842A pdb=" N ASP E 303 " --> pdb=" O LEU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 385 removed outlier: 3.746A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 30 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 77 through 83 removed outlier: 3.527A pdb=" N VAL F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 104 Processing helix chain 'F' and resid 109 through 131 removed outlier: 4.226A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 150 removed outlier: 3.668A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 213 removed outlier: 3.539A pdb=" N GLN F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.615A pdb=" N ALA F 264 " --> pdb=" O ALA F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 350 Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.692A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 462 Processing helix chain 'F' and resid 481 through 490 removed outlier: 3.657A pdb=" N LYS F 485 " --> pdb=" O ARG F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.848A pdb=" N TYR F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR F 506 " --> pdb=" O PHE F 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 502 through 506' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.751A pdb=" N LYS B 2 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 414 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS A 167 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.636A pdb=" N TYR A 210 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 186 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 286 Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.826A pdb=" N LYS A 328 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 394 removed outlier: 3.532A pdb=" N VAL A 401 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AB3, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.916A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 278 through 279 removed outlier: 3.746A pdb=" N LYS B 447 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 420 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 443 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 284 through 287 removed outlier: 3.553A pdb=" N VAL B 284 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 300 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.639A pdb=" N THR B 431 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 33 through 34 removed outlier: 5.864A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE E 6 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL E 63 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER E 8 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE E 60 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU E 97 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU E 62 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ILE E 118 " --> pdb=" O ILE E 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 410 through 415 removed outlier: 3.718A pdb=" N VAL E 414 " --> pdb=" O LYS E 167 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LYS E 167 " --> pdb=" O VAL E 414 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.514A pdb=" N LEU E 176 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 324 " --> pdb=" O SER E 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.754A pdb=" N TYR E 210 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 214 " --> pdb=" O HIS E 188 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE E 187 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 283 through 286 Processing sheet with id=AC3, first strand: chain 'E' and resid 390 through 394 Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 6 removed outlier: 6.651A pdb=" N SER F 417 " --> pdb=" O VAL F 413 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 386 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS F 279 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N HIS F 360 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU F 281 " --> pdb=" O HIS F 360 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL F 278 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 305 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN F 296 " --> pdb=" O TRP F 320 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP F 320 " --> pdb=" O ASN F 296 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS F 298 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY F 318 " --> pdb=" O CYS F 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE F 304 " --> pdb=" O VAL F 312 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.532A pdb=" N CYS F 20 " --> pdb=" O ILE F 12 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.195A pdb=" N SER F 41 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N LYS F 94 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL F 43 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TRP F 139 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE F 224 " --> pdb=" O TRP F 139 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL F 141 " --> pdb=" O PHE F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.608A pdb=" N VAL F 426 " --> pdb=" O THR F 431 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 526 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 7.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3910 1.33 - 1.45: 3799 1.45 - 1.57: 8903 1.57 - 1.69: 160 1.69 - 1.81: 66 Bond restraints: 16838 Sorted by residual: bond pdb=" N ASN F 293 " pdb=" CA ASN F 293 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.11e-02 8.12e+03 1.00e+01 bond pdb=" N LYS F 290 " pdb=" CA LYS F 290 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.86e+00 bond pdb=" N LYS F 292 " pdb=" CA LYS F 292 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.40e+00 bond pdb=" N SER F 291 " pdb=" CA SER F 291 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.10e+00 bond pdb=" CA SER F 291 " pdb=" CB SER F 291 " ideal model delta sigma weight residual 1.530 1.507 0.023 1.53e-02 4.27e+03 2.29e+00 ... (remaining 16833 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.86: 865 106.86 - 113.66: 9209 113.66 - 120.45: 6404 120.45 - 127.24: 6337 127.24 - 134.03: 313 Bond angle restraints: 23128 Sorted by residual: angle pdb=" N VAL F 288 " pdb=" CA VAL F 288 " pdb=" C VAL F 288 " ideal model delta sigma weight residual 111.00 107.06 3.94 1.09e+00 8.42e-01 1.31e+01 angle pdb=" C GLU F 289 " pdb=" CA GLU F 289 " pdb=" CB GLU F 289 " ideal model delta sigma weight residual 116.34 111.56 4.78 1.40e+00 5.10e-01 1.17e+01 angle pdb=" C ASN F 293 " pdb=" N PRO F 294 " pdb=" CA PRO F 294 " ideal model delta sigma weight residual 119.05 122.62 -3.57 1.11e+00 8.12e-01 1.03e+01 angle pdb=" N HIS E 9 " pdb=" CA HIS E 9 " pdb=" C HIS E 9 " ideal model delta sigma weight residual 108.34 112.48 -4.14 1.31e+00 5.83e-01 9.97e+00 angle pdb=" N PHE E 93 " pdb=" CA PHE E 93 " pdb=" C PHE E 93 " ideal model delta sigma weight residual 114.56 110.60 3.96 1.27e+00 6.20e-01 9.74e+00 ... (remaining 23123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9702 35.92 - 71.83: 296 71.83 - 107.75: 14 107.75 - 143.67: 1 143.67 - 179.58: 11 Dihedral angle restraints: 10024 sinusoidal: 4786 harmonic: 5238 Sorted by residual: dihedral pdb=" O4' U G 17 " pdb=" C1' U G 17 " pdb=" N1 U G 17 " pdb=" C2 U G 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.58 -179.58 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U C 17 " pdb=" C1' U C 17 " pdb=" N1 U C 17 " pdb=" C2 U C 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.58 -179.58 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U C 13 " pdb=" C1' U C 13 " pdb=" N1 U C 13 " pdb=" C2 U C 13 " ideal model delta sinusoidal sigma weight residual -160.00 15.36 -175.36 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 10021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2111 0.054 - 0.108: 369 0.108 - 0.162: 55 0.162 - 0.216: 2 0.216 - 0.270: 1 Chirality restraints: 2538 Sorted by residual: chirality pdb=" CA VAL F 288 " pdb=" N VAL F 288 " pdb=" C VAL F 288 " pdb=" CB VAL F 288 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE B 248 " pdb=" CA ILE B 248 " pdb=" CG1 ILE B 248 " pdb=" CG2 ILE B 248 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CB ILE E 418 " pdb=" CA ILE E 418 " pdb=" CG1 ILE E 418 " pdb=" CG2 ILE E 418 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 2535 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 287 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C LYS F 287 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS F 287 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL F 288 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A G 11 " -0.026 2.00e-02 2.50e+03 1.27e-02 4.41e+00 pdb=" N9 A G 11 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A G 11 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A G 11 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A G 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A G 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A G 11 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A G 11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A G 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A G 11 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A G 11 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 11 " -0.025 2.00e-02 2.50e+03 1.13e-02 3.50e+00 pdb=" N9 A C 11 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A C 11 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A C 11 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C 11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 11 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A C 11 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A C 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 11 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A C 11 " 0.003 2.00e-02 2.50e+03 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 25 2.35 - 2.99: 7775 2.99 - 3.62: 22892 3.62 - 4.26: 35565 4.26 - 4.90: 59364 Nonbonded interactions: 125621 Sorted by model distance: nonbonded pdb=" OE2 GLU E 260 " pdb=" O2' A G 16 " model vdw 1.710 2.440 nonbonded pdb=" NZ LYS B 247 " pdb=" O2 DC H 22 " model vdw 1.871 2.520 nonbonded pdb=" OP2 U C 1 " pdb="MG MG B 601 " model vdw 1.967 2.170 nonbonded pdb=" OP2 U G 1 " pdb="MG MG F 601 " model vdw 2.051 2.170 nonbonded pdb=" O2' A C 11 " pdb=" O5' A C 12 " model vdw 2.062 2.440 ... (remaining 125616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.590 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 49.820 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16838 Z= 0.202 Angle : 0.527 9.409 23128 Z= 0.295 Chirality : 0.042 0.270 2538 Planarity : 0.003 0.043 2632 Dihedral : 17.606 179.584 6640 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1764 helix: 1.75 (0.24), residues: 543 sheet: -0.37 (0.31), residues: 318 loop : -1.74 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 192 HIS 0.005 0.001 HIS F 207 PHE 0.014 0.001 PHE A 321 TYR 0.010 0.001 TYR B 321 ARG 0.003 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.668 Fit side-chains REVERT: A 210 TYR cc_start: 0.8318 (t80) cc_final: 0.8080 (t80) REVERT: A 279 ASP cc_start: 0.7897 (t0) cc_final: 0.7682 (t0) REVERT: A 348 LYS cc_start: 0.6948 (ttpp) cc_final: 0.6724 (ttpp) REVERT: B 68 ASN cc_start: 0.7607 (t0) cc_final: 0.7377 (m-40) REVERT: B 143 VAL cc_start: 0.7275 (t) cc_final: 0.7051 (p) REVERT: B 324 LYS cc_start: 0.7276 (tppt) cc_final: 0.7019 (tppt) REVERT: B 358 PHE cc_start: 0.7916 (m-80) cc_final: 0.7593 (m-80) REVERT: E 269 LEU cc_start: 0.6442 (mp) cc_final: 0.6216 (mt) REVERT: E 276 ARG cc_start: 0.7064 (tpt90) cc_final: 0.6637 (tpt90) REVERT: F 95 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7170 (tm-30) REVERT: F 226 GLU cc_start: 0.7333 (tt0) cc_final: 0.6631 (tt0) REVERT: F 295 ARG cc_start: 0.7024 (ttp-170) cc_final: 0.6670 (mtp85) REVERT: F 296 ASN cc_start: 0.6898 (m-40) cc_final: 0.6440 (p0) REVERT: F 468 ASN cc_start: 0.7127 (t160) cc_final: 0.6829 (t0) REVERT: F 488 GLU cc_start: 0.6723 (pp20) cc_final: 0.6518 (pp20) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3259 time to fit residues: 95.2606 Evaluate side-chains 183 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 165 optimal weight: 0.4980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 ASN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS F 302 GLN F 325 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16838 Z= 0.239 Angle : 0.569 9.535 23128 Z= 0.300 Chirality : 0.042 0.164 2538 Planarity : 0.004 0.043 2632 Dihedral : 18.415 179.355 3014 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.50 % Allowed : 6.98 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1764 helix: 1.82 (0.24), residues: 549 sheet: -0.25 (0.30), residues: 335 loop : -1.81 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 192 HIS 0.007 0.001 HIS F 207 PHE 0.016 0.002 PHE A 391 TYR 0.012 0.001 TYR E 392 ARG 0.004 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 1.645 Fit side-chains revert: symmetry clash REVERT: A 348 LYS cc_start: 0.6916 (ttpp) cc_final: 0.6708 (ttpp) REVERT: B 324 LYS cc_start: 0.7301 (tppt) cc_final: 0.6992 (tppt) REVERT: E 276 ARG cc_start: 0.7075 (tpt90) cc_final: 0.6856 (tpt90) REVERT: F 296 ASN cc_start: 0.6811 (m-40) cc_final: 0.6375 (p0) REVERT: F 468 ASN cc_start: 0.7512 (t0) cc_final: 0.7223 (t0) outliers start: 8 outliers final: 7 residues processed: 189 average time/residue: 0.3298 time to fit residues: 90.2138 Evaluate side-chains 180 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 173 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 357 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16838 Z= 0.345 Angle : 0.633 10.449 23128 Z= 0.335 Chirality : 0.045 0.185 2538 Planarity : 0.004 0.043 2632 Dihedral : 18.559 175.338 3014 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.64 % Allowed : 9.94 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1764 helix: 1.61 (0.23), residues: 549 sheet: -0.38 (0.30), residues: 334 loop : -1.97 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 192 HIS 0.009 0.001 HIS F 207 PHE 0.024 0.002 PHE A 321 TYR 0.015 0.002 TYR B 280 ARG 0.005 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.6802 (mtt) cc_final: 0.6534 (mtt) REVERT: A 348 LYS cc_start: 0.7003 (ttpp) cc_final: 0.6779 (ttpp) REVERT: B 68 ASN cc_start: 0.7602 (t0) cc_final: 0.7364 (m-40) REVERT: B 324 LYS cc_start: 0.7392 (tppt) cc_final: 0.7088 (tppt) REVERT: B 358 PHE cc_start: 0.8089 (m-80) cc_final: 0.7460 (m-80) REVERT: E 276 ARG cc_start: 0.7177 (tpt90) cc_final: 0.6934 (tpt90) REVERT: F 226 GLU cc_start: 0.7437 (tt0) cc_final: 0.7051 (tt0) outliers start: 26 outliers final: 19 residues processed: 208 average time/residue: 0.3320 time to fit residues: 101.9914 Evaluate side-chains 209 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 445 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 0.0030 chunk 86 optimal weight: 0.4980 chunk 157 optimal weight: 0.6980 chunk 47 optimal weight: 0.0070 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16838 Z= 0.177 Angle : 0.526 7.775 23128 Z= 0.279 Chirality : 0.041 0.176 2538 Planarity : 0.003 0.043 2632 Dihedral : 18.369 178.843 3014 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.70 % Allowed : 11.95 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1764 helix: 1.95 (0.24), residues: 550 sheet: -0.38 (0.30), residues: 350 loop : -1.81 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 192 HIS 0.004 0.001 HIS F 207 PHE 0.020 0.001 PHE A 305 TYR 0.011 0.001 TYR E 392 ARG 0.003 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7548 (tppp) cc_final: 0.7166 (tppt) REVERT: A 348 LYS cc_start: 0.6908 (ttpp) cc_final: 0.6691 (ttpp) REVERT: B 324 LYS cc_start: 0.7313 (tppt) cc_final: 0.7025 (tppt) REVERT: E 276 ARG cc_start: 0.6937 (tpt90) cc_final: 0.6684 (tpt90) REVERT: F 226 GLU cc_start: 0.7233 (tt0) cc_final: 0.6885 (tt0) REVERT: F 303 MET cc_start: 0.8027 (ttp) cc_final: 0.7591 (ttp) outliers start: 27 outliers final: 21 residues processed: 193 average time/residue: 0.3195 time to fit residues: 89.5128 Evaluate side-chains 201 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 150 optimal weight: 0.5980 chunk 121 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16838 Z= 0.251 Angle : 0.563 8.924 23128 Z= 0.298 Chirality : 0.042 0.193 2538 Planarity : 0.004 0.045 2632 Dihedral : 18.446 177.149 3014 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.95 % Allowed : 13.40 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1764 helix: 1.86 (0.23), residues: 551 sheet: -0.32 (0.30), residues: 343 loop : -1.86 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 192 HIS 0.006 0.001 HIS F 207 PHE 0.026 0.002 PHE A 305 TYR 0.011 0.001 TYR B 397 ARG 0.003 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7661 (tppp) cc_final: 0.7214 (tppt) REVERT: A 348 LYS cc_start: 0.6973 (ttpp) cc_final: 0.6749 (ttpp) REVERT: B 324 LYS cc_start: 0.7351 (tppt) cc_final: 0.7067 (tppt) REVERT: E 276 ARG cc_start: 0.7042 (tpt90) cc_final: 0.6802 (tpt90) REVERT: F 226 GLU cc_start: 0.7306 (tt0) cc_final: 0.7003 (tt0) REVERT: F 296 ASN cc_start: 0.6742 (m-40) cc_final: 0.6279 (p0) REVERT: F 468 ASN cc_start: 0.7656 (t0) cc_final: 0.7307 (t0) outliers start: 31 outliers final: 22 residues processed: 201 average time/residue: 0.3205 time to fit residues: 95.0939 Evaluate side-chains 206 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 chunk 43 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16838 Z= 0.268 Angle : 0.572 8.385 23128 Z= 0.303 Chirality : 0.043 0.192 2538 Planarity : 0.004 0.050 2632 Dihedral : 18.538 176.188 3014 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.52 % Allowed : 14.40 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1764 helix: 1.82 (0.23), residues: 550 sheet: -0.43 (0.30), residues: 348 loop : -1.90 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 254 HIS 0.007 0.001 HIS F 207 PHE 0.026 0.002 PHE A 305 TYR 0.014 0.001 TYR B 397 ARG 0.004 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.603 Fit side-chains REVERT: A 336 MET cc_start: 0.6764 (mtt) cc_final: 0.6507 (mtt) REVERT: A 348 LYS cc_start: 0.7002 (ttpp) cc_final: 0.6773 (ttpp) REVERT: A 411 LYS cc_start: 0.7985 (pttt) cc_final: 0.7683 (pttm) REVERT: B 324 LYS cc_start: 0.7359 (tppt) cc_final: 0.7086 (tppt) REVERT: B 435 MET cc_start: 0.6520 (mpp) cc_final: 0.5813 (mpp) REVERT: E 276 ARG cc_start: 0.7035 (tpt90) cc_final: 0.6760 (tpt90) REVERT: F 95 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6935 (tm-30) REVERT: F 296 ASN cc_start: 0.6749 (m-40) cc_final: 0.6281 (p0) REVERT: F 468 ASN cc_start: 0.7684 (t0) cc_final: 0.7335 (t0) outliers start: 40 outliers final: 29 residues processed: 209 average time/residue: 0.3325 time to fit residues: 102.0790 Evaluate side-chains 214 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 445 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 0.0030 chunk 128 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 175 optimal weight: 0.0030 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 0.0070 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16838 Z= 0.158 Angle : 0.513 6.788 23128 Z= 0.273 Chirality : 0.040 0.184 2538 Planarity : 0.003 0.045 2632 Dihedral : 18.432 178.347 3014 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.95 % Allowed : 15.35 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1764 helix: 2.07 (0.23), residues: 550 sheet: -0.33 (0.30), residues: 348 loop : -1.83 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 294 HIS 0.003 0.001 HIS E 320 PHE 0.016 0.001 PHE E 217 TYR 0.011 0.001 TYR E 392 ARG 0.003 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 1.863 Fit side-chains REVERT: A 348 LYS cc_start: 0.6885 (ttpp) cc_final: 0.6671 (ttpp) REVERT: A 364 GLN cc_start: 0.7296 (mm-40) cc_final: 0.7057 (mm-40) REVERT: A 411 LYS cc_start: 0.7942 (pttt) cc_final: 0.7632 (pttm) REVERT: B 324 LYS cc_start: 0.7326 (tppt) cc_final: 0.7043 (tppt) REVERT: B 435 MET cc_start: 0.6495 (mpp) cc_final: 0.5850 (mpp) REVERT: E 276 ARG cc_start: 0.6905 (tpt90) cc_final: 0.6610 (tpt90) REVERT: F 95 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6747 (tm-30) REVERT: F 303 MET cc_start: 0.8060 (ttp) cc_final: 0.7624 (ttp) outliers start: 31 outliers final: 24 residues processed: 206 average time/residue: 0.3139 time to fit residues: 94.5312 Evaluate side-chains 213 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 445 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 104 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 119 optimal weight: 0.0570 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16838 Z= 0.193 Angle : 0.529 7.433 23128 Z= 0.279 Chirality : 0.041 0.211 2538 Planarity : 0.003 0.043 2632 Dihedral : 18.424 177.844 3014 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.08 % Allowed : 15.97 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1764 helix: 2.04 (0.23), residues: 552 sheet: -0.32 (0.29), residues: 347 loop : -1.86 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 192 HIS 0.005 0.001 HIS F 207 PHE 0.022 0.001 PHE A 305 TYR 0.012 0.001 TYR E 392 ARG 0.004 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.908 Fit side-chains REVERT: A 348 LYS cc_start: 0.6921 (ttpp) cc_final: 0.6707 (ttpp) REVERT: A 411 LYS cc_start: 0.7957 (pttt) cc_final: 0.7675 (pttm) REVERT: B 324 LYS cc_start: 0.7336 (tppt) cc_final: 0.7058 (tppt) REVERT: B 435 MET cc_start: 0.6581 (mpp) cc_final: 0.5927 (mpp) REVERT: E 276 ARG cc_start: 0.6953 (tpt90) cc_final: 0.6711 (tpt90) REVERT: F 95 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6440 (tm-30) REVERT: F 208 ASP cc_start: 0.7218 (m-30) cc_final: 0.6983 (m-30) REVERT: F 296 ASN cc_start: 0.6715 (m-40) cc_final: 0.6279 (p0) REVERT: F 303 MET cc_start: 0.8011 (ttp) cc_final: 0.7533 (ttp) REVERT: F 468 ASN cc_start: 0.7631 (t0) cc_final: 0.7302 (t0) outliers start: 33 outliers final: 29 residues processed: 210 average time/residue: 0.3035 time to fit residues: 94.0241 Evaluate side-chains 217 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 445 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 153 optimal weight: 0.2980 chunk 163 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16838 Z= 0.272 Angle : 0.586 8.809 23128 Z= 0.309 Chirality : 0.043 0.241 2538 Planarity : 0.004 0.049 2632 Dihedral : 18.555 174.230 3014 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.08 % Allowed : 16.29 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1764 helix: 1.85 (0.23), residues: 552 sheet: -0.57 (0.29), residues: 357 loop : -1.87 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 294 HIS 0.008 0.001 HIS F 207 PHE 0.014 0.002 PHE A 321 TYR 0.012 0.001 TYR B 397 ARG 0.004 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.724 Fit side-chains REVERT: A 280 LYS cc_start: 0.7637 (tppp) cc_final: 0.7218 (tppt) REVERT: A 348 LYS cc_start: 0.6996 (ttpp) cc_final: 0.6795 (ttpp) REVERT: B 1 MET cc_start: 0.8148 (mmt) cc_final: 0.7834 (tpt) REVERT: B 324 LYS cc_start: 0.7406 (tppt) cc_final: 0.7128 (tppt) REVERT: B 435 MET cc_start: 0.6446 (mpp) cc_final: 0.5762 (mpp) REVERT: E 276 ARG cc_start: 0.7022 (tpt90) cc_final: 0.6810 (tpt90) REVERT: F 50 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7312 (mt) REVERT: F 87 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6847 (mm-30) REVERT: F 95 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6698 (tm-30) REVERT: F 296 ASN cc_start: 0.6762 (m-40) cc_final: 0.6289 (p0) REVERT: F 468 ASN cc_start: 0.7686 (t0) cc_final: 0.7334 (t0) outliers start: 33 outliers final: 27 residues processed: 209 average time/residue: 0.3032 time to fit residues: 93.2473 Evaluate side-chains 216 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 445 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 166 optimal weight: 0.0000 chunk 144 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16838 Z= 0.276 Angle : 0.584 8.196 23128 Z= 0.308 Chirality : 0.043 0.250 2538 Planarity : 0.004 0.052 2632 Dihedral : 18.544 173.416 3014 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.01 % Allowed : 16.79 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1764 helix: 1.82 (0.23), residues: 552 sheet: -0.56 (0.29), residues: 352 loop : -1.92 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 294 HIS 0.008 0.001 HIS F 207 PHE 0.025 0.002 PHE A 305 TYR 0.012 0.001 TYR B 115 ARG 0.004 0.000 ARG B 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 1.906 Fit side-chains REVERT: A 280 LYS cc_start: 0.7667 (tppp) cc_final: 0.7254 (tppt) REVERT: A 348 LYS cc_start: 0.6994 (ttpp) cc_final: 0.6793 (ttpp) REVERT: B 1 MET cc_start: 0.8180 (mmt) cc_final: 0.7852 (tpt) REVERT: B 324 LYS cc_start: 0.7376 (tppt) cc_final: 0.7118 (tppt) REVERT: B 435 MET cc_start: 0.6456 (mpp) cc_final: 0.5761 (mpp) REVERT: E 276 ARG cc_start: 0.6997 (tpt90) cc_final: 0.6763 (tpt90) REVERT: F 50 LEU cc_start: 0.7554 (mm) cc_final: 0.7339 (mt) REVERT: F 95 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6716 (tm-30) REVERT: F 296 ASN cc_start: 0.6729 (m-40) cc_final: 0.6280 (p0) REVERT: F 468 ASN cc_start: 0.7682 (t0) cc_final: 0.7328 (t0) outliers start: 32 outliers final: 29 residues processed: 199 average time/residue: 0.3186 time to fit residues: 92.8376 Evaluate side-chains 210 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 445 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.3980 chunk 153 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 0.0870 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.0970 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 325 ASN B 446 ASN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.205499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.172108 restraints weight = 22386.203| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.01 r_work: 0.3917 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16838 Z= 0.162 Angle : 0.517 6.995 23128 Z= 0.274 Chirality : 0.041 0.201 2538 Planarity : 0.003 0.047 2632 Dihedral : 18.327 176.618 3014 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.08 % Allowed : 16.92 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1764 helix: 2.08 (0.23), residues: 553 sheet: -0.37 (0.29), residues: 347 loop : -1.87 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 294 HIS 0.004 0.001 HIS A 320 PHE 0.025 0.001 PHE A 305 TYR 0.012 0.001 TYR E 392 ARG 0.003 0.000 ARG B 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3924.67 seconds wall clock time: 73 minutes 52.52 seconds (4432.52 seconds total)