Starting phenix.real_space_refine on Tue Apr 9 19:15:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/04_2024/5zqz_6940.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/04_2024/5zqz_6940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/04_2024/5zqz_6940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/04_2024/5zqz_6940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/04_2024/5zqz_6940.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/04_2024/5zqz_6940.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10916 2.51 5 N 2944 2.21 5 O 3214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 549": "NH1" <-> "NH2" Residue "C PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 680": "NH1" <-> "NH2" Residue "C ARG 732": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 444": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17174 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5410 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 33, 'TRANS': 677} Chain breaks: 2 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3177 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "C" Number of atoms: 5410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5410 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 33, 'TRANS': 677} Chain breaks: 2 Chain: "D" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3177 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Time building chain proxies: 9.24, per 1000 atoms: 0.54 Number of scatterers: 17174 At special positions: 0 Unit cell: (109.56, 183.48, 104.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3214 8.00 N 2944 7.00 C 10916 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: 6.75 Conformation dependent library (CDL) restraints added in 3.2 seconds 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4132 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 16 sheets defined 43.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 removed outlier: 4.977A pdb=" N GLU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.578A pdb=" N ALA A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.503A pdb=" N SER A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.839A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 183 through 186 removed outlier: 3.633A pdb=" N GLN A 186 " --> pdb=" O GLY A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 193 through 202 removed outlier: 4.171A pdb=" N ASP A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.346A pdb=" N LYS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 removed outlier: 3.790A pdb=" N LEU A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.657A pdb=" N TYR A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.564A pdb=" N ILE A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.684A pdb=" N LEU A 321 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 removed outlier: 4.327A pdb=" N GLY A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.695A pdb=" N VAL A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 396 removed outlier: 3.785A pdb=" N ALA A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.680A pdb=" N GLN A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.841A pdb=" N ASP A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.512A pdb=" N ARG A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 462 removed outlier: 3.635A pdb=" N ARG A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.554A pdb=" N VAL A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Proline residue: A 553 - end of helix Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.664A pdb=" N ILE A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 562' Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.576A pdb=" N ASP A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 592 removed outlier: 4.115A pdb=" N GLY A 592 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 removed outlier: 3.597A pdb=" N ALA A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 4.009A pdb=" N LYS A 625 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 626 " --> pdb=" O MET A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.648A pdb=" N LYS A 631 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 removed outlier: 3.981A pdb=" N ILE A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 688 Processing helix chain 'A' and resid 696 through 699 Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.609A pdb=" N ALA A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 720 removed outlier: 3.977A pdb=" N PHE A 720 " --> pdb=" O PRO A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.921A pdb=" N ALA A 751 " --> pdb=" O CYS A 747 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.898A pdb=" N ASP B 73 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.724A pdb=" N ARG B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 4.358A pdb=" N GLU B 118 " --> pdb=" O ASN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 194 through 201 removed outlier: 3.874A pdb=" N SER B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 removed outlier: 3.986A pdb=" N SER B 226 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 4.428A pdb=" N TYR B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 354 through 357 removed outlier: 3.775A pdb=" N TYR B 357 " --> pdb=" O GLY B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 357' Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.838A pdb=" N GLU B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 438 through 448 removed outlier: 4.319A pdb=" N ARG B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 81 removed outlier: 4.977A pdb=" N GLU C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLU C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.578A pdb=" N ALA C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.504A pdb=" N SER C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 126 " --> pdb=" O GLU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.839A pdb=" N LEU C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 183 through 186 removed outlier: 3.633A pdb=" N GLN C 186 " --> pdb=" O GLY C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 193 through 202 removed outlier: 4.171A pdb=" N ASP C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 216 removed outlier: 4.345A pdb=" N LYS C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 253 removed outlier: 3.789A pdb=" N LEU C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.657A pdb=" N TYR C 283 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 removed outlier: 3.564A pdb=" N ILE C 305 " --> pdb=" O PRO C 301 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL C 307 " --> pdb=" O LYS C 303 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 3.684A pdb=" N LEU C 321 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 332 removed outlier: 4.327A pdb=" N GLY C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU C 329 " --> pdb=" O GLN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.694A pdb=" N VAL C 379 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 396 removed outlier: 3.785A pdb=" N ALA C 396 " --> pdb=" O THR C 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 393 through 396' Processing helix chain 'C' and resid 397 through 405 removed outlier: 3.679A pdb=" N GLN C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 removed outlier: 3.840A pdb=" N ASP C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS C 411 " --> pdb=" O GLY C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 427 removed outlier: 3.511A pdb=" N ARG C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 462 removed outlier: 3.635A pdb=" N ARG C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS C 460 " --> pdb=" O HIS C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.553A pdb=" N VAL C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Proline residue: C 553 - end of helix Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.664A pdb=" N ILE C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU C 562 " --> pdb=" O VAL C 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 562' Processing helix chain 'C' and resid 568 through 579 removed outlier: 3.575A pdb=" N ASP C 572 " --> pdb=" O PRO C 568 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 592 removed outlier: 4.115A pdb=" N GLY C 592 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.596A pdb=" N ALA C 596 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS C 598 " --> pdb=" O ASP C 594 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU C 603 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 626 removed outlier: 4.009A pdb=" N LYS C 625 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY C 626 " --> pdb=" O MET C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.648A pdb=" N LYS C 631 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 657 removed outlier: 3.982A pdb=" N ILE C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 656 " --> pdb=" O MET C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 688 Processing helix chain 'C' and resid 696 through 699 Processing helix chain 'C' and resid 700 through 705 removed outlier: 3.610A pdb=" N ALA C 704 " --> pdb=" O GLY C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 720 removed outlier: 3.977A pdb=" N PHE C 720 " --> pdb=" O PRO C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 736 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.920A pdb=" N ALA C 751 " --> pdb=" O CYS C 747 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 removed outlier: 3.898A pdb=" N ASP D 73 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.724A pdb=" N ARG D 81 " --> pdb=" O HIS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 122 removed outlier: 4.358A pdb=" N GLU D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'D' and resid 194 through 201 removed outlier: 3.875A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.985A pdb=" N SER D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 259 removed outlier: 4.427A pdb=" N TYR D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 354 through 357 removed outlier: 3.776A pdb=" N TYR D 357 " --> pdb=" O GLY D 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 354 through 357' Processing helix chain 'D' and resid 358 through 367 removed outlier: 3.839A pdb=" N GLU D 364 " --> pdb=" O PRO D 360 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 392 Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 438 through 448 removed outlier: 4.320A pdb=" N ARG D 444 " --> pdb=" O ALA D 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.534A pdb=" N ASN A 42 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 46 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.534A pdb=" N ASN A 42 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA A 88 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 146 removed outlier: 6.459A pdb=" N CYS A 145 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.604A pdb=" N ALA A 161 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA6, first strand: chain 'A' and resid 496 through 498 Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.889A pdb=" N VAL B 161 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 132 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS D 132 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 161 " --> pdb=" O TYR D 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 336 removed outlier: 3.777A pdb=" N ALA B 335 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU B 319 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 161 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 132 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS D 132 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 161 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU D 319 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 335 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 341 removed outlier: 6.788A pdb=" N GLU B 377 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N CYS B 458 " --> pdb=" O GLU B 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.534A pdb=" N ASN C 42 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 46 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.534A pdb=" N ASN C 42 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA C 88 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.459A pdb=" N CYS C 145 " --> pdb=" O GLY C 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.604A pdb=" N ALA C 161 " --> pdb=" O GLN C 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AB6, first strand: chain 'C' and resid 496 through 498 Processing sheet with id=AB7, first strand: chain 'D' and resid 340 through 341 removed outlier: 6.788A pdb=" N GLU D 377 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N CYS D 458 " --> pdb=" O GLU D 377 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1524 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: 5.49 Time building geometry restraints manager: 7.23 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: 5119 1.33 - 1.45: 2905 1.45 - 1.57: 9269 1.57 - 1.69: 3 1.69 - 1.81: 170 Bond restraints: 17466 Sorted by residual: bond pdb=" CA GLU C 67 " pdb=" C GLU C 67 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.38e-02 5.25e+03 1.06e+01 bond pdb=" CA GLU A 67 " pdb=" C GLU A 67 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.38e-02 5.25e+03 1.02e+01 bond pdb=" CB MET D 136 " pdb=" CG MET D 136 " ideal model delta sigma weight residual 1.520 1.430 0.090 3.00e-02 1.11e+03 8.97e+00 bond pdb=" CB MET B 136 " pdb=" CG MET B 136 " ideal model delta sigma weight residual 1.520 1.430 0.090 3.00e-02 1.11e+03 8.90e+00 bond pdb=" CG1 ILE D 102 " pdb=" CD1 ILE D 102 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.09e+00 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 94.61 - 102.96: 147 102.96 - 111.32: 6713 111.32 - 119.67: 8740 119.67 - 128.03: 7823 128.03 - 136.38: 129 Bond angle restraints: 23552 Sorted by residual: angle pdb=" CA GLU B 118 " pdb=" CB GLU B 118 " pdb=" CG GLU B 118 " ideal model delta sigma weight residual 114.10 132.97 -18.87 2.00e+00 2.50e-01 8.90e+01 angle pdb=" CA GLU D 118 " pdb=" CB GLU D 118 " pdb=" CG GLU D 118 " ideal model delta sigma weight residual 114.10 132.94 -18.84 2.00e+00 2.50e-01 8.88e+01 angle pdb=" CB GLU D 118 " pdb=" CG GLU D 118 " pdb=" CD GLU D 118 " ideal model delta sigma weight residual 112.60 126.54 -13.94 1.70e+00 3.46e-01 6.72e+01 angle pdb=" CB GLU B 118 " pdb=" CG GLU B 118 " pdb=" CD GLU B 118 " ideal model delta sigma weight residual 112.60 126.49 -13.89 1.70e+00 3.46e-01 6.68e+01 angle pdb=" CA ARG A 159 " pdb=" CB ARG A 159 " pdb=" CG ARG A 159 " ideal model delta sigma weight residual 114.10 128.96 -14.86 2.00e+00 2.50e-01 5.52e+01 ... (remaining 23547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9728 17.92 - 35.84: 751 35.84 - 53.76: 176 53.76 - 71.68: 37 71.68 - 89.60: 8 Dihedral angle restraints: 10700 sinusoidal: 4264 harmonic: 6436 Sorted by residual: dihedral pdb=" CA PHE B 376 " pdb=" C PHE B 376 " pdb=" N GLU B 377 " pdb=" CA GLU B 377 " ideal model delta harmonic sigma weight residual 180.00 139.38 40.62 0 5.00e+00 4.00e-02 6.60e+01 dihedral pdb=" CA PHE D 376 " pdb=" C PHE D 376 " pdb=" N GLU D 377 " pdb=" CA GLU D 377 " ideal model delta harmonic sigma weight residual 180.00 139.41 40.59 0 5.00e+00 4.00e-02 6.59e+01 dihedral pdb=" CA ASN D 142 " pdb=" C ASN D 142 " pdb=" N GLN D 143 " pdb=" CA GLN D 143 " ideal model delta harmonic sigma weight residual 180.00 141.30 38.70 0 5.00e+00 4.00e-02 5.99e+01 ... (remaining 10697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2082 0.082 - 0.164: 543 0.164 - 0.246: 64 0.246 - 0.329: 13 0.329 - 0.411: 2 Chirality restraints: 2704 Sorted by residual: chirality pdb=" CB ILE C 275 " pdb=" CA ILE C 275 " pdb=" CG1 ILE C 275 " pdb=" CG2 ILE C 275 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE A 275 " pdb=" CA ILE A 275 " pdb=" CG1 ILE A 275 " pdb=" CG2 ILE A 275 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA ASN D 114 " pdb=" N ASN D 114 " pdb=" C ASN D 114 " pdb=" CB ASN D 114 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2701 not shown) Planarity restraints: 3026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 662 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO C 663 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 663 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 663 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 662 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 663 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 663 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 663 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 298 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO D 299 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.043 5.00e-02 4.00e+02 ... (remaining 3023 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2427 2.74 - 3.28: 17004 3.28 - 3.82: 27674 3.82 - 4.36: 31707 4.36 - 4.90: 51028 Nonbonded interactions: 129840 Sorted by model distance: nonbonded pdb=" OH TYR D 357 " pdb=" O TYR D 402 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR B 357 " pdb=" O TYR B 402 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR D 244 " pdb=" OE2 GLU D 380 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR B 244 " pdb=" OE2 GLU B 380 " model vdw 2.232 2.440 nonbonded pdb=" O GLY D 422 " pdb=" OG SER D 425 " model vdw 2.272 2.440 ... (remaining 129835 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.380 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: 0.010 Extract box with map and model: 2.410 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 46.700 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.009 0.104 17466 Z= 0.595 Angle : 1.415 18.869 23552 Z= 0.768 Chirality : 0.073 0.411 2704 Planarity : 0.009 0.081 3026 Dihedral : 14.223 89.604 6568 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.22 % Favored : 87.29 % Rotamer: Outliers : 3.84 % Allowed : 13.74 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.14), residues: 2242 helix: -3.83 (0.11), residues: 740 sheet: -2.73 (0.29), residues: 252 loop : -3.14 (0.15), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP C 80 HIS 0.012 0.003 HIS B 465 PHE 0.030 0.004 PHE C 545 TYR 0.030 0.004 TYR D 100 ARG 0.018 0.002 ARG B 436 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 470 time to evaluate : 2.365 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: A 42 ASN cc_start: 0.8381 (p0) cc_final: 0.8160 (p0) REVERT: A 166 LYS cc_start: 0.8327 (tptm) cc_final: 0.8112 (tptm) REVERT: A 198 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7947 (tm) REVERT: A 273 MET cc_start: 0.4865 (ptt) cc_final: 0.4542 (ptm) REVERT: A 321 LEU cc_start: 0.8666 (pp) cc_final: 0.8255 (tp) REVERT: A 330 LEU cc_start: 0.8684 (pt) cc_final: 0.7758 (mp) REVERT: A 382 ASP cc_start: 0.8123 (p0) cc_final: 0.7632 (p0) REVERT: A 497 MET cc_start: 0.8993 (mtt) cc_final: 0.8513 (mtp) REVERT: A 509 LEU cc_start: 0.9028 (mm) cc_final: 0.8781 (mm) REVERT: A 536 ILE cc_start: 0.9026 (tp) cc_final: 0.8761 (tp) REVERT: A 718 PHE cc_start: 0.7757 (t80) cc_final: 0.7375 (t80) REVERT: A 722 ASP cc_start: 0.7477 (p0) cc_final: 0.7016 (p0) REVERT: B 73 ASP cc_start: 0.7518 (t0) cc_final: 0.7299 (t0) REVERT: B 107 ILE cc_start: 0.8511 (mm) cc_final: 0.7636 (pt) REVERT: B 142 ASN cc_start: 0.8332 (t0) cc_final: 0.7925 (t0) REVERT: B 143 GLN cc_start: 0.9310 (tm130) cc_final: 0.9000 (tm-30) REVERT: B 206 PHE cc_start: 0.6925 (p90) cc_final: 0.6209 (p90) REVERT: B 258 GLU cc_start: 0.7649 (tp30) cc_final: 0.7203 (tp30) REVERT: B 318 MET cc_start: 0.9210 (ptp) cc_final: 0.8986 (ptp) REVERT: B 341 MET cc_start: 0.8396 (tpt) cc_final: 0.8129 (tpp) REVERT: B 371 ASN cc_start: 0.8408 (p0) cc_final: 0.8153 (t0) REVERT: B 387 LEU cc_start: 0.9380 (pp) cc_final: 0.8967 (tp) REVERT: B 390 PHE cc_start: 0.8083 (m-10) cc_final: 0.7863 (m-10) REVERT: B 418 ASN cc_start: 0.7817 (t0) cc_final: 0.7433 (t0) REVERT: B 423 SER cc_start: 0.8483 (t) cc_final: 0.7700 (t) REVERT: B 451 GLN cc_start: 0.7909 (pt0) cc_final: 0.7555 (pt0) REVERT: C 198 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7755 (tm) REVERT: C 200 MET cc_start: 0.8831 (ttt) cc_final: 0.8283 (tmm) REVERT: C 219 ASP cc_start: 0.7336 (p0) cc_final: 0.7104 (p0) REVERT: C 273 MET cc_start: 0.5151 (ptt) cc_final: 0.4777 (ptm) REVERT: C 330 LEU cc_start: 0.8670 (pt) cc_final: 0.7840 (mp) REVERT: C 382 ASP cc_start: 0.8337 (p0) cc_final: 0.7991 (p0) REVERT: C 383 LYS cc_start: 0.8074 (ptpp) cc_final: 0.7658 (pttt) REVERT: C 462 VAL cc_start: 0.8722 (t) cc_final: 0.8217 (p) REVERT: C 497 MET cc_start: 0.9077 (mtt) cc_final: 0.8837 (mtt) REVERT: C 536 ILE cc_start: 0.9036 (tp) cc_final: 0.8786 (tp) REVERT: C 718 PHE cc_start: 0.7755 (t80) cc_final: 0.7290 (t80) REVERT: C 722 ASP cc_start: 0.7284 (p0) cc_final: 0.6779 (p0) REVERT: D 107 ILE cc_start: 0.8630 (mm) cc_final: 0.7792 (pt) REVERT: D 136 MET cc_start: 0.7337 (mtp) cc_final: 0.7078 (mtp) REVERT: D 142 ASN cc_start: 0.8437 (t0) cc_final: 0.8020 (t0) REVERT: D 143 GLN cc_start: 0.9257 (tm130) cc_final: 0.8919 (tm-30) REVERT: D 206 PHE cc_start: 0.6389 (p90) cc_final: 0.5758 (p90) REVERT: D 221 GLU cc_start: 0.8085 (pp20) cc_final: 0.7528 (pp20) REVERT: D 341 MET cc_start: 0.8338 (tpt) cc_final: 0.8060 (tpp) REVERT: D 371 ASN cc_start: 0.8403 (p0) cc_final: 0.8140 (t0) REVERT: D 387 LEU cc_start: 0.9393 (pp) cc_final: 0.8946 (tp) REVERT: D 390 PHE cc_start: 0.8174 (m-10) cc_final: 0.7918 (m-10) REVERT: D 418 ASN cc_start: 0.7879 (t0) cc_final: 0.7370 (t0) REVERT: D 423 SER cc_start: 0.8579 (t) cc_final: 0.7808 (t) outliers start: 71 outliers final: 21 residues processed: 507 average time/residue: 0.3270 time to fit residues: 239.8358 Evaluate side-chains 320 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 297 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17466 Z= 0.247 Angle : 0.799 8.538 23552 Z= 0.414 Chirality : 0.049 0.181 2704 Planarity : 0.006 0.079 3026 Dihedral : 7.329 38.398 2394 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 0.38 % Allowed : 6.60 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.16), residues: 2242 helix: -2.76 (0.15), residues: 808 sheet: -2.30 (0.31), residues: 240 loop : -2.91 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 80 HIS 0.003 0.001 HIS D 379 PHE 0.021 0.002 PHE A 277 TYR 0.017 0.002 TYR C 239 ARG 0.013 0.001 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 450 time to evaluate : 2.032 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: A 273 MET cc_start: 0.5135 (ptt) cc_final: 0.4829 (ptm) REVERT: A 321 LEU cc_start: 0.8730 (pp) cc_final: 0.8337 (tp) REVERT: A 330 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.7831 (mp) REVERT: A 383 LYS cc_start: 0.8236 (pttt) cc_final: 0.7449 (pttt) REVERT: A 401 GLN cc_start: 0.9000 (mp-120) cc_final: 0.8374 (mp10) REVERT: A 497 MET cc_start: 0.8998 (mtt) cc_final: 0.8781 (mtt) REVERT: A 722 ASP cc_start: 0.7132 (p0) cc_final: 0.6620 (p0) REVERT: A 724 TYR cc_start: 0.5852 (t80) cc_final: 0.5524 (t80) REVERT: A 728 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8505 (ttmm) REVERT: A 748 GLN cc_start: 0.8283 (mp-120) cc_final: 0.8059 (mm-40) REVERT: B 107 ILE cc_start: 0.8329 (mm) cc_final: 0.7642 (pt) REVERT: B 206 PHE cc_start: 0.6715 (p90) cc_final: 0.6031 (p90) REVERT: B 350 GLN cc_start: 0.8790 (mp10) cc_final: 0.8273 (mp10) REVERT: B 380 GLU cc_start: 0.8189 (pm20) cc_final: 0.7941 (pm20) REVERT: B 387 LEU cc_start: 0.9215 (pp) cc_final: 0.8612 (tp) REVERT: B 451 GLN cc_start: 0.7512 (pt0) cc_final: 0.6962 (pt0) REVERT: C 103 ASP cc_start: 0.8179 (t0) cc_final: 0.7967 (t70) REVERT: C 200 MET cc_start: 0.8765 (ttt) cc_final: 0.8117 (tmm) REVERT: C 219 ASP cc_start: 0.7257 (p0) cc_final: 0.6853 (p0) REVERT: C 273 MET cc_start: 0.5082 (ptt) cc_final: 0.4752 (ptm) REVERT: C 321 LEU cc_start: 0.8763 (pp) cc_final: 0.8280 (tp) REVERT: C 330 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.7853 (mp) REVERT: C 382 ASP cc_start: 0.8228 (p0) cc_final: 0.7916 (p0) REVERT: C 383 LYS cc_start: 0.8016 (ptpp) cc_final: 0.7574 (pttt) REVERT: C 435 TYR cc_start: 0.7842 (m-80) cc_final: 0.7504 (m-80) REVERT: C 722 ASP cc_start: 0.7083 (p0) cc_final: 0.6590 (p0) REVERT: C 724 TYR cc_start: 0.5872 (t80) cc_final: 0.5552 (t80) REVERT: C 728 LYS cc_start: 0.9085 (mtpt) cc_final: 0.8561 (ttmm) REVERT: C 748 GLN cc_start: 0.8308 (mp-120) cc_final: 0.7958 (mm-40) REVERT: D 100 TYR cc_start: 0.8728 (t80) cc_final: 0.8452 (t80) REVERT: D 107 ILE cc_start: 0.8420 (mm) cc_final: 0.7696 (pt) REVERT: D 166 GLU cc_start: 0.8530 (pm20) cc_final: 0.8303 (pm20) REVERT: D 206 PHE cc_start: 0.6328 (p90) cc_final: 0.5776 (p90) REVERT: D 221 GLU cc_start: 0.7740 (pp20) cc_final: 0.7331 (pp20) REVERT: D 340 PHE cc_start: 0.8569 (p90) cc_final: 0.8113 (p90) REVERT: D 350 GLN cc_start: 0.8706 (mp10) cc_final: 0.8231 (mp10) REVERT: D 387 LEU cc_start: 0.9184 (pp) cc_final: 0.8647 (tp) REVERT: D 451 GLN cc_start: 0.7439 (pt0) cc_final: 0.6952 (pt0) outliers start: 7 outliers final: 2 residues processed: 452 average time/residue: 0.3151 time to fit residues: 210.7847 Evaluate side-chains 292 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 288 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 222 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 70 optimal weight: 0.2980 chunk 164 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN D 418 ASN D 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17466 Z= 0.207 Angle : 0.741 9.435 23552 Z= 0.377 Chirality : 0.047 0.212 2704 Planarity : 0.005 0.074 3026 Dihedral : 6.607 32.188 2394 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.16), residues: 2242 helix: -2.36 (0.16), residues: 808 sheet: -2.04 (0.30), residues: 258 loop : -2.76 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 80 HIS 0.006 0.001 HIS D 465 PHE 0.022 0.002 PHE C 72 TYR 0.015 0.002 TYR C 239 ARG 0.007 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 406 time to evaluate : 1.942 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: A 41 ILE cc_start: 0.9231 (mm) cc_final: 0.8956 (mm) REVERT: A 128 GLU cc_start: 0.8432 (mp0) cc_final: 0.7652 (mp0) REVERT: A 273 MET cc_start: 0.4964 (ptt) cc_final: 0.4633 (ptm) REVERT: A 305 ILE cc_start: 0.9138 (mm) cc_final: 0.8505 (mm) REVERT: A 321 LEU cc_start: 0.8704 (pp) cc_final: 0.8305 (tp) REVERT: A 372 MET cc_start: 0.7995 (mmp) cc_final: 0.7687 (mmp) REVERT: A 401 GLN cc_start: 0.8574 (mp-120) cc_final: 0.8264 (mp10) REVERT: A 423 ASP cc_start: 0.7681 (t70) cc_final: 0.7392 (t0) REVERT: A 536 ILE cc_start: 0.8914 (tp) cc_final: 0.8640 (tp) REVERT: A 678 VAL cc_start: 0.8999 (t) cc_final: 0.8656 (p) REVERT: A 722 ASP cc_start: 0.7098 (p0) cc_final: 0.6470 (p0) REVERT: B 107 ILE cc_start: 0.8415 (mm) cc_final: 0.7712 (pt) REVERT: B 206 PHE cc_start: 0.6671 (p90) cc_final: 0.6007 (p90) REVERT: B 387 LEU cc_start: 0.9284 (pp) cc_final: 0.8646 (tp) REVERT: B 430 PHE cc_start: 0.7568 (t80) cc_final: 0.7298 (t80) REVERT: B 451 GLN cc_start: 0.7567 (pt0) cc_final: 0.7106 (pt0) REVERT: C 41 ILE cc_start: 0.9285 (mm) cc_final: 0.8984 (mm) REVERT: C 103 ASP cc_start: 0.8075 (t0) cc_final: 0.7874 (t70) REVERT: C 128 GLU cc_start: 0.8315 (mp0) cc_final: 0.7540 (mp0) REVERT: C 200 MET cc_start: 0.8779 (ttt) cc_final: 0.8178 (tmm) REVERT: C 273 MET cc_start: 0.5153 (ptt) cc_final: 0.4794 (ptm) REVERT: C 321 LEU cc_start: 0.8742 (pp) cc_final: 0.8259 (tp) REVERT: C 372 MET cc_start: 0.7952 (mmp) cc_final: 0.7671 (mmp) REVERT: C 401 GLN cc_start: 0.8640 (mp-120) cc_final: 0.8254 (mp10) REVERT: C 435 TYR cc_start: 0.8066 (m-80) cc_final: 0.6486 (m-80) REVERT: C 536 ILE cc_start: 0.8938 (tp) cc_final: 0.8666 (tp) REVERT: C 678 VAL cc_start: 0.8945 (t) cc_final: 0.8586 (p) REVERT: C 708 LEU cc_start: 0.8281 (tt) cc_final: 0.7886 (mt) REVERT: C 722 ASP cc_start: 0.7059 (p0) cc_final: 0.6523 (p0) REVERT: D 107 ILE cc_start: 0.8358 (mm) cc_final: 0.7732 (pt) REVERT: D 206 PHE cc_start: 0.6367 (p90) cc_final: 0.5796 (p90) REVERT: D 221 GLU cc_start: 0.7664 (pp20) cc_final: 0.7325 (pp20) REVERT: D 387 LEU cc_start: 0.9281 (pp) cc_final: 0.8653 (tp) REVERT: D 451 GLN cc_start: 0.7576 (pt0) cc_final: 0.7193 (pt0) outliers start: 2 outliers final: 0 residues processed: 408 average time/residue: 0.3004 time to fit residues: 183.0435 Evaluate side-chains 314 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 218 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 17466 Z= 0.480 Angle : 0.896 12.603 23552 Z= 0.462 Chirality : 0.052 0.205 2704 Planarity : 0.006 0.077 3026 Dihedral : 7.057 34.558 2394 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.45 % Favored : 85.46 % Rotamer: Outliers : 0.11 % Allowed : 7.52 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.17), residues: 2242 helix: -2.21 (0.16), residues: 848 sheet: -2.25 (0.29), residues: 272 loop : -2.69 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 80 HIS 0.010 0.002 HIS D 465 PHE 0.021 0.003 PHE B 430 TYR 0.031 0.003 TYR B 472 ARG 0.011 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 356 time to evaluate : 2.224 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: A 45 VAL cc_start: 0.6971 (p) cc_final: 0.6646 (m) REVERT: A 131 GLU cc_start: 0.7303 (pm20) cc_final: 0.6189 (tm-30) REVERT: A 198 LEU cc_start: 0.8478 (tp) cc_final: 0.8173 (tp) REVERT: A 273 MET cc_start: 0.5480 (ptt) cc_final: 0.5031 (ptm) REVERT: A 321 LEU cc_start: 0.8791 (pp) cc_final: 0.8231 (tp) REVERT: A 383 LYS cc_start: 0.8293 (pttm) cc_final: 0.7942 (pttt) REVERT: A 391 ASP cc_start: 0.8100 (t0) cc_final: 0.7784 (t0) REVERT: A 401 GLN cc_start: 0.8672 (mp-120) cc_final: 0.8203 (mp10) REVERT: A 507 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 536 ILE cc_start: 0.9213 (tp) cc_final: 0.8985 (tp) REVERT: A 687 MET cc_start: 0.7823 (ttt) cc_final: 0.7541 (ttm) REVERT: A 722 ASP cc_start: 0.7359 (p0) cc_final: 0.6764 (p0) REVERT: B 73 ASP cc_start: 0.7511 (t70) cc_final: 0.7220 (t0) REVERT: B 107 ILE cc_start: 0.8708 (mm) cc_final: 0.8020 (pt) REVERT: B 127 ASP cc_start: 0.8382 (m-30) cc_final: 0.8098 (m-30) REVERT: B 206 PHE cc_start: 0.6648 (p90) cc_final: 0.5916 (p90) REVERT: B 221 GLU cc_start: 0.7859 (pp20) cc_final: 0.7314 (pp20) REVERT: B 340 PHE cc_start: 0.8805 (p90) cc_final: 0.8170 (p90) REVERT: B 341 MET cc_start: 0.8291 (tpt) cc_final: 0.7998 (tpp) REVERT: B 387 LEU cc_start: 0.9417 (pp) cc_final: 0.8824 (tp) REVERT: C 128 GLU cc_start: 0.8639 (mp0) cc_final: 0.7714 (mp0) REVERT: C 200 MET cc_start: 0.8813 (ttt) cc_final: 0.8233 (tmm) REVERT: C 273 MET cc_start: 0.5166 (ptt) cc_final: 0.4802 (ptm) REVERT: C 391 ASP cc_start: 0.8262 (t0) cc_final: 0.7939 (t0) REVERT: C 497 MET cc_start: 0.9146 (mtt) cc_final: 0.8577 (mtp) REVERT: C 507 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8023 (tm-30) REVERT: C 536 ILE cc_start: 0.9228 (tp) cc_final: 0.8986 (tp) REVERT: C 722 ASP cc_start: 0.7283 (p0) cc_final: 0.6682 (p0) REVERT: D 73 ASP cc_start: 0.7381 (t70) cc_final: 0.7090 (t0) REVERT: D 107 ILE cc_start: 0.8627 (mm) cc_final: 0.7954 (pt) REVERT: D 127 ASP cc_start: 0.8423 (m-30) cc_final: 0.8078 (m-30) REVERT: D 179 MET cc_start: 0.7995 (mmt) cc_final: 0.7631 (mtt) REVERT: D 206 PHE cc_start: 0.6535 (p90) cc_final: 0.5956 (p90) REVERT: D 221 GLU cc_start: 0.7799 (pp20) cc_final: 0.7279 (pp20) REVERT: D 341 MET cc_start: 0.8369 (tpt) cc_final: 0.8165 (tpp) REVERT: D 387 LEU cc_start: 0.9417 (pp) cc_final: 0.8814 (tp) outliers start: 2 outliers final: 1 residues processed: 358 average time/residue: 0.2930 time to fit residues: 159.8662 Evaluate side-chains 277 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17466 Z= 0.231 Angle : 0.748 9.934 23552 Z= 0.378 Chirality : 0.048 0.191 2704 Planarity : 0.005 0.067 3026 Dihedral : 6.476 31.489 2394 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.17), residues: 2242 helix: -1.89 (0.17), residues: 822 sheet: -2.15 (0.30), residues: 262 loop : -2.53 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.004 0.001 HIS B 465 PHE 0.030 0.002 PHE D 417 TYR 0.016 0.002 TYR B 331 ARG 0.005 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9258 (mm) cc_final: 0.8962 (mm) REVERT: A 128 GLU cc_start: 0.8395 (mp0) cc_final: 0.7723 (mp0) REVERT: A 200 MET cc_start: 0.8938 (ttt) cc_final: 0.8126 (tmm) REVERT: A 321 LEU cc_start: 0.8800 (pp) cc_final: 0.8356 (tp) REVERT: A 391 ASP cc_start: 0.7912 (t0) cc_final: 0.7638 (t0) REVERT: A 435 TYR cc_start: 0.7335 (m-80) cc_final: 0.7020 (m-80) REVERT: A 536 ILE cc_start: 0.9093 (tp) cc_final: 0.8855 (tp) REVERT: A 678 VAL cc_start: 0.9049 (t) cc_final: 0.8712 (p) REVERT: A 722 ASP cc_start: 0.7034 (p0) cc_final: 0.6438 (p0) REVERT: A 731 ASP cc_start: 0.8307 (m-30) cc_final: 0.8090 (m-30) REVERT: B 73 ASP cc_start: 0.7443 (t70) cc_final: 0.7131 (t0) REVERT: B 107 ILE cc_start: 0.8570 (mm) cc_final: 0.7867 (pt) REVERT: B 206 PHE cc_start: 0.6598 (p90) cc_final: 0.5878 (p90) REVERT: B 350 GLN cc_start: 0.8884 (mp10) cc_final: 0.8298 (mp10) REVERT: B 352 LEU cc_start: 0.8933 (mp) cc_final: 0.8713 (mp) REVERT: B 387 LEU cc_start: 0.9327 (pp) cc_final: 0.8664 (tp) REVERT: B 463 GLN cc_start: 0.8945 (mp10) cc_final: 0.8639 (mp10) REVERT: C 41 ILE cc_start: 0.9256 (mm) cc_final: 0.8943 (mm) REVERT: C 128 GLU cc_start: 0.8362 (mp0) cc_final: 0.7664 (mp0) REVERT: C 200 MET cc_start: 0.8707 (ttt) cc_final: 0.8170 (tmm) REVERT: C 273 MET cc_start: 0.5010 (ptt) cc_final: 0.4627 (ptm) REVERT: C 305 ILE cc_start: 0.9194 (mm) cc_final: 0.8617 (mm) REVERT: C 309 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8181 (ptpt) REVERT: C 497 MET cc_start: 0.9054 (mtt) cc_final: 0.8652 (mtp) REVERT: C 536 ILE cc_start: 0.9059 (tp) cc_final: 0.8828 (tp) REVERT: C 722 ASP cc_start: 0.7069 (p0) cc_final: 0.6473 (p0) REVERT: D 73 ASP cc_start: 0.7322 (t70) cc_final: 0.7025 (t0) REVERT: D 107 ILE cc_start: 0.8374 (mm) cc_final: 0.7540 (pt) REVERT: D 179 MET cc_start: 0.8124 (mmt) cc_final: 0.7758 (mtt) REVERT: D 206 PHE cc_start: 0.6503 (p90) cc_final: 0.5918 (p90) REVERT: D 281 ILE cc_start: 0.8857 (mt) cc_final: 0.8651 (mt) REVERT: D 387 LEU cc_start: 0.9401 (pp) cc_final: 0.8690 (tp) REVERT: D 418 ASN cc_start: 0.7282 (t0) cc_final: 0.6909 (t0) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2934 time to fit residues: 176.2109 Evaluate side-chains 283 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 181 optimal weight: 0.0470 chunk 101 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN C 401 GLN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 443 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17466 Z= 0.241 Angle : 0.746 9.929 23552 Z= 0.375 Chirality : 0.048 0.210 2704 Planarity : 0.005 0.065 3026 Dihedral : 6.295 31.387 2394 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.17), residues: 2242 helix: -1.66 (0.18), residues: 814 sheet: -2.01 (0.31), residues: 262 loop : -2.38 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 420 HIS 0.009 0.001 HIS C 69 PHE 0.014 0.002 PHE D 125 TYR 0.022 0.002 TYR C 283 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9255 (mm) cc_final: 0.8978 (mm) REVERT: A 200 MET cc_start: 0.8926 (ttt) cc_final: 0.8229 (tmm) REVERT: A 273 MET cc_start: 0.4450 (ptt) cc_final: 0.4179 (ptm) REVERT: A 321 LEU cc_start: 0.8804 (pp) cc_final: 0.8350 (tp) REVERT: A 372 MET cc_start: 0.7977 (mmp) cc_final: 0.7582 (mmp) REVERT: A 391 ASP cc_start: 0.7915 (t0) cc_final: 0.7609 (t0) REVERT: A 423 ASP cc_start: 0.7624 (t70) cc_final: 0.7074 (t0) REVERT: A 507 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 536 ILE cc_start: 0.9073 (tp) cc_final: 0.8865 (tp) REVERT: A 678 VAL cc_start: 0.8994 (t) cc_final: 0.8672 (p) REVERT: A 722 ASP cc_start: 0.7093 (p0) cc_final: 0.6518 (p0) REVERT: A 731 ASP cc_start: 0.8288 (m-30) cc_final: 0.8057 (m-30) REVERT: B 73 ASP cc_start: 0.7396 (t70) cc_final: 0.7101 (t0) REVERT: B 107 ILE cc_start: 0.8506 (mm) cc_final: 0.7785 (pt) REVERT: B 143 GLN cc_start: 0.9276 (tp40) cc_final: 0.9066 (tp40) REVERT: B 179 MET cc_start: 0.7964 (mmt) cc_final: 0.7663 (mtt) REVERT: B 206 PHE cc_start: 0.6621 (p90) cc_final: 0.6034 (p90) REVERT: B 340 PHE cc_start: 0.8812 (p90) cc_final: 0.8074 (p90) REVERT: B 387 LEU cc_start: 0.9326 (pp) cc_final: 0.8740 (tp) REVERT: B 430 PHE cc_start: 0.7926 (t80) cc_final: 0.7698 (t80) REVERT: C 41 ILE cc_start: 0.9246 (mm) cc_final: 0.8946 (mm) REVERT: C 200 MET cc_start: 0.8792 (ttt) cc_final: 0.8291 (tmm) REVERT: C 273 MET cc_start: 0.5003 (ptt) cc_final: 0.4631 (ptm) REVERT: C 305 ILE cc_start: 0.9237 (mm) cc_final: 0.8662 (mm) REVERT: C 309 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8158 (ptpt) REVERT: C 372 MET cc_start: 0.7929 (mmp) cc_final: 0.7552 (mmp) REVERT: C 497 MET cc_start: 0.9078 (mtt) cc_final: 0.8635 (mtp) REVERT: C 536 ILE cc_start: 0.9098 (tp) cc_final: 0.8858 (tp) REVERT: C 722 ASP cc_start: 0.7023 (p0) cc_final: 0.6412 (p0) REVERT: C 731 ASP cc_start: 0.8456 (m-30) cc_final: 0.8238 (m-30) REVERT: D 73 ASP cc_start: 0.7338 (t70) cc_final: 0.6993 (t0) REVERT: D 206 PHE cc_start: 0.6503 (p90) cc_final: 0.5932 (p90) REVERT: D 281 ILE cc_start: 0.8877 (mt) cc_final: 0.8640 (mt) REVERT: D 387 LEU cc_start: 0.9396 (pp) cc_final: 0.8750 (tp) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.2812 time to fit residues: 157.8446 Evaluate side-chains 278 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 159 optimal weight: 0.4980 chunk 123 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 463 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17466 Z= 0.249 Angle : 0.758 10.373 23552 Z= 0.380 Chirality : 0.048 0.196 2704 Planarity : 0.005 0.063 3026 Dihedral : 6.184 30.773 2394 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.17), residues: 2242 helix: -1.65 (0.17), residues: 828 sheet: -1.91 (0.32), residues: 262 loop : -2.36 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 397 HIS 0.003 0.001 HIS C 69 PHE 0.017 0.002 PHE C 72 TYR 0.018 0.002 TYR A 239 ARG 0.011 0.001 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9250 (mm) cc_final: 0.8896 (mm) REVERT: A 42 ASN cc_start: 0.8350 (p0) cc_final: 0.8067 (p0) REVERT: A 200 MET cc_start: 0.8912 (ttt) cc_final: 0.8155 (tmm) REVERT: A 201 MET cc_start: 0.8931 (pmm) cc_final: 0.8727 (pmm) REVERT: A 273 MET cc_start: 0.4471 (ptt) cc_final: 0.4204 (ptm) REVERT: A 321 LEU cc_start: 0.8796 (pp) cc_final: 0.8338 (tp) REVERT: A 372 MET cc_start: 0.7925 (mmp) cc_final: 0.7532 (mmp) REVERT: A 391 ASP cc_start: 0.7884 (t0) cc_final: 0.7582 (t0) REVERT: A 401 GLN cc_start: 0.8685 (mp10) cc_final: 0.8398 (mp10) REVERT: A 497 MET cc_start: 0.9008 (mtt) cc_final: 0.8562 (mtp) REVERT: A 507 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 536 ILE cc_start: 0.9111 (tp) cc_final: 0.8857 (tp) REVERT: A 722 ASP cc_start: 0.7070 (p0) cc_final: 0.6484 (p0) REVERT: A 731 ASP cc_start: 0.8212 (m-30) cc_final: 0.7975 (m-30) REVERT: B 73 ASP cc_start: 0.7447 (t70) cc_final: 0.7182 (t0) REVERT: B 206 PHE cc_start: 0.6111 (p90) cc_final: 0.5696 (p90) REVERT: B 387 LEU cc_start: 0.9329 (pp) cc_final: 0.8719 (tp) REVERT: B 451 GLN cc_start: 0.7500 (pt0) cc_final: 0.7294 (pt0) REVERT: C 41 ILE cc_start: 0.9234 (mm) cc_final: 0.8929 (mm) REVERT: C 200 MET cc_start: 0.8763 (ttt) cc_final: 0.8259 (tmm) REVERT: C 273 MET cc_start: 0.5015 (ptt) cc_final: 0.4632 (ptm) REVERT: C 305 ILE cc_start: 0.9235 (mm) cc_final: 0.8646 (mm) REVERT: C 309 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8164 (ptpt) REVERT: C 372 MET cc_start: 0.7898 (mmp) cc_final: 0.7572 (mmp) REVERT: C 497 MET cc_start: 0.9061 (mtt) cc_final: 0.8630 (mtp) REVERT: C 507 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7790 (tm-30) REVERT: C 536 ILE cc_start: 0.9094 (tp) cc_final: 0.8865 (tp) REVERT: C 555 MET cc_start: 0.8453 (tpt) cc_final: 0.8027 (mmm) REVERT: C 722 ASP cc_start: 0.6975 (p0) cc_final: 0.6422 (p0) REVERT: C 731 ASP cc_start: 0.8402 (m-30) cc_final: 0.8176 (m-30) REVERT: D 73 ASP cc_start: 0.7388 (t70) cc_final: 0.7093 (t0) REVERT: D 179 MET cc_start: 0.8242 (mtt) cc_final: 0.7667 (mtt) REVERT: D 206 PHE cc_start: 0.6569 (p90) cc_final: 0.5921 (p90) REVERT: D 281 ILE cc_start: 0.8867 (mt) cc_final: 0.8639 (mt) REVERT: D 387 LEU cc_start: 0.9418 (pp) cc_final: 0.8756 (tp) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2709 time to fit residues: 156.2352 Evaluate side-chains 276 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 138 optimal weight: 0.0270 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN B 379 HIS B 443 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 HIS D 389 ASN D 443 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17466 Z= 0.195 Angle : 0.762 11.160 23552 Z= 0.378 Chirality : 0.048 0.183 2704 Planarity : 0.005 0.063 3026 Dihedral : 5.953 29.521 2394 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.17), residues: 2242 helix: -1.51 (0.18), residues: 820 sheet: -1.70 (0.33), residues: 234 loop : -2.27 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 397 HIS 0.011 0.001 HIS A 69 PHE 0.032 0.002 PHE D 64 TYR 0.023 0.002 TYR C 283 ARG 0.007 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9188 (mm) cc_final: 0.8848 (mm) REVERT: A 42 ASN cc_start: 0.8362 (p0) cc_final: 0.8026 (p0) REVERT: A 200 MET cc_start: 0.8809 (ttt) cc_final: 0.8131 (tmm) REVERT: A 273 MET cc_start: 0.4767 (ptt) cc_final: 0.4316 (ptm) REVERT: A 321 LEU cc_start: 0.8773 (pp) cc_final: 0.8334 (tp) REVERT: A 372 MET cc_start: 0.7872 (mmp) cc_final: 0.7586 (mmp) REVERT: A 423 ASP cc_start: 0.7592 (t70) cc_final: 0.7143 (t70) REVERT: A 551 LEU cc_start: 0.9039 (tp) cc_final: 0.8835 (tp) REVERT: A 554 MET cc_start: 0.8288 (tmm) cc_final: 0.8022 (tmm) REVERT: A 555 MET cc_start: 0.8299 (tpt) cc_final: 0.7891 (mmm) REVERT: A 701 ASP cc_start: 0.8480 (p0) cc_final: 0.8175 (t0) REVERT: A 722 ASP cc_start: 0.6938 (p0) cc_final: 0.6384 (p0) REVERT: B 100 TYR cc_start: 0.8748 (t80) cc_final: 0.8410 (t80) REVERT: B 118 GLU cc_start: 0.7628 (pp20) cc_final: 0.7334 (pp20) REVERT: B 179 MET cc_start: 0.7824 (mmt) cc_final: 0.7524 (mmt) REVERT: B 206 PHE cc_start: 0.6232 (p90) cc_final: 0.5781 (p90) REVERT: B 387 LEU cc_start: 0.9322 (pp) cc_final: 0.8666 (tp) REVERT: B 430 PHE cc_start: 0.7549 (t80) cc_final: 0.7020 (t80) REVERT: C 41 ILE cc_start: 0.9185 (mm) cc_final: 0.8892 (mm) REVERT: C 200 MET cc_start: 0.8676 (ttt) cc_final: 0.8059 (tmm) REVERT: C 201 MET cc_start: 0.8893 (pmm) cc_final: 0.8602 (pmm) REVERT: C 273 MET cc_start: 0.4885 (ptt) cc_final: 0.4532 (ptm) REVERT: C 305 ILE cc_start: 0.9196 (mm) cc_final: 0.8620 (mm) REVERT: C 372 MET cc_start: 0.7827 (mmp) cc_final: 0.7541 (mmp) REVERT: C 497 MET cc_start: 0.9002 (mtt) cc_final: 0.8527 (mtp) REVERT: C 555 MET cc_start: 0.8331 (tpt) cc_final: 0.8032 (mmm) REVERT: C 701 ASP cc_start: 0.8430 (p0) cc_final: 0.8071 (t0) REVERT: C 722 ASP cc_start: 0.6849 (p0) cc_final: 0.6298 (p0) REVERT: D 73 ASP cc_start: 0.7287 (t70) cc_final: 0.6954 (t0) REVERT: D 179 MET cc_start: 0.8206 (mtt) cc_final: 0.7577 (mtt) REVERT: D 206 PHE cc_start: 0.6555 (p90) cc_final: 0.5878 (p90) REVERT: D 216 GLU cc_start: 0.7784 (mp0) cc_final: 0.7460 (mt-10) REVERT: D 221 GLU cc_start: 0.7633 (pp20) cc_final: 0.7312 (pp20) REVERT: D 387 LEU cc_start: 0.9357 (pp) cc_final: 0.8765 (tp) REVERT: D 451 GLN cc_start: 0.7632 (pt0) cc_final: 0.7391 (pt0) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.2760 time to fit residues: 169.3348 Evaluate side-chains 291 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.0980 chunk 190 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 HIS ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17466 Z= 0.225 Angle : 0.764 11.200 23552 Z= 0.381 Chirality : 0.048 0.173 2704 Planarity : 0.005 0.061 3026 Dihedral : 5.931 29.261 2394 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.66 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.17), residues: 2242 helix: -1.48 (0.18), residues: 824 sheet: -1.53 (0.33), residues: 246 loop : -2.17 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 420 HIS 0.004 0.001 HIS C 69 PHE 0.035 0.002 PHE B 64 TYR 0.018 0.002 TYR C 283 ARG 0.007 0.001 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9178 (mm) cc_final: 0.8900 (mm) REVERT: A 200 MET cc_start: 0.8750 (ttt) cc_final: 0.8088 (tmm) REVERT: A 201 MET cc_start: 0.8837 (pmm) cc_final: 0.8627 (pmm) REVERT: A 273 MET cc_start: 0.4752 (ptt) cc_final: 0.4381 (ptm) REVERT: A 321 LEU cc_start: 0.8740 (pp) cc_final: 0.8296 (tp) REVERT: A 372 MET cc_start: 0.7889 (mmp) cc_final: 0.7604 (mmp) REVERT: A 536 ILE cc_start: 0.9160 (tp) cc_final: 0.8910 (tp) REVERT: A 554 MET cc_start: 0.8323 (tmm) cc_final: 0.8019 (tmm) REVERT: A 555 MET cc_start: 0.8342 (tpt) cc_final: 0.7974 (mmm) REVERT: A 722 ASP cc_start: 0.7004 (p0) cc_final: 0.6432 (p0) REVERT: B 73 ASP cc_start: 0.7363 (t70) cc_final: 0.7137 (t0) REVERT: B 118 GLU cc_start: 0.7660 (pp20) cc_final: 0.7301 (pp20) REVERT: B 179 MET cc_start: 0.7864 (mmt) cc_final: 0.7553 (mmt) REVERT: B 206 PHE cc_start: 0.6263 (p90) cc_final: 0.5792 (p90) REVERT: B 223 MET cc_start: 0.7125 (tpt) cc_final: 0.6878 (tpt) REVERT: B 288 GLN cc_start: 0.8391 (mm110) cc_final: 0.8143 (pt0) REVERT: B 387 LEU cc_start: 0.9326 (pp) cc_final: 0.8680 (tp) REVERT: C 41 ILE cc_start: 0.9183 (mm) cc_final: 0.8890 (mm) REVERT: C 200 MET cc_start: 0.8652 (ttt) cc_final: 0.8011 (tmm) REVERT: C 273 MET cc_start: 0.4897 (ptt) cc_final: 0.4538 (ptm) REVERT: C 372 MET cc_start: 0.7870 (mmp) cc_final: 0.7569 (mmp) REVERT: C 497 MET cc_start: 0.9013 (mtt) cc_final: 0.8532 (mtp) REVERT: C 536 ILE cc_start: 0.9145 (tp) cc_final: 0.8874 (tp) REVERT: C 701 ASP cc_start: 0.8356 (p0) cc_final: 0.8146 (t0) REVERT: C 722 ASP cc_start: 0.6841 (p0) cc_final: 0.6228 (p0) REVERT: D 73 ASP cc_start: 0.7323 (t70) cc_final: 0.7075 (t0) REVERT: D 179 MET cc_start: 0.8170 (mtt) cc_final: 0.7554 (mtt) REVERT: D 206 PHE cc_start: 0.6533 (p90) cc_final: 0.5848 (p90) REVERT: D 288 GLN cc_start: 0.8416 (mm110) cc_final: 0.8118 (pt0) REVERT: D 341 MET cc_start: 0.8654 (tpp) cc_final: 0.8424 (tpp) REVERT: D 387 LEU cc_start: 0.9392 (pp) cc_final: 0.8813 (tp) REVERT: D 389 ASN cc_start: 0.9177 (m-40) cc_final: 0.8888 (m-40) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2799 time to fit residues: 159.5539 Evaluate side-chains 287 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 225 optimal weight: 0.0050 chunk 207 optimal weight: 10.0000 chunk 179 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17466 Z= 0.194 Angle : 0.776 11.695 23552 Z= 0.383 Chirality : 0.047 0.169 2704 Planarity : 0.005 0.062 3026 Dihedral : 5.688 27.238 2394 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.17), residues: 2242 helix: -1.36 (0.18), residues: 814 sheet: -1.48 (0.33), residues: 234 loop : -2.13 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 420 HIS 0.012 0.001 HIS A 69 PHE 0.025 0.002 PHE A 681 TYR 0.017 0.001 TYR C 283 ARG 0.009 0.000 ARG D 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9108 (mm) cc_final: 0.8842 (mm) REVERT: A 130 LEU cc_start: 0.8427 (pt) cc_final: 0.8130 (pp) REVERT: A 200 MET cc_start: 0.8785 (ttt) cc_final: 0.8371 (tmm) REVERT: A 273 MET cc_start: 0.4699 (ptt) cc_final: 0.4297 (ptm) REVERT: A 321 LEU cc_start: 0.8700 (pp) cc_final: 0.8304 (tp) REVERT: A 340 MET cc_start: 0.6669 (mmp) cc_final: 0.5826 (tpt) REVERT: A 372 MET cc_start: 0.7755 (mmp) cc_final: 0.7521 (mmp) REVERT: A 507 GLN cc_start: 0.7481 (pp30) cc_final: 0.6513 (pp30) REVERT: A 536 ILE cc_start: 0.9125 (tp) cc_final: 0.8875 (tp) REVERT: A 722 ASP cc_start: 0.6860 (p0) cc_final: 0.6413 (p0) REVERT: B 73 ASP cc_start: 0.7160 (t70) cc_final: 0.6954 (t0) REVERT: B 100 TYR cc_start: 0.8782 (t80) cc_final: 0.8393 (t80) REVERT: B 179 MET cc_start: 0.7895 (mmt) cc_final: 0.7599 (mmt) REVERT: B 206 PHE cc_start: 0.6258 (p90) cc_final: 0.5799 (p90) REVERT: B 216 GLU cc_start: 0.7746 (mp0) cc_final: 0.7501 (mt-10) REVERT: B 288 GLN cc_start: 0.8420 (mm110) cc_final: 0.8147 (pt0) REVERT: B 387 LEU cc_start: 0.9279 (pp) cc_final: 0.8579 (tp) REVERT: B 451 GLN cc_start: 0.7464 (pt0) cc_final: 0.7245 (pt0) REVERT: C 41 ILE cc_start: 0.9128 (mm) cc_final: 0.8747 (mm) REVERT: C 130 LEU cc_start: 0.8421 (pt) cc_final: 0.8172 (pp) REVERT: C 200 MET cc_start: 0.8610 (ttt) cc_final: 0.8042 (tmm) REVERT: C 273 MET cc_start: 0.5188 (ptt) cc_final: 0.4785 (ptm) REVERT: C 321 LEU cc_start: 0.8698 (pp) cc_final: 0.8281 (tp) REVERT: C 340 MET cc_start: 0.6533 (mmp) cc_final: 0.5787 (tpt) REVERT: C 372 MET cc_start: 0.7730 (mmp) cc_final: 0.7461 (mmp) REVERT: C 427 SER cc_start: 0.8552 (m) cc_final: 0.8271 (p) REVERT: C 507 GLN cc_start: 0.7879 (pp30) cc_final: 0.7604 (pp30) REVERT: C 536 ILE cc_start: 0.9095 (tp) cc_final: 0.8876 (tp) REVERT: C 722 ASP cc_start: 0.6849 (p0) cc_final: 0.6201 (p0) REVERT: D 100 TYR cc_start: 0.8748 (t80) cc_final: 0.8390 (t80) REVERT: D 179 MET cc_start: 0.8119 (mtt) cc_final: 0.7484 (mtt) REVERT: D 206 PHE cc_start: 0.6492 (p90) cc_final: 0.5878 (p90) REVERT: D 216 GLU cc_start: 0.8360 (mp0) cc_final: 0.7865 (mp0) REVERT: D 223 MET cc_start: 0.7174 (tpt) cc_final: 0.6970 (tpt) REVERT: D 263 ASP cc_start: 0.7151 (p0) cc_final: 0.6535 (p0) REVERT: D 288 GLN cc_start: 0.8366 (mm110) cc_final: 0.8080 (pt0) REVERT: D 356 THR cc_start: 0.8439 (p) cc_final: 0.7906 (p) REVERT: D 387 LEU cc_start: 0.9355 (pp) cc_final: 0.8795 (tp) REVERT: D 389 ASN cc_start: 0.9070 (m-40) cc_final: 0.8768 (m-40) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2697 time to fit residues: 169.7973 Evaluate side-chains 295 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN C 42 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 HIS ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108479 restraints weight = 35433.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108518 restraints weight = 26365.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109746 restraints weight = 21085.585| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17466 Z= 0.225 Angle : 0.776 11.378 23552 Z= 0.386 Chirality : 0.048 0.172 2704 Planarity : 0.005 0.071 3026 Dihedral : 5.682 26.964 2394 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.35 % Favored : 89.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.17), residues: 2242 helix: -1.27 (0.18), residues: 818 sheet: -1.47 (0.33), residues: 232 loop : -2.08 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 420 HIS 0.004 0.001 HIS B 379 PHE 0.021 0.002 PHE A 681 TYR 0.021 0.002 TYR C 283 ARG 0.007 0.000 ARG A 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3832.36 seconds wall clock time: 71 minutes 8.10 seconds (4268.10 seconds total)