Starting phenix.real_space_refine on Sun Mar 17 09:14:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvc_30216/03_2024/7bvc_30216_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 7 5.49 5 S 60 5.16 5 C 11110 2.51 5 N 2914 2.21 5 O 3113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ARG 886": "NH1" <-> "NH2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A ARG 1033": "NH1" <-> "NH2" Residue "A GLU 1044": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B GLU 679": "OE1" <-> "OE2" Residue "B ARG 681": "NH1" <-> "NH2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B ARG 777": "NH1" <-> "NH2" Residue "B ARG 784": "NH1" <-> "NH2" Residue "B ARG 849": "NH1" <-> "NH2" Residue "B ARG 854": "NH1" <-> "NH2" Residue "B GLU 871": "OE1" <-> "OE2" Residue "B ASP 926": "OD1" <-> "OD2" Residue "B ARG 931": "NH1" <-> "NH2" Residue "B ARG 951": "NH1" <-> "NH2" Residue "B GLU 954": "OE1" <-> "OE2" Residue "B ARG 997": "NH1" <-> "NH2" Residue "B ASP 1052": "OD1" <-> "OD2" Residue "B ARG 1079": "NH1" <-> "NH2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P ASP 38": "OD1" <-> "OD2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17206 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8147 Classifications: {'peptide': 1078} Link IDs: {'PCIS': 2, 'PTRANS': 77, 'TRANS': 998} Chain: "B" Number of atoms: 8105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8105 Classifications: {'peptide': 1063} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 985} Chain: "P" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 673 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {' CA': 1, 'CDL': 1, 'F8L': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'F8L:plan-2': 1, 'F8L:plan-1': 1, 'F8L:plan-10': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {' CA': 1, '95E': 1, 'CDL': 1, 'PNS': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 9.35, per 1000 atoms: 0.54 Number of scatterers: 17206 At special positions: 0 Unit cell: (123.82, 134.48, 123.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 60 16.00 P 7 15.00 O 3113 8.00 N 2914 7.00 C 11110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 145 " distance=2.78 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: 6.29 Conformation dependent library (CDL) restraints added in 3.4 seconds 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4060 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 15 sheets defined 35.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 6 through 14 removed outlier: 3.817A pdb=" N LEU A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 196 through 221 removed outlier: 3.547A pdb=" N LEU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.735A pdb=" N THR A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 4.543A pdb=" N GLY A 263 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR A 264 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 265 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 266 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 271 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.736A pdb=" N VAL A 298 " --> pdb=" O TRP A 294 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 312 No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 332 through 335 No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 345 through 357 Processing helix chain 'A' and resid 366 through 385 removed outlier: 4.164A pdb=" N ALA A 371 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET A 379 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 404 removed outlier: 3.716A pdb=" N ILE A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 3.684A pdb=" N LEU A 411 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 412 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 413 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 4.233A pdb=" N VAL A 419 " --> pdb=" O PRO A 416 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 421 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG A 422 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 429 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 457 Proline residue: A 443 - end of helix removed outlier: 3.740A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 484 through 490 Processing helix chain 'A' and resid 502 through 522 removed outlier: 3.502A pdb=" N LEU A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 549 removed outlier: 3.645A pdb=" N TRP A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 580 removed outlier: 3.806A pdb=" N ALA A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 563 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY A 564 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 566 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 567 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY A 571 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 577 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 579 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 604 removed outlier: 3.773A pdb=" N ALA A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 652 removed outlier: 3.832A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 652 " --> pdb=" O TRP A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 695 removed outlier: 4.258A pdb=" N MET A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 953 through 956 No H-bonds generated for 'chain 'A' and resid 953 through 956' Processing helix chain 'A' and resid 997 through 1007 removed outlier: 3.519A pdb=" N VAL A1002 " --> pdb=" O LYS A 998 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASN A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 removed outlier: 3.739A pdb=" N TRP B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 39 No H-bonds generated for 'chain 'B' and resid 36 through 39' Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 231 through 247 removed outlier: 4.152A pdb=" N LEU B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASP B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.613A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 320 through 328 removed outlier: 3.598A pdb=" N LEU B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 391 through 411 Processing helix chain 'B' and resid 415 through 428 removed outlier: 3.871A pdb=" N ILE B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.875A pdb=" N LEU B 435 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 436 " --> pdb=" O THR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 446 through 455 removed outlier: 3.696A pdb=" N ILE B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 485 through 498 Processing helix chain 'B' and resid 504 through 512 removed outlier: 5.093A pdb=" N ASN B 508 " --> pdb=" O TRP B 505 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 509 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 545 removed outlier: 4.201A pdb=" N THR B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Proline residue: B 538 - end of helix removed outlier: 3.696A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 570 removed outlier: 3.591A pdb=" N LEU B 560 " --> pdb=" O PRO B 556 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 599 removed outlier: 3.957A pdb=" N LEU B 584 " --> pdb=" O HIS B 581 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 585 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA B 587 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY B 589 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B 593 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 594 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 597 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 625 Processing helix chain 'B' and resid 654 through 675 Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 690 through 712 removed outlier: 3.809A pdb=" N MET B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 710 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 728 removed outlier: 4.492A pdb=" N PHE B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 728 " --> pdb=" O ILE B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 735 No H-bonds generated for 'chain 'B' and resid 733 through 735' Processing helix chain 'B' and resid 794 through 796 No H-bonds generated for 'chain 'B' and resid 794 through 796' Processing helix chain 'B' and resid 851 through 854 No H-bonds generated for 'chain 'B' and resid 851 through 854' Processing helix chain 'B' and resid 958 through 961 No H-bonds generated for 'chain 'B' and resid 958 through 961' Processing helix chain 'B' and resid 1002 through 1007 removed outlier: 3.979A pdb=" N GLN B1007 " --> pdb=" O TYR B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1017 No H-bonds generated for 'chain 'B' and resid 1015 through 1017' Processing helix chain 'B' and resid 1024 through 1027 No H-bonds generated for 'chain 'B' and resid 1024 through 1027' Processing helix chain 'P' and resid 5 through 19 removed outlier: 3.566A pdb=" N ALA P 10 " --> pdb=" O GLU P 6 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU P 14 " --> pdb=" O ALA P 10 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE P 15 " --> pdb=" O GLY P 11 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 52 removed outlier: 4.012A pdb=" N GLU P 46 " --> pdb=" O LEU P 42 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 83 Processing sheet with id= A, first strand: chain 'A' and resid 33 through 35 Processing sheet with id= B, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.878A pdb=" N ALA A 64 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 724 through 727 Processing sheet with id= D, first strand: chain 'A' and resid 825 through 827 removed outlier: 3.702A pdb=" N MET A 826 " --> pdb=" O PHE A 942 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 855 through 857 Processing sheet with id= F, first strand: chain 'A' and resid 926 through 929 removed outlier: 3.619A pdb=" N VAL A 928 " --> pdb=" O LYS A 879 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 963 through 965 removed outlier: 6.699A pdb=" N TYR A 991 " --> pdb=" O LEU A 964 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1023 through 1025 Processing sheet with id= I, first strand: chain 'B' and resid 216 through 218 removed outlier: 3.870A pdb=" N GLY B1065 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 205 through 207 removed outlier: 4.764A pdb=" N ALA B 81 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 123 through 127 removed outlier: 4.252A pdb=" N PHE B 99 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 118 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU B 97 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 737 through 739 Processing sheet with id= M, first strand: chain 'B' and resid 837 through 840 Processing sheet with id= N, first strand: chain 'B' and resid 860 through 864 Processing sheet with id= O, first strand: chain 'B' and resid 968 through 970 removed outlier: 6.542A pdb=" N PHE B 996 " --> pdb=" O LEU B 969 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1227 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: 5.20 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2745 1.26 - 1.40: 4172 1.40 - 1.54: 10174 1.54 - 1.68: 440 1.68 - 1.82: 102 Bond restraints: 17633 Sorted by residual: bond pdb=" C61 F8L A1102 " pdb=" O56 F8L A1102 " ideal model delta sigma weight residual 1.272 1.531 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" OA3 CDL B1204 " pdb=" PA1 CDL B1204 " ideal model delta sigma weight residual 1.529 1.416 0.113 1.00e-02 1.00e+04 1.27e+02 bond pdb=" CA7 CDL B1204 " pdb=" OA8 CDL B1204 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C59 F8L A1102 " pdb=" C61 F8L A1102 " ideal model delta sigma weight residual 1.568 1.366 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OB3 CDL B1204 " pdb=" PB2 CDL B1204 " ideal model delta sigma weight residual 1.529 1.430 0.099 1.00e-02 1.00e+04 9.71e+01 ... (remaining 17628 not shown) Histogram of bond angle deviations from ideal: 90.61 - 99.32: 5 99.32 - 108.04: 1082 108.04 - 116.76: 11232 116.76 - 125.47: 11368 125.47 - 134.19: 420 Bond angle restraints: 24107 Sorted by residual: angle pdb=" C46 F8L A1102 " pdb=" C47 F8L A1102 " pdb=" C48 F8L A1102 " ideal model delta sigma weight residual 74.51 120.00 -45.49 3.00e+00 1.11e-01 2.30e+02 angle pdb=" C26 F8L A1102 " pdb=" C27 F8L A1102 " pdb=" C28 F8L A1102 " ideal model delta sigma weight residual 74.52 119.88 -45.36 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C31 F8L A1102 " pdb=" C32 F8L A1102 " pdb=" C33 F8L A1102 " ideal model delta sigma weight residual 74.51 119.61 -45.10 3.00e+00 1.11e-01 2.26e+02 angle pdb=" C21 F8L A1102 " pdb=" C22 F8L A1102 " pdb=" C23 F8L A1102 " ideal model delta sigma weight residual 74.51 119.55 -45.04 3.00e+00 1.11e-01 2.25e+02 angle pdb=" C36 F8L A1102 " pdb=" C37 F8L A1102 " pdb=" C38 F8L A1102 " ideal model delta sigma weight residual 74.50 119.52 -45.02 3.00e+00 1.11e-01 2.25e+02 ... (remaining 24102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.77: 10101 30.77 - 61.54: 317 61.54 - 92.32: 19 92.32 - 123.09: 2 123.09 - 153.86: 1 Dihedral angle restraints: 10440 sinusoidal: 4091 harmonic: 6349 Sorted by residual: dihedral pdb=" CA TRP B 58 " pdb=" C TRP B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta harmonic sigma weight residual 180.00 73.55 106.45 0 5.00e+00 4.00e-02 4.53e+02 dihedral pdb=" CA TYR A 698 " pdb=" C TYR A 698 " pdb=" N PRO A 699 " pdb=" CA PRO A 699 " ideal model delta harmonic sigma weight residual 0.00 42.66 -42.66 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CB CYS B 85 " pdb=" SG CYS B 85 " pdb=" SG CYS B 145 " pdb=" CB CYS B 145 " ideal model delta sinusoidal sigma weight residual -86.00 -22.88 -63.12 1 1.00e+01 1.00e-02 5.26e+01 ... (remaining 10437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2655 0.101 - 0.203: 99 0.203 - 0.304: 5 0.304 - 0.405: 0 0.405 - 0.507: 1 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CA THR B 716 " pdb=" N THR B 716 " pdb=" C THR B 716 " pdb=" CB THR B 716 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA ARG A 697 " pdb=" N ARG A 697 " pdb=" C ARG A 697 " pdb=" CB ARG A 697 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C10 95E B1203 " pdb=" C11 95E B1203 " pdb=" C13 95E B1203 " pdb=" N9 95E B1203 " both_signs ideal model delta sigma weight residual False 2.35 2.62 -0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2757 not shown) Planarity restraints: 3082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 698 " 0.048 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR A 698 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 698 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 698 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 698 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 698 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 698 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 698 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 699 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C PRO A 699 " 0.063 2.00e-02 2.50e+03 pdb=" O PRO A 699 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 700 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 715 " -0.017 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C PRO B 715 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO B 715 " -0.024 2.00e-02 2.50e+03 pdb=" N THR B 716 " -0.021 2.00e-02 2.50e+03 ... (remaining 3079 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 370 2.69 - 3.24: 16303 3.24 - 3.79: 24989 3.79 - 4.35: 34749 4.35 - 4.90: 59117 Nonbonded interactions: 135528 Sorted by model distance: nonbonded pdb=" O27 PNS B1201 " pdb=" O33 PNS B1201 " model vdw 2.134 2.440 nonbonded pdb=" OG1 THR B 576 " pdb=" O1 PO4 B1202 " model vdw 2.208 2.440 nonbonded pdb=" N TRP A 864 " pdb=" O GLN A 876 " model vdw 2.232 2.520 nonbonded pdb=" OE2 GLU B 781 " pdb=" OH TYR B 816 " model vdw 2.237 2.440 nonbonded pdb=" O SER B1070 " pdb=" OG SER B1070 " model vdw 2.250 2.440 ... (remaining 135523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.140 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 45.650 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.259 17633 Z= 0.425 Angle : 1.190 45.489 24107 Z= 0.562 Chirality : 0.046 0.507 2760 Planarity : 0.005 0.052 3082 Dihedral : 14.392 153.860 6377 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.22 % Favored : 91.64 % Rotamer: Outliers : 0.17 % Allowed : 3.14 % Favored : 96.69 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.15), residues: 2225 helix: -2.20 (0.15), residues: 857 sheet: -2.36 (0.32), residues: 225 loop : -3.58 (0.14), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 864 HIS 0.003 0.001 HIS B1069 PHE 0.011 0.001 PHE B 99 TYR 0.048 0.002 TYR A 698 ARG 0.010 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 267 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8011 (mt) cc_final: 0.7645 (mm) REVERT: A 72 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7811 (ttm-80) REVERT: A 225 ARG cc_start: 0.5667 (ttt-90) cc_final: 0.5391 (ttt-90) REVERT: A 495 SER cc_start: 0.8675 (t) cc_final: 0.8423 (p) REVERT: A 577 PHE cc_start: 0.8044 (m-80) cc_final: 0.7673 (m-10) REVERT: A 622 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8273 (pttp) REVERT: A 648 TRP cc_start: 0.7862 (t60) cc_final: 0.7488 (t60) REVERT: A 699 PRO cc_start: 0.9249 (OUTLIER) cc_final: 0.9034 (Cg_endo) REVERT: A 837 LYS cc_start: 0.7238 (pptt) cc_final: 0.6554 (ptpt) REVERT: A 879 LYS cc_start: 0.8459 (mttt) cc_final: 0.8063 (mttp) REVERT: A 906 LYS cc_start: 0.8005 (mttm) cc_final: 0.7682 (mtmm) REVERT: B 24 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7263 (ttp-170) REVERT: B 28 TRP cc_start: 0.7762 (m100) cc_final: 0.7373 (m100) REVERT: B 146 GLN cc_start: 0.7390 (mt0) cc_final: 0.7063 (mt0) REVERT: B 174 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7737 (pttm) REVERT: B 227 LEU cc_start: 0.8063 (mp) cc_final: 0.7795 (tp) REVERT: B 428 LEU cc_start: 0.8822 (tt) cc_final: 0.8609 (tp) REVERT: B 781 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7696 (mt-10) REVERT: B 801 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8023 (mmmt) REVERT: B 821 LYS cc_start: 0.7819 (mmtp) cc_final: 0.7052 (pttp) outliers start: 3 outliers final: 3 residues processed: 270 average time/residue: 1.5770 time to fit residues: 466.1593 Evaluate side-chains 168 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 PRO Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 713 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 1.9990 chunk 168 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 174 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.0000 chunk 129 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 361 ASN A 482 GLN A 667 ASN A 741 GLN A 760 ASN A 832 ASN ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN B 291 GLN B 393 GLN B 610 ASN B 653 GLN B 719 ASN B 956 GLN B 959 GLN B1013 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17633 Z= 0.159 Angle : 0.843 26.254 24107 Z= 0.352 Chirality : 0.042 0.145 2760 Planarity : 0.005 0.055 3082 Dihedral : 10.955 137.380 2670 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.09 % Favored : 91.82 % Rotamer: Outliers : 1.65 % Allowed : 10.38 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.16), residues: 2225 helix: -1.28 (0.18), residues: 842 sheet: -1.97 (0.32), residues: 234 loop : -3.05 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 864 HIS 0.003 0.001 HIS B 217 PHE 0.017 0.001 PHE A 620 TYR 0.011 0.001 TYR A 746 ARG 0.006 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7953 (mt) cc_final: 0.7705 (mm) REVERT: A 105 ASN cc_start: 0.7139 (t0) cc_final: 0.6702 (t0) REVERT: A 577 PHE cc_start: 0.7804 (m-80) cc_final: 0.7452 (m-10) REVERT: A 622 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8294 (pttp) REVERT: A 648 TRP cc_start: 0.7937 (t60) cc_final: 0.7392 (t-100) REVERT: A 837 LYS cc_start: 0.7247 (pptt) cc_final: 0.6698 (ptpt) REVERT: A 879 LYS cc_start: 0.8261 (mttt) cc_final: 0.7902 (mttp) REVERT: A 906 LYS cc_start: 0.8015 (mttm) cc_final: 0.7677 (mtmm) REVERT: A 1042 SER cc_start: 0.8612 (t) cc_final: 0.8362 (p) REVERT: A 1052 GLN cc_start: 0.8002 (tt0) cc_final: 0.7587 (tm-30) REVERT: B 146 GLN cc_start: 0.7323 (mt0) cc_final: 0.7053 (mt0) REVERT: B 174 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7794 (ptmm) REVERT: B 202 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7452 (mm-40) REVERT: B 227 LEU cc_start: 0.8093 (mp) cc_final: 0.7776 (tp) REVERT: B 503 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: B 506 THR cc_start: 0.8964 (m) cc_final: 0.8741 (p) REVERT: B 543 MET cc_start: 0.8292 (mtp) cc_final: 0.8045 (mtp) REVERT: B 821 LYS cc_start: 0.7676 (mmtp) cc_final: 0.6871 (pttp) outliers start: 29 outliers final: 10 residues processed: 206 average time/residue: 1.4505 time to fit residues: 330.2512 Evaluate side-chains 176 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 0.0670 chunk 218 optimal weight: 0.0010 chunk 179 optimal weight: 0.0020 chunk 200 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN B 719 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17633 Z= 0.165 Angle : 0.830 26.238 24107 Z= 0.344 Chirality : 0.042 0.143 2760 Planarity : 0.005 0.100 3082 Dihedral : 9.952 127.209 2660 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.55 % Favored : 92.40 % Rotamer: Outliers : 1.88 % Allowed : 12.04 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.78 (0.17), residues: 2225 helix: -0.79 (0.18), residues: 833 sheet: -1.69 (0.32), residues: 250 loop : -2.77 (0.16), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 864 HIS 0.003 0.001 HIS B 217 PHE 0.014 0.001 PHE A 620 TYR 0.012 0.001 TYR B 288 ARG 0.009 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7423 (ttt90) REVERT: A 10 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7906 (pt) REVERT: A 105 ASN cc_start: 0.7207 (t0) cc_final: 0.6720 (t0) REVERT: A 367 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: A 577 PHE cc_start: 0.7835 (m-80) cc_final: 0.7488 (m-10) REVERT: A 622 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8236 (pttp) REVERT: A 648 TRP cc_start: 0.7954 (t60) cc_final: 0.7403 (t-100) REVERT: A 837 LYS cc_start: 0.7348 (pptt) cc_final: 0.6773 (ptpt) REVERT: A 848 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5917 (mpt180) REVERT: A 879 LYS cc_start: 0.8201 (mttt) cc_final: 0.7859 (mttp) REVERT: A 906 LYS cc_start: 0.8077 (mttm) cc_final: 0.7732 (mtmm) REVERT: A 1042 SER cc_start: 0.8581 (t) cc_final: 0.8311 (p) REVERT: A 1052 GLN cc_start: 0.7959 (tt0) cc_final: 0.7597 (tm-30) REVERT: B 28 TRP cc_start: 0.7793 (m100) cc_final: 0.7237 (m100) REVERT: B 121 THR cc_start: 0.7498 (p) cc_final: 0.7150 (t) REVERT: B 146 GLN cc_start: 0.7310 (mt0) cc_final: 0.6946 (mt0) REVERT: B 174 LYS cc_start: 0.8340 (mmtp) cc_final: 0.7811 (ptmm) REVERT: B 227 LEU cc_start: 0.8125 (mp) cc_final: 0.7791 (tp) REVERT: B 503 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: B 543 MET cc_start: 0.8227 (mtp) cc_final: 0.7970 (mtt) REVERT: B 821 LYS cc_start: 0.7604 (mmtp) cc_final: 0.6726 (pttp) REVERT: B 930 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7920 (p) outliers start: 33 outliers final: 12 residues processed: 197 average time/residue: 1.5200 time to fit residues: 331.6195 Evaluate side-chains 175 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 105 optimal weight: 0.0270 chunk 192 optimal weight: 0.0270 chunk 57 optimal weight: 0.5980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17633 Z= 0.147 Angle : 0.820 25.757 24107 Z= 0.337 Chirality : 0.041 0.150 2760 Planarity : 0.004 0.104 3082 Dihedral : 9.321 118.582 2660 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.10 % Favored : 92.85 % Rotamer: Outliers : 2.22 % Allowed : 12.78 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.41 (0.17), residues: 2225 helix: -0.46 (0.19), residues: 831 sheet: -1.67 (0.32), residues: 263 loop : -2.53 (0.16), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 864 HIS 0.003 0.001 HIS B 673 PHE 0.011 0.001 PHE A 620 TYR 0.011 0.001 TYR B 288 ARG 0.008 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7434 (ttt90) REVERT: A 72 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.7078 (mmp80) REVERT: A 105 ASN cc_start: 0.7131 (t0) cc_final: 0.6652 (t0) REVERT: A 367 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: A 577 PHE cc_start: 0.7773 (m-80) cc_final: 0.7472 (m-10) REVERT: A 622 LYS cc_start: 0.8525 (ptpp) cc_final: 0.8174 (pttp) REVERT: A 648 TRP cc_start: 0.7947 (t60) cc_final: 0.7406 (t-100) REVERT: A 837 LYS cc_start: 0.7359 (pptt) cc_final: 0.6703 (ptpt) REVERT: A 848 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5917 (mpt180) REVERT: A 879 LYS cc_start: 0.8074 (mttt) cc_final: 0.7744 (mttp) REVERT: A 906 LYS cc_start: 0.8083 (mttm) cc_final: 0.7745 (mtmm) REVERT: A 1042 SER cc_start: 0.8526 (t) cc_final: 0.8252 (p) REVERT: A 1052 GLN cc_start: 0.7918 (tt0) cc_final: 0.7592 (tm-30) REVERT: B 121 THR cc_start: 0.7778 (p) cc_final: 0.7371 (t) REVERT: B 146 GLN cc_start: 0.7325 (mt0) cc_final: 0.6928 (mt0) REVERT: B 149 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: B 174 LYS cc_start: 0.8336 (mmtp) cc_final: 0.7769 (ptmm) REVERT: B 202 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7433 (mm-40) REVERT: B 227 LEU cc_start: 0.8164 (mp) cc_final: 0.7812 (tp) REVERT: B 543 MET cc_start: 0.8173 (mtp) cc_final: 0.7891 (mtt) REVERT: B 676 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7694 (mtt-85) REVERT: B 821 LYS cc_start: 0.7563 (mmtp) cc_final: 0.6705 (pttp) REVERT: B 930 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7808 (p) outliers start: 39 outliers final: 18 residues processed: 194 average time/residue: 1.4388 time to fit residues: 308.5504 Evaluate side-chains 181 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 183 optimal weight: 0.0020 chunk 148 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 192 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 overall best weight: 1.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 789 ASN ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17633 Z= 0.233 Angle : 0.850 25.143 24107 Z= 0.355 Chirality : 0.043 0.157 2760 Planarity : 0.005 0.089 3082 Dihedral : 9.250 117.465 2660 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.18 % Favored : 91.78 % Rotamer: Outliers : 2.51 % Allowed : 13.41 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.34 (0.17), residues: 2225 helix: -0.57 (0.19), residues: 848 sheet: -1.31 (0.33), residues: 253 loop : -2.44 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 864 HIS 0.003 0.001 HIS B 580 PHE 0.014 0.001 PHE A 610 TYR 0.014 0.001 TYR B 288 ARG 0.005 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7441 (ttt90) REVERT: A 105 ASN cc_start: 0.7506 (t0) cc_final: 0.6946 (t0) REVERT: A 367 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: A 577 PHE cc_start: 0.7843 (m-80) cc_final: 0.7534 (m-10) REVERT: A 622 LYS cc_start: 0.8516 (ptpp) cc_final: 0.8172 (pttp) REVERT: A 648 TRP cc_start: 0.7946 (t60) cc_final: 0.7442 (t-100) REVERT: A 837 LYS cc_start: 0.7501 (pptt) cc_final: 0.6596 (ptmt) REVERT: A 848 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.5782 (mpt180) REVERT: A 879 LYS cc_start: 0.8125 (mttt) cc_final: 0.7785 (mttp) REVERT: A 906 LYS cc_start: 0.8157 (mttm) cc_final: 0.7560 (mtmm) REVERT: A 960 GLN cc_start: 0.8223 (tp40) cc_final: 0.7995 (mm-40) REVERT: A 1042 SER cc_start: 0.8557 (t) cc_final: 0.8276 (p) REVERT: A 1052 GLN cc_start: 0.7909 (tt0) cc_final: 0.7568 (tm-30) REVERT: B 28 TRP cc_start: 0.7840 (m100) cc_final: 0.7269 (m100) REVERT: B 121 THR cc_start: 0.7843 (p) cc_final: 0.7381 (t) REVERT: B 146 GLN cc_start: 0.7336 (mt0) cc_final: 0.6926 (mt0) REVERT: B 149 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: B 174 LYS cc_start: 0.8360 (mmtp) cc_final: 0.7781 (pttm) REVERT: B 227 LEU cc_start: 0.8170 (mp) cc_final: 0.7806 (tp) REVERT: B 273 MET cc_start: 0.8045 (tpp) cc_final: 0.7728 (mmt) REVERT: B 543 MET cc_start: 0.8193 (mtp) cc_final: 0.7963 (mtt) REVERT: B 676 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7773 (mtt-85) REVERT: B 821 LYS cc_start: 0.7642 (mmtp) cc_final: 0.6759 (pttp) REVERT: B 935 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6253 (mt-10) outliers start: 44 outliers final: 21 residues processed: 195 average time/residue: 1.4341 time to fit residues: 310.5289 Evaluate side-chains 186 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain B residue 1070 SER Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 0.0170 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17633 Z= 0.171 Angle : 0.826 24.335 24107 Z= 0.341 Chirality : 0.042 0.135 2760 Planarity : 0.004 0.078 3082 Dihedral : 8.899 112.142 2660 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.46 % Favored : 92.49 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.10 (0.17), residues: 2225 helix: -0.35 (0.19), residues: 836 sheet: -1.19 (0.33), residues: 261 loop : -2.30 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 864 HIS 0.002 0.001 HIS B 217 PHE 0.010 0.001 PHE B 99 TYR 0.011 0.001 TYR B 288 ARG 0.014 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7390 (ttt180) REVERT: A 10 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7903 (pt) REVERT: A 105 ASN cc_start: 0.7277 (t0) cc_final: 0.6780 (t0) REVERT: A 367 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: A 577 PHE cc_start: 0.7834 (m-80) cc_final: 0.7543 (m-10) REVERT: A 622 LYS cc_start: 0.8491 (ptpp) cc_final: 0.8169 (pttp) REVERT: A 648 TRP cc_start: 0.7962 (t60) cc_final: 0.7431 (t-100) REVERT: A 837 LYS cc_start: 0.7511 (pptt) cc_final: 0.6562 (ptmt) REVERT: A 848 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5720 (mpt180) REVERT: A 879 LYS cc_start: 0.8069 (mttt) cc_final: 0.7731 (mttp) REVERT: A 906 LYS cc_start: 0.8134 (mttm) cc_final: 0.7535 (mtmm) REVERT: A 960 GLN cc_start: 0.8218 (tp40) cc_final: 0.8003 (mm-40) REVERT: A 1042 SER cc_start: 0.8530 (t) cc_final: 0.8247 (p) REVERT: A 1052 GLN cc_start: 0.7929 (tt0) cc_final: 0.7586 (tm-30) REVERT: B 121 THR cc_start: 0.7863 (p) cc_final: 0.7406 (t) REVERT: B 146 GLN cc_start: 0.7357 (mt0) cc_final: 0.6931 (mt0) REVERT: B 149 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: B 174 LYS cc_start: 0.8333 (mmtp) cc_final: 0.7774 (pttm) REVERT: B 202 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7449 (mm-40) REVERT: B 227 LEU cc_start: 0.8143 (mp) cc_final: 0.7802 (tp) REVERT: B 273 MET cc_start: 0.8066 (tpp) cc_final: 0.7765 (mmt) REVERT: B 543 MET cc_start: 0.8115 (mtp) cc_final: 0.7896 (mtt) REVERT: B 676 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7721 (mtt-85) REVERT: B 821 LYS cc_start: 0.7599 (mmtp) cc_final: 0.6713 (pttp) REVERT: B 935 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6248 (mt-10) outliers start: 38 outliers final: 20 residues processed: 195 average time/residue: 1.4947 time to fit residues: 321.2001 Evaluate side-chains 187 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 0.0870 chunk 156 optimal weight: 0.0570 chunk 121 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 119 optimal weight: 0.0040 chunk 213 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.4288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 ASN B 875 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17633 Z= 0.153 Angle : 0.819 23.988 24107 Z= 0.336 Chirality : 0.041 0.136 2760 Planarity : 0.004 0.076 3082 Dihedral : 8.631 109.173 2660 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.46 % Favored : 92.49 % Rotamer: Outliers : 2.34 % Allowed : 13.75 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.18), residues: 2225 helix: -0.22 (0.19), residues: 844 sheet: -1.13 (0.32), residues: 271 loop : -2.21 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 864 HIS 0.002 0.000 HIS B 217 PHE 0.016 0.001 PHE A 101 TYR 0.011 0.001 TYR B 288 ARG 0.011 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7372 (ttt180) REVERT: A 72 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7186 (mtp85) REVERT: A 105 ASN cc_start: 0.7216 (t0) cc_final: 0.6729 (t0) REVERT: A 367 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: A 577 PHE cc_start: 0.7849 (m-80) cc_final: 0.7553 (m-10) REVERT: A 622 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8148 (pttp) REVERT: A 648 TRP cc_start: 0.7951 (t60) cc_final: 0.7408 (t-100) REVERT: A 837 LYS cc_start: 0.7458 (pptt) cc_final: 0.6462 (ptmt) REVERT: A 848 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5837 (mpt180) REVERT: A 879 LYS cc_start: 0.8015 (mttt) cc_final: 0.7688 (mttp) REVERT: A 906 LYS cc_start: 0.8122 (mttm) cc_final: 0.7529 (mtmm) REVERT: A 960 GLN cc_start: 0.8208 (tp40) cc_final: 0.7997 (mm-40) REVERT: A 1042 SER cc_start: 0.8520 (t) cc_final: 0.8239 (p) REVERT: A 1052 GLN cc_start: 0.7898 (tt0) cc_final: 0.7580 (tm-30) REVERT: B 114 MET cc_start: 0.8375 (ttm) cc_final: 0.8175 (ttp) REVERT: B 121 THR cc_start: 0.7883 (p) cc_final: 0.7424 (t) REVERT: B 146 GLN cc_start: 0.7330 (mt0) cc_final: 0.6912 (mt0) REVERT: B 174 LYS cc_start: 0.8326 (mmtp) cc_final: 0.7759 (pttm) REVERT: B 202 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7509 (mm-40) REVERT: B 227 LEU cc_start: 0.8114 (mp) cc_final: 0.7772 (tp) REVERT: B 273 MET cc_start: 0.8061 (tpp) cc_final: 0.7767 (mmt) REVERT: B 821 LYS cc_start: 0.7615 (mmtp) cc_final: 0.6671 (pttp) REVERT: B 935 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6325 (mt-10) outliers start: 41 outliers final: 23 residues processed: 192 average time/residue: 1.4835 time to fit residues: 316.0898 Evaluate side-chains 184 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17633 Z= 0.245 Angle : 0.853 23.942 24107 Z= 0.357 Chirality : 0.043 0.138 2760 Planarity : 0.005 0.076 3082 Dihedral : 8.783 110.854 2660 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.22 % Favored : 91.73 % Rotamer: Outliers : 2.40 % Allowed : 14.38 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2225 helix: -0.30 (0.19), residues: 835 sheet: -1.19 (0.32), residues: 266 loop : -2.18 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 864 HIS 0.003 0.001 HIS B 580 PHE 0.024 0.001 PHE A 101 TYR 0.015 0.001 TYR A 746 ARG 0.013 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7465 (ttt90) REVERT: A 10 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7957 (pt) REVERT: A 72 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7268 (mtp85) REVERT: A 105 ASN cc_start: 0.7478 (t0) cc_final: 0.6906 (t0) REVERT: A 367 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: A 577 PHE cc_start: 0.7891 (m-80) cc_final: 0.7593 (m-10) REVERT: A 622 LYS cc_start: 0.8495 (ptpp) cc_final: 0.8169 (pttp) REVERT: A 648 TRP cc_start: 0.7977 (t60) cc_final: 0.7443 (t-100) REVERT: A 837 LYS cc_start: 0.7474 (pptt) cc_final: 0.6461 (ptmt) REVERT: A 848 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5684 (mpt180) REVERT: A 879 LYS cc_start: 0.8022 (mttt) cc_final: 0.7677 (mttp) REVERT: A 906 LYS cc_start: 0.8163 (mttm) cc_final: 0.7579 (mtmm) REVERT: A 1042 SER cc_start: 0.8588 (t) cc_final: 0.8306 (p) REVERT: A 1052 GLN cc_start: 0.7935 (tt0) cc_final: 0.7595 (tm-30) REVERT: B 121 THR cc_start: 0.7891 (p) cc_final: 0.7417 (t) REVERT: B 146 GLN cc_start: 0.7365 (mt0) cc_final: 0.6937 (mt0) REVERT: B 149 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 174 LYS cc_start: 0.8339 (mmtp) cc_final: 0.7764 (pttm) REVERT: B 227 LEU cc_start: 0.8145 (mp) cc_final: 0.7825 (tp) REVERT: B 273 MET cc_start: 0.8086 (tpp) cc_final: 0.7771 (mmt) REVERT: B 821 LYS cc_start: 0.7618 (mmtp) cc_final: 0.6714 (pttp) REVERT: B 935 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6393 (mt-10) outliers start: 42 outliers final: 26 residues processed: 187 average time/residue: 1.4985 time to fit residues: 309.3678 Evaluate side-chains 186 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain B residue 1070 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.8980 chunk 204 optimal weight: 0.3980 chunk 187 optimal weight: 0.0670 chunk 199 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 180 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17633 Z= 0.156 Angle : 0.827 23.545 24107 Z= 0.340 Chirality : 0.041 0.136 2760 Planarity : 0.004 0.072 3082 Dihedral : 8.500 107.395 2660 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.06 % Favored : 92.90 % Rotamer: Outliers : 2.28 % Allowed : 14.55 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.18), residues: 2225 helix: -0.13 (0.19), residues: 837 sheet: -1.11 (0.33), residues: 268 loop : -2.09 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 864 HIS 0.002 0.001 HIS A 135 PHE 0.021 0.001 PHE A 101 TYR 0.012 0.001 TYR A 746 ARG 0.014 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7381 (ttt180) REVERT: A 10 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7948 (pt) REVERT: A 72 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.7201 (mtp85) REVERT: A 105 ASN cc_start: 0.7279 (t0) cc_final: 0.6782 (t0) REVERT: A 367 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: A 577 PHE cc_start: 0.7852 (m-80) cc_final: 0.7572 (m-10) REVERT: A 622 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8151 (pttp) REVERT: A 648 TRP cc_start: 0.7956 (t60) cc_final: 0.7412 (t-100) REVERT: A 837 LYS cc_start: 0.7411 (pptt) cc_final: 0.6394 (ptmt) REVERT: A 848 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.5712 (mpt180) REVERT: A 879 LYS cc_start: 0.7955 (mttt) cc_final: 0.7621 (mttp) REVERT: A 906 LYS cc_start: 0.8151 (mttm) cc_final: 0.7562 (mtmm) REVERT: A 1042 SER cc_start: 0.8523 (t) cc_final: 0.8238 (p) REVERT: A 1052 GLN cc_start: 0.7886 (tt0) cc_final: 0.7580 (tm-30) REVERT: B 146 GLN cc_start: 0.7372 (mt0) cc_final: 0.6991 (mt0) REVERT: B 149 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: B 174 LYS cc_start: 0.8336 (mmtp) cc_final: 0.7776 (pttm) REVERT: B 202 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7476 (mm-40) REVERT: B 227 LEU cc_start: 0.8126 (mp) cc_final: 0.7829 (tp) REVERT: B 273 MET cc_start: 0.8057 (tpp) cc_final: 0.7781 (mmt) REVERT: B 676 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7709 (mtt-85) REVERT: B 801 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8088 (mmpt) REVERT: B 821 LYS cc_start: 0.7624 (mmtp) cc_final: 0.6665 (pttp) REVERT: B 935 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6318 (mt-10) REVERT: P 80 LEU cc_start: 0.8359 (tt) cc_final: 0.8142 (tp) outliers start: 40 outliers final: 23 residues processed: 191 average time/residue: 1.4274 time to fit residues: 302.6240 Evaluate side-chains 188 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 146 optimal weight: 0.1980 chunk 221 optimal weight: 0.0970 chunk 203 optimal weight: 0.0070 chunk 176 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 ASN B 875 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17633 Z= 0.145 Angle : 0.820 23.363 24107 Z= 0.335 Chirality : 0.041 0.135 2760 Planarity : 0.004 0.072 3082 Dihedral : 8.260 105.031 2660 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.24 % Favored : 92.72 % Rotamer: Outliers : 1.65 % Allowed : 15.57 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2225 helix: 0.01 (0.19), residues: 843 sheet: -1.03 (0.33), residues: 268 loop : -2.00 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 864 HIS 0.002 0.000 HIS A 135 PHE 0.019 0.001 PHE A 101 TYR 0.017 0.001 TYR A 746 ARG 0.014 0.000 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7962 (pt) REVERT: A 105 ASN cc_start: 0.7204 (t0) cc_final: 0.6722 (t0) REVERT: A 225 ARG cc_start: 0.5541 (ttt180) cc_final: 0.3841 (ttm170) REVERT: A 367 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: A 401 MET cc_start: 0.8340 (mmm) cc_final: 0.8004 (mmp) REVERT: A 577 PHE cc_start: 0.7852 (m-80) cc_final: 0.7577 (m-10) REVERT: A 622 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8133 (pttp) REVERT: A 648 TRP cc_start: 0.7950 (t60) cc_final: 0.7395 (t-100) REVERT: A 837 LYS cc_start: 0.7342 (pptt) cc_final: 0.6346 (ptmt) REVERT: A 848 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.5721 (mpt180) REVERT: A 879 LYS cc_start: 0.7921 (mttt) cc_final: 0.7589 (mttp) REVERT: A 906 LYS cc_start: 0.8116 (mttm) cc_final: 0.7532 (mtmm) REVERT: A 1042 SER cc_start: 0.8494 (t) cc_final: 0.8226 (p) REVERT: A 1052 GLN cc_start: 0.7834 (tt0) cc_final: 0.7596 (tm-30) REVERT: B 146 GLN cc_start: 0.7378 (mt0) cc_final: 0.6914 (mt0) REVERT: B 149 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: B 174 LYS cc_start: 0.8331 (mmtp) cc_final: 0.7777 (pttm) REVERT: B 202 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7533 (mm-40) REVERT: B 227 LEU cc_start: 0.8079 (mp) cc_final: 0.7797 (tp) REVERT: B 273 MET cc_start: 0.8056 (tpp) cc_final: 0.7782 (mmt) REVERT: B 821 LYS cc_start: 0.7597 (mmtp) cc_final: 0.6648 (pttp) REVERT: B 935 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6303 (mt-10) REVERT: P 18 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: P 80 LEU cc_start: 0.8358 (tt) cc_final: 0.8138 (tp) outliers start: 29 outliers final: 18 residues processed: 186 average time/residue: 1.4671 time to fit residues: 301.3830 Evaluate side-chains 182 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.0980 chunk 187 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 73 optimal weight: 0.0770 chunk 181 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 ASN B 767 GLN B 835 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112720 restraints weight = 22119.103| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.87 r_work: 0.3251 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17633 Z= 0.148 Angle : 0.822 23.272 24107 Z= 0.335 Chirality : 0.041 0.252 2760 Planarity : 0.004 0.067 3082 Dihedral : 8.118 103.914 2660 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.76 % Rotamer: Outliers : 1.54 % Allowed : 15.74 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.18), residues: 2225 helix: 0.10 (0.19), residues: 845 sheet: -0.99 (0.33), residues: 268 loop : -1.94 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 864 HIS 0.003 0.000 HIS B 673 PHE 0.021 0.001 PHE A 101 TYR 0.019 0.001 TYR A 746 ARG 0.014 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6275.33 seconds wall clock time: 111 minutes 23.03 seconds (6683.03 seconds total)