Starting phenix.real_space_refine on Mon Mar 18 11:56:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/03_2024/6pvn_20494.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/03_2024/6pvn_20494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/03_2024/6pvn_20494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/03_2024/6pvn_20494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/03_2024/6pvn_20494.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/03_2024/6pvn_20494.pdb" } resolution = 4.07 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= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 Na 2 4.78 5 C 13560 2.51 5 N 3464 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "C ARG 712": "NH1" <-> "NH2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 758": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.30, per 1000 atoms: 0.54 Number of scatterers: 20874 At special positions: 0 Unit cell: (143.1, 143.1, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 Na 2 11.00 O 3724 8.00 N 3464 7.00 C 13560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 3.8 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 57.9% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.640A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.802A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.669A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.542A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.904A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.609A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG A 371 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 459 removed outlier: 3.687A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 535 removed outlier: 3.566A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 565 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.809A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 586 through 610 removed outlier: 3.852A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 132 through 149 removed outlier: 3.640A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.525A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.803A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.670A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.542A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.903A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 459 removed outlier: 3.687A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 505 removed outlier: 3.524A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 565 Processing helix chain 'B' and resid 570 through 576 removed outlier: 3.808A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 586 through 610 removed outlier: 3.852A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 634 removed outlier: 4.005A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 132 through 149 removed outlier: 3.639A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.802A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.670A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.543A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.903A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.668A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG C 371 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.937A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 459 removed outlier: 3.688A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 565 Processing helix chain 'C' and resid 570 through 576 removed outlier: 3.810A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 586 Processing helix chain 'C' and resid 586 through 610 removed outlier: 3.853A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 132 through 149 removed outlier: 3.639A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.803A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.669A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.543A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.904A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER D 372 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 459 removed outlier: 3.688A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 501 " --> pdb=" O ILE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.926A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 565 Processing helix chain 'D' and resid 570 through 576 removed outlier: 3.809A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 Processing helix chain 'D' and resid 586 through 610 removed outlier: 3.853A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE D 656 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA2, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'D' and resid 387 through 388 764 hydrogen bonds defined for protein. 2244 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: 5.22 Time building geometry restraints manager: 8.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6542 1.34 - 1.46: 5002 1.46 - 1.58: 9576 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 21324 Sorted by residual: bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.80e+00 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C ASP D 752 " pdb=" N PRO D 753 " ideal model delta sigma weight residual 1.328 1.360 -0.032 1.25e-02 6.40e+03 6.44e+00 ... (remaining 21319 not shown) Histogram of bond angle deviations from ideal: 98.95 - 106.10: 358 106.10 - 113.26: 11441 113.26 - 120.42: 8775 120.42 - 127.58: 8090 127.58 - 134.74: 208 Bond angle restraints: 28872 Sorted by residual: angle pdb=" N ILE B 652 " pdb=" CA ILE B 652 " pdb=" C ILE B 652 " ideal model delta sigma weight residual 112.29 105.14 7.15 9.40e-01 1.13e+00 5.78e+01 angle pdb=" N ILE A 652 " pdb=" CA ILE A 652 " pdb=" C ILE A 652 " ideal model delta sigma weight residual 112.29 105.19 7.10 9.40e-01 1.13e+00 5.70e+01 angle pdb=" N ILE C 652 " pdb=" CA ILE C 652 " pdb=" C ILE C 652 " ideal model delta sigma weight residual 112.29 105.19 7.10 9.40e-01 1.13e+00 5.70e+01 angle pdb=" N ILE D 652 " pdb=" CA ILE D 652 " pdb=" C ILE D 652 " ideal model delta sigma weight residual 112.29 105.22 7.07 9.40e-01 1.13e+00 5.65e+01 angle pdb=" N LYS D 686 " pdb=" CA LYS D 686 " pdb=" C LYS D 686 " ideal model delta sigma weight residual 114.39 105.24 9.15 1.45e+00 4.76e-01 3.98e+01 ... (remaining 28867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 11599 15.63 - 31.27: 853 31.27 - 46.90: 244 46.90 - 62.54: 28 62.54 - 78.17: 28 Dihedral angle restraints: 12752 sinusoidal: 5152 harmonic: 7600 Sorted by residual: dihedral pdb=" CA SER A 648 " pdb=" C SER A 648 " pdb=" N THR A 649 " pdb=" CA THR A 649 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.37e+01 dihedral pdb=" CA SER D 648 " pdb=" C SER D 648 " pdb=" N THR D 649 " pdb=" CA THR D 649 " ideal model delta harmonic sigma weight residual -180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 dihedral pdb=" CA SER B 648 " pdb=" C SER B 648 " pdb=" N THR B 649 " pdb=" CA THR B 649 " ideal model delta harmonic sigma weight residual -180.00 -131.66 -48.34 0 5.00e+00 4.00e-02 9.35e+01 ... (remaining 12749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2310 0.051 - 0.103: 710 0.103 - 0.154: 190 0.154 - 0.205: 74 0.205 - 0.257: 24 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CB THR D 740 " pdb=" CA THR D 740 " pdb=" OG1 THR D 740 " pdb=" CG2 THR D 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR C 740 " pdb=" CA THR C 740 " pdb=" OG1 THR C 740 " pdb=" CG2 THR C 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR A 740 " pdb=" CA THR A 740 " pdb=" OG1 THR A 740 " pdb=" CG2 THR A 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3305 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 754 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO B 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 755 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 754 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO A 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 755 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 754 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO D 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 755 " -0.042 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 5115 2.78 - 3.31: 19004 3.31 - 3.84: 31607 3.84 - 4.37: 36282 4.37 - 4.90: 61241 Nonbonded interactions: 153249 Sorted by model distance: nonbonded pdb=" NH2 ARG C 464 " pdb=" O GLU C 467 " model vdw 2.256 2.520 nonbonded pdb=" NH2 ARG A 464 " pdb=" O GLU A 467 " model vdw 2.256 2.520 nonbonded pdb=" NH2 ARG B 464 " pdb=" O GLU B 467 " model vdw 2.256 2.520 nonbonded pdb=" NH2 ARG D 464 " pdb=" O GLU D 467 " model vdw 2.256 2.520 nonbonded pdb=" OE2 GLU A 751 " pdb=" NZ LYS B 174 " model vdw 2.298 2.520 ... (remaining 153244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 115 through 758) selection = (chain 'B' and resid 115 through 758) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.930 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 51.340 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 0.065 21324 Z= 0.398 Angle : 1.328 14.338 28872 Z= 0.769 Chirality : 0.060 0.257 3308 Planarity : 0.007 0.078 3608 Dihedral : 12.870 78.173 7816 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.21 % Favored : 85.32 % Rotamer: Outliers : 1.23 % Allowed : 8.11 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.44 % 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: -6.84 (0.09), residues: 2568 helix: -4.54 (0.06), residues: 1420 sheet: None (None), residues: 0 loop : -4.50 (0.13), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 692 HIS 0.012 0.002 HIS B 301 PHE 0.043 0.003 PHE D 542 TYR 0.036 0.002 TYR D 213 ARG 0.011 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 848 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7882 (tpp) cc_final: 0.7556 (tpp) REVERT: A 335 THR cc_start: 0.9343 (p) cc_final: 0.9079 (t) REVERT: A 353 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8545 (mmtm) REVERT: A 397 THR cc_start: 0.8472 (m) cc_final: 0.8127 (p) REVERT: A 438 LYS cc_start: 0.8236 (tttp) cc_final: 0.8012 (ttpp) REVERT: A 479 MET cc_start: 0.0779 (mmm) cc_final: 0.0305 (mtm) REVERT: A 540 TYR cc_start: 0.6049 (t80) cc_final: 0.5802 (t80) REVERT: A 584 LEU cc_start: 0.8308 (tm) cc_final: 0.8043 (tt) REVERT: A 677 MET cc_start: 0.8402 (mtt) cc_final: 0.8048 (mtt) REVERT: A 687 GLU cc_start: 0.7629 (tp30) cc_final: 0.7386 (pp20) REVERT: A 734 ILE cc_start: 0.7687 (mt) cc_final: 0.7369 (mm) REVERT: A 748 PHE cc_start: 0.7359 (p90) cc_final: 0.6787 (p90) REVERT: B 159 MET cc_start: 0.7754 (tpp) cc_final: 0.6872 (tpp) REVERT: B 250 PHE cc_start: 0.7777 (p90) cc_final: 0.7547 (p90) REVERT: B 251 ASN cc_start: 0.5207 (t0) cc_final: 0.4891 (t0) REVERT: B 282 MET cc_start: 0.8352 (mmm) cc_final: 0.8012 (mmt) REVERT: B 335 THR cc_start: 0.9306 (p) cc_final: 0.9020 (t) REVERT: B 479 MET cc_start: 0.0663 (mmm) cc_final: 0.0182 (mtm) REVERT: B 497 ILE cc_start: 0.9165 (tp) cc_final: 0.8828 (tt) REVERT: B 661 TYR cc_start: 0.9453 (t80) cc_final: 0.8548 (t80) REVERT: B 677 MET cc_start: 0.8290 (mtt) cc_final: 0.7824 (mtt) REVERT: B 722 LYS cc_start: 0.6287 (ttmt) cc_final: 0.6041 (ttmt) REVERT: B 734 ILE cc_start: 0.7914 (mt) cc_final: 0.7588 (mm) REVERT: B 748 PHE cc_start: 0.7556 (p90) cc_final: 0.7050 (p90) REVERT: C 159 MET cc_start: 0.7880 (tpp) cc_final: 0.7564 (tpp) REVERT: C 335 THR cc_start: 0.9344 (p) cc_final: 0.9115 (t) REVERT: C 353 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8508 (mmtm) REVERT: C 397 THR cc_start: 0.8462 (m) cc_final: 0.8123 (p) REVERT: C 438 LYS cc_start: 0.8211 (tttp) cc_final: 0.7997 (ttpp) REVERT: C 479 MET cc_start: 0.0804 (mmm) cc_final: 0.0325 (mtm) REVERT: C 540 TYR cc_start: 0.6072 (t80) cc_final: 0.5827 (t80) REVERT: C 584 LEU cc_start: 0.8317 (tm) cc_final: 0.8020 (tt) REVERT: C 605 LEU cc_start: 0.9091 (mp) cc_final: 0.8871 (mt) REVERT: C 677 MET cc_start: 0.8332 (mtt) cc_final: 0.7990 (mtt) REVERT: C 687 GLU cc_start: 0.7591 (tp30) cc_final: 0.7356 (pp20) REVERT: C 734 ILE cc_start: 0.7683 (mt) cc_final: 0.7351 (mm) REVERT: C 748 PHE cc_start: 0.7428 (p90) cc_final: 0.7009 (p90) REVERT: D 159 MET cc_start: 0.7876 (tpp) cc_final: 0.7541 (tpp) REVERT: D 335 THR cc_start: 0.9339 (p) cc_final: 0.9109 (t) REVERT: D 353 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8499 (mmtm) REVERT: D 397 THR cc_start: 0.8468 (m) cc_final: 0.8116 (p) REVERT: D 438 LYS cc_start: 0.8215 (tttp) cc_final: 0.8004 (ttpp) REVERT: D 479 MET cc_start: 0.0774 (mmm) cc_final: 0.0303 (mtm) REVERT: D 540 TYR cc_start: 0.6091 (t80) cc_final: 0.5836 (t80) REVERT: D 584 LEU cc_start: 0.8311 (tm) cc_final: 0.8015 (tt) REVERT: D 605 LEU cc_start: 0.9087 (mp) cc_final: 0.8880 (mt) REVERT: D 677 MET cc_start: 0.8340 (mtt) cc_final: 0.7998 (mtt) REVERT: D 687 GLU cc_start: 0.7577 (tp30) cc_final: 0.7352 (pp20) REVERT: D 734 ILE cc_start: 0.7690 (mt) cc_final: 0.7309 (mm) REVERT: D 748 PHE cc_start: 0.7396 (p90) cc_final: 0.6947 (p90) outliers start: 28 outliers final: 8 residues processed: 868 average time/residue: 0.3209 time to fit residues: 430.9276 Evaluate side-chains 487 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 479 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 HIS A 483 GLN A 570 GLN A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 HIS B 426 HIS B 483 GLN B 570 GLN B 585 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS C 483 GLN C 570 GLN C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 483 GLN D 570 GLN D 585 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 21324 Z= 0.364 Angle : 0.880 13.076 28872 Z= 0.462 Chirality : 0.049 0.247 3308 Planarity : 0.006 0.071 3608 Dihedral : 7.763 45.305 2804 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.56 % Favored : 85.24 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: -4.83 (0.13), residues: 2568 helix: -2.39 (0.11), residues: 1456 sheet: None (None), residues: 0 loop : -4.41 (0.14), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 739 HIS 0.005 0.001 HIS D 417 PHE 0.036 0.002 PHE C 249 TYR 0.024 0.002 TYR D 213 ARG 0.004 0.001 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 159 MET cc_start: 0.7822 (tpp) cc_final: 0.6717 (tpp) REVERT: A 163 THR cc_start: 0.8643 (m) cc_final: 0.8337 (p) REVERT: A 207 GLU cc_start: 0.8027 (pt0) cc_final: 0.7825 (pm20) REVERT: A 335 THR cc_start: 0.9296 (p) cc_final: 0.8941 (t) REVERT: A 540 TYR cc_start: 0.6511 (t80) cc_final: 0.6160 (t80) REVERT: A 659 ILE cc_start: 0.9077 (pt) cc_final: 0.8808 (mm) REVERT: A 677 MET cc_start: 0.7836 (mtt) cc_final: 0.7616 (mtt) REVERT: A 734 ILE cc_start: 0.7693 (mt) cc_final: 0.6782 (tt) REVERT: B 129 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 131 CYS cc_start: 0.8332 (t) cc_final: 0.7358 (t) REVERT: B 146 CYS cc_start: 0.7591 (t) cc_final: 0.7376 (t) REVERT: B 159 MET cc_start: 0.7743 (tpp) cc_final: 0.6636 (tpp) REVERT: B 282 MET cc_start: 0.8256 (mmm) cc_final: 0.7943 (mmt) REVERT: B 335 THR cc_start: 0.9326 (p) cc_final: 0.8919 (t) REVERT: B 479 MET cc_start: 0.0755 (mmm) cc_final: 0.0471 (mtm) REVERT: B 497 ILE cc_start: 0.9187 (tp) cc_final: 0.8711 (tt) REVERT: B 534 ILE cc_start: 0.9239 (tp) cc_final: 0.9035 (tp) REVERT: B 569 PHE cc_start: 0.8112 (m-10) cc_final: 0.7879 (m-10) REVERT: B 605 LEU cc_start: 0.9008 (mp) cc_final: 0.8519 (mt) REVERT: B 677 MET cc_start: 0.7768 (mtt) cc_final: 0.7469 (mtt) REVERT: C 129 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 159 MET cc_start: 0.7839 (tpp) cc_final: 0.6732 (tpp) REVERT: C 163 THR cc_start: 0.8643 (m) cc_final: 0.8343 (p) REVERT: C 207 GLU cc_start: 0.8050 (pt0) cc_final: 0.7836 (pm20) REVERT: C 335 THR cc_start: 0.9298 (p) cc_final: 0.8944 (t) REVERT: C 513 LEU cc_start: 0.8113 (mt) cc_final: 0.7896 (mt) REVERT: C 540 TYR cc_start: 0.6529 (t80) cc_final: 0.6155 (t80) REVERT: C 605 LEU cc_start: 0.9147 (mp) cc_final: 0.8609 (mt) REVERT: C 659 ILE cc_start: 0.9082 (pt) cc_final: 0.8826 (mm) REVERT: C 677 MET cc_start: 0.7835 (mtt) cc_final: 0.7617 (mtt) REVERT: C 734 ILE cc_start: 0.7682 (mt) cc_final: 0.6797 (tt) REVERT: D 129 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 159 MET cc_start: 0.7825 (tpp) cc_final: 0.6719 (tpp) REVERT: D 163 THR cc_start: 0.8647 (m) cc_final: 0.8343 (p) REVERT: D 207 GLU cc_start: 0.8038 (pt0) cc_final: 0.7820 (pm20) REVERT: D 335 THR cc_start: 0.9298 (p) cc_final: 0.8939 (t) REVERT: D 540 TYR cc_start: 0.6539 (t80) cc_final: 0.6179 (t80) REVERT: D 605 LEU cc_start: 0.9134 (mp) cc_final: 0.8611 (mt) REVERT: D 659 ILE cc_start: 0.9083 (pt) cc_final: 0.8785 (mm) REVERT: D 677 MET cc_start: 0.7852 (mtt) cc_final: 0.7618 (mtt) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.2959 time to fit residues: 301.6925 Evaluate side-chains 444 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 256 HIS A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS D 585 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21324 Z= 0.344 Angle : 0.833 12.050 28872 Z= 0.431 Chirality : 0.048 0.275 3308 Planarity : 0.005 0.071 3608 Dihedral : 7.269 37.706 2804 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.30 % Favored : 84.50 % Rotamer: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -3.97 (0.14), residues: 2568 helix: -1.53 (0.12), residues: 1476 sheet: -6.16 (0.27), residues: 20 loop : -4.25 (0.15), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 481 HIS 0.004 0.001 HIS B 160 PHE 0.039 0.002 PHE A 249 TYR 0.023 0.002 TYR B 213 ARG 0.003 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 569 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7747 (tpp) cc_final: 0.7539 (tpp) REVERT: A 207 GLU cc_start: 0.8083 (pt0) cc_final: 0.7825 (pm20) REVERT: A 335 THR cc_start: 0.9312 (p) cc_final: 0.8948 (t) REVERT: A 540 TYR cc_start: 0.6624 (t80) cc_final: 0.6234 (t80) REVERT: A 659 ILE cc_start: 0.9046 (pt) cc_final: 0.8748 (mm) REVERT: A 677 MET cc_start: 0.7819 (mtt) cc_final: 0.7608 (mtt) REVERT: A 734 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.6676 (tt) REVERT: B 129 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 159 MET cc_start: 0.7365 (tpp) cc_final: 0.6825 (tpp) REVERT: B 335 THR cc_start: 0.9368 (p) cc_final: 0.8955 (t) REVERT: B 351 MET cc_start: 0.8524 (mmm) cc_final: 0.8307 (mmm) REVERT: B 555 MET cc_start: 0.8866 (ttp) cc_final: 0.8658 (ttm) REVERT: B 605 LEU cc_start: 0.9074 (mp) cc_final: 0.8564 (mt) REVERT: B 677 MET cc_start: 0.7795 (mtt) cc_final: 0.7556 (mtt) REVERT: C 129 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 159 MET cc_start: 0.7766 (tpp) cc_final: 0.7549 (tpp) REVERT: C 207 GLU cc_start: 0.8110 (pt0) cc_final: 0.7836 (pm20) REVERT: C 335 THR cc_start: 0.9315 (p) cc_final: 0.8948 (t) REVERT: C 540 TYR cc_start: 0.6635 (t80) cc_final: 0.6224 (t80) REVERT: C 605 LEU cc_start: 0.9153 (mp) cc_final: 0.8667 (mt) REVERT: C 627 ASP cc_start: 0.7599 (t70) cc_final: 0.7384 (t0) REVERT: C 659 ILE cc_start: 0.9050 (pt) cc_final: 0.8769 (mm) REVERT: C 734 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.6661 (tt) REVERT: D 129 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7539 (tm-30) REVERT: D 159 MET cc_start: 0.7736 (tpp) cc_final: 0.7533 (tpp) REVERT: D 207 GLU cc_start: 0.8085 (pt0) cc_final: 0.7811 (pm20) REVERT: D 335 THR cc_start: 0.9316 (p) cc_final: 0.8956 (t) REVERT: D 540 TYR cc_start: 0.6659 (t80) cc_final: 0.6254 (t80) REVERT: D 605 LEU cc_start: 0.9167 (mp) cc_final: 0.8692 (mt) REVERT: D 627 ASP cc_start: 0.7608 (t70) cc_final: 0.7385 (t0) REVERT: D 659 ILE cc_start: 0.9049 (pt) cc_final: 0.8756 (mm) REVERT: D 677 MET cc_start: 0.7887 (mtt) cc_final: 0.7666 (mtt) outliers start: 2 outliers final: 0 residues processed: 569 average time/residue: 0.2716 time to fit residues: 248.4057 Evaluate side-chains 429 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 427 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 9.9990 chunk 175 optimal weight: 0.0070 chunk 120 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 233 optimal weight: 0.3980 chunk 247 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 297 ASN A 585 HIS B 197 ASN C 197 ASN C 244 HIS C 297 ASN C 585 HIS D 197 ASN D 244 HIS D 297 ASN D 585 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21324 Z= 0.183 Angle : 0.738 8.912 28872 Z= 0.385 Chirality : 0.045 0.317 3308 Planarity : 0.005 0.057 3608 Dihedral : 6.763 38.871 2804 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.33 % Favored : 85.51 % Rotamer: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -3.51 (0.15), residues: 2568 helix: -1.08 (0.13), residues: 1464 sheet: -5.92 (0.28), residues: 20 loop : -4.14 (0.15), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 481 HIS 0.003 0.001 HIS B 301 PHE 0.021 0.001 PHE A 250 TYR 0.036 0.002 TYR C 650 ARG 0.003 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 576 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8498 (mm) cc_final: 0.8283 (mt) REVERT: A 159 MET cc_start: 0.7704 (tpp) cc_final: 0.7486 (tpp) REVERT: A 207 GLU cc_start: 0.8021 (pt0) cc_final: 0.7780 (pm20) REVERT: A 335 THR cc_start: 0.9343 (p) cc_final: 0.8963 (t) REVERT: A 540 TYR cc_start: 0.6620 (t80) cc_final: 0.6229 (t80) REVERT: A 659 ILE cc_start: 0.8980 (pt) cc_final: 0.8698 (mm) REVERT: A 677 MET cc_start: 0.7653 (mtt) cc_final: 0.7408 (mtt) REVERT: B 129 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 131 CYS cc_start: 0.8062 (t) cc_final: 0.6909 (t) REVERT: B 159 MET cc_start: 0.7254 (tpp) cc_final: 0.6760 (tpp) REVERT: B 335 THR cc_start: 0.9328 (p) cc_final: 0.8914 (t) REVERT: B 555 MET cc_start: 0.8853 (ttp) cc_final: 0.8581 (ttm) REVERT: B 562 MET cc_start: 0.8783 (ttt) cc_final: 0.8547 (ttt) REVERT: B 605 LEU cc_start: 0.9039 (mp) cc_final: 0.8564 (mt) REVERT: B 677 MET cc_start: 0.7410 (mtt) cc_final: 0.7168 (mtt) REVERT: C 119 LEU cc_start: 0.8483 (mm) cc_final: 0.8258 (mt) REVERT: C 207 GLU cc_start: 0.8051 (pt0) cc_final: 0.7788 (pm20) REVERT: C 335 THR cc_start: 0.9338 (p) cc_final: 0.8952 (t) REVERT: C 540 TYR cc_start: 0.6637 (t80) cc_final: 0.6226 (t80) REVERT: C 605 LEU cc_start: 0.9130 (mp) cc_final: 0.8670 (mt) REVERT: C 627 ASP cc_start: 0.7550 (t70) cc_final: 0.7314 (t0) REVERT: C 659 ILE cc_start: 0.8964 (pt) cc_final: 0.8663 (mm) REVERT: D 119 LEU cc_start: 0.8493 (mm) cc_final: 0.8276 (mt) REVERT: D 159 MET cc_start: 0.7703 (tpp) cc_final: 0.7493 (tpp) REVERT: D 207 GLU cc_start: 0.8024 (pt0) cc_final: 0.7773 (pm20) REVERT: D 335 THR cc_start: 0.9342 (p) cc_final: 0.8941 (t) REVERT: D 540 TYR cc_start: 0.6684 (t80) cc_final: 0.6264 (t80) REVERT: D 605 LEU cc_start: 0.9113 (mp) cc_final: 0.8628 (mt) REVERT: D 627 ASP cc_start: 0.7546 (t70) cc_final: 0.7323 (t0) REVERT: D 659 ILE cc_start: 0.8990 (pt) cc_final: 0.8706 (mm) outliers start: 1 outliers final: 0 residues processed: 577 average time/residue: 0.2709 time to fit residues: 252.9813 Evaluate side-chains 423 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.6980 chunk 140 optimal weight: 0.3980 chunk 3 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN D 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21324 Z= 0.235 Angle : 0.749 10.236 28872 Z= 0.385 Chirality : 0.045 0.231 3308 Planarity : 0.005 0.061 3608 Dihedral : 6.454 37.121 2804 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.84 % Favored : 85.01 % Rotamer: Outliers : 0.31 % Allowed : 4.37 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -3.13 (0.15), residues: 2568 helix: -0.72 (0.13), residues: 1484 sheet: -5.82 (0.30), residues: 20 loop : -4.10 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 493 HIS 0.003 0.001 HIS B 160 PHE 0.027 0.002 PHE C 249 TYR 0.017 0.002 TYR D 208 ARG 0.003 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 553 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8683 (mm) cc_final: 0.8414 (mt) REVERT: A 327 ARG cc_start: 0.6593 (tpt170) cc_final: 0.6322 (tpt-90) REVERT: A 335 THR cc_start: 0.9352 (p) cc_final: 0.8955 (t) REVERT: A 488 MET cc_start: 0.7494 (mtt) cc_final: 0.7021 (mtm) REVERT: A 540 TYR cc_start: 0.6590 (t80) cc_final: 0.6280 (t80) REVERT: A 605 LEU cc_start: 0.9259 (mt) cc_final: 0.9033 (mm) REVERT: A 659 ILE cc_start: 0.9095 (pt) cc_final: 0.8735 (mm) REVERT: B 129 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 139 LEU cc_start: 0.9029 (mm) cc_final: 0.8807 (tp) REVERT: B 159 MET cc_start: 0.7322 (tpp) cc_final: 0.6786 (tpp) REVERT: B 251 ASN cc_start: 0.5702 (t0) cc_final: 0.5490 (t0) REVERT: B 335 THR cc_start: 0.9302 (p) cc_final: 0.8892 (t) REVERT: B 488 MET cc_start: 0.7347 (mtt) cc_final: 0.6894 (mtm) REVERT: B 555 MET cc_start: 0.8848 (ttp) cc_final: 0.8555 (ttm) REVERT: B 562 MET cc_start: 0.8851 (ttt) cc_final: 0.8563 (ttt) REVERT: B 677 MET cc_start: 0.7561 (mtt) cc_final: 0.7301 (mtt) REVERT: C 119 LEU cc_start: 0.8664 (mm) cc_final: 0.8386 (mt) REVERT: C 129 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7578 (tm-30) REVERT: C 327 ARG cc_start: 0.6591 (tpt170) cc_final: 0.6354 (tpt-90) REVERT: C 335 THR cc_start: 0.9341 (p) cc_final: 0.8955 (t) REVERT: C 488 MET cc_start: 0.7435 (mtt) cc_final: 0.6972 (mtm) REVERT: C 540 TYR cc_start: 0.6605 (t80) cc_final: 0.6276 (t80) REVERT: C 605 LEU cc_start: 0.9104 (mp) cc_final: 0.8645 (mt) REVERT: C 627 ASP cc_start: 0.7538 (t70) cc_final: 0.7326 (t0) REVERT: C 659 ILE cc_start: 0.9082 (pt) cc_final: 0.8787 (mm) REVERT: D 119 LEU cc_start: 0.8678 (mm) cc_final: 0.8419 (mt) REVERT: D 129 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7528 (tm-30) REVERT: D 159 MET cc_start: 0.7697 (tpp) cc_final: 0.7491 (tpp) REVERT: D 207 GLU cc_start: 0.8090 (pt0) cc_final: 0.7888 (pm20) REVERT: D 327 ARG cc_start: 0.6603 (tpt170) cc_final: 0.6361 (tpt-90) REVERT: D 335 THR cc_start: 0.9343 (p) cc_final: 0.8962 (t) REVERT: D 488 MET cc_start: 0.7481 (mtt) cc_final: 0.6995 (mtm) REVERT: D 540 TYR cc_start: 0.6638 (t80) cc_final: 0.6315 (t80) REVERT: D 627 ASP cc_start: 0.7537 (t70) cc_final: 0.7334 (t0) REVERT: D 659 ILE cc_start: 0.9091 (pt) cc_final: 0.8760 (mm) outliers start: 7 outliers final: 4 residues processed: 560 average time/residue: 0.2733 time to fit residues: 245.6184 Evaluate side-chains 428 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 424 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.3980 chunk 222 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 61 optimal weight: 0.0270 chunk 247 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 130 optimal weight: 5.9990 overall best weight: 1.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21324 Z= 0.197 Angle : 0.730 8.188 28872 Z= 0.376 Chirality : 0.046 0.406 3308 Planarity : 0.004 0.059 3608 Dihedral : 6.186 37.200 2804 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.47 % Favored : 86.37 % Rotamer: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -2.85 (0.16), residues: 2568 helix: -0.49 (0.13), residues: 1492 sheet: -5.40 (0.37), residues: 20 loop : -4.04 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 493 HIS 0.002 0.001 HIS A 417 PHE 0.020 0.001 PHE C 249 TYR 0.019 0.002 TYR C 661 ARG 0.005 0.000 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 560 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8683 (mm) cc_final: 0.8404 (mt) REVERT: A 335 THR cc_start: 0.9331 (p) cc_final: 0.8988 (t) REVERT: A 531 VAL cc_start: 0.9637 (m) cc_final: 0.9316 (p) REVERT: A 540 TYR cc_start: 0.6583 (t80) cc_final: 0.6252 (t80) REVERT: A 659 ILE cc_start: 0.9038 (pt) cc_final: 0.8730 (mm) REVERT: A 677 MET cc_start: 0.7639 (mtt) cc_final: 0.7432 (mtt) REVERT: B 119 LEU cc_start: 0.8726 (mm) cc_final: 0.8518 (mt) REVERT: B 129 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 131 CYS cc_start: 0.8177 (t) cc_final: 0.6967 (t) REVERT: B 159 MET cc_start: 0.7353 (tpp) cc_final: 0.6799 (tpp) REVERT: B 335 THR cc_start: 0.9277 (p) cc_final: 0.8892 (t) REVERT: B 488 MET cc_start: 0.7507 (mtt) cc_final: 0.6914 (mtm) REVERT: B 555 MET cc_start: 0.8793 (ttp) cc_final: 0.8551 (ttm) REVERT: B 562 MET cc_start: 0.8814 (ttt) cc_final: 0.8581 (ttt) REVERT: B 722 LYS cc_start: 0.6866 (tttt) cc_final: 0.6592 (tttt) REVERT: C 119 LEU cc_start: 0.8640 (mm) cc_final: 0.8390 (mt) REVERT: C 129 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7581 (tm-30) REVERT: C 335 THR cc_start: 0.9292 (p) cc_final: 0.8957 (t) REVERT: C 488 MET cc_start: 0.7464 (mtt) cc_final: 0.6978 (mtm) REVERT: C 540 TYR cc_start: 0.6561 (t80) cc_final: 0.6226 (t80) REVERT: C 605 LEU cc_start: 0.9076 (mp) cc_final: 0.8607 (mt) REVERT: C 627 ASP cc_start: 0.7526 (t70) cc_final: 0.7286 (t0) REVERT: C 659 ILE cc_start: 0.9074 (pt) cc_final: 0.8725 (mm) REVERT: D 119 LEU cc_start: 0.8665 (mm) cc_final: 0.8371 (mt) REVERT: D 335 THR cc_start: 0.9298 (p) cc_final: 0.8955 (t) REVERT: D 531 VAL cc_start: 0.9632 (m) cc_final: 0.9307 (p) REVERT: D 540 TYR cc_start: 0.6624 (t80) cc_final: 0.6283 (t80) REVERT: D 627 ASP cc_start: 0.7519 (t70) cc_final: 0.7315 (t0) REVERT: D 659 ILE cc_start: 0.9061 (pt) cc_final: 0.8776 (mm) REVERT: D 677 MET cc_start: 0.7625 (mtt) cc_final: 0.7425 (mtt) outliers start: 1 outliers final: 0 residues processed: 561 average time/residue: 0.2729 time to fit residues: 249.1018 Evaluate side-chains 404 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.0270 chunk 27 optimal weight: 0.9980 chunk 141 optimal weight: 0.4980 chunk 180 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21324 Z= 0.175 Angle : 0.706 10.054 28872 Z= 0.363 Chirality : 0.043 0.319 3308 Planarity : 0.004 0.061 3608 Dihedral : 6.011 36.927 2804 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.10 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.62 (0.16), residues: 2568 helix: -0.23 (0.13), residues: 1472 sheet: -5.13 (0.42), residues: 20 loop : -4.00 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 493 HIS 0.002 0.001 HIS D 301 PHE 0.018 0.001 PHE B 506 TYR 0.024 0.002 TYR B 213 ARG 0.003 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8654 (mm) cc_final: 0.8375 (mt) REVERT: A 163 THR cc_start: 0.8460 (m) cc_final: 0.8239 (p) REVERT: A 335 THR cc_start: 0.9301 (p) cc_final: 0.8933 (t) REVERT: A 540 TYR cc_start: 0.6548 (t80) cc_final: 0.6232 (t80) REVERT: B 119 LEU cc_start: 0.8604 (mm) cc_final: 0.8377 (mt) REVERT: B 129 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 131 CYS cc_start: 0.8201 (t) cc_final: 0.7000 (t) REVERT: B 159 MET cc_start: 0.7311 (tpp) cc_final: 0.6734 (tpp) REVERT: B 335 THR cc_start: 0.9280 (p) cc_final: 0.8907 (t) REVERT: B 371 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.8346 (ttp-170) REVERT: B 555 MET cc_start: 0.8745 (ttp) cc_final: 0.8499 (ttm) REVERT: B 562 MET cc_start: 0.8814 (ttt) cc_final: 0.8560 (ttt) REVERT: B 722 LYS cc_start: 0.6884 (tttt) cc_final: 0.6477 (tttt) REVERT: C 119 LEU cc_start: 0.8620 (mm) cc_final: 0.8323 (mt) REVERT: C 163 THR cc_start: 0.8459 (m) cc_final: 0.8242 (p) REVERT: C 335 THR cc_start: 0.9269 (p) cc_final: 0.8915 (t) REVERT: C 360 ILE cc_start: 0.9448 (tp) cc_final: 0.9227 (tt) REVERT: C 540 TYR cc_start: 0.6564 (t80) cc_final: 0.6234 (t80) REVERT: C 627 ASP cc_start: 0.7521 (t70) cc_final: 0.7320 (t0) REVERT: C 659 ILE cc_start: 0.9024 (pt) cc_final: 0.8661 (mm) REVERT: D 119 LEU cc_start: 0.8666 (mm) cc_final: 0.8351 (mt) REVERT: D 163 THR cc_start: 0.8446 (m) cc_final: 0.8236 (p) REVERT: D 335 THR cc_start: 0.9287 (p) cc_final: 0.8928 (t) REVERT: D 540 TYR cc_start: 0.6580 (t80) cc_final: 0.6257 (t80) REVERT: D 659 ILE cc_start: 0.9033 (pt) cc_final: 0.8646 (mm) REVERT: D 677 MET cc_start: 0.7415 (mtt) cc_final: 0.7209 (mtt) outliers start: 0 outliers final: 0 residues processed: 568 average time/residue: 0.2811 time to fit residues: 256.1694 Evaluate side-chains 411 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 147 optimal weight: 0.0070 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 645 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21324 Z= 0.209 Angle : 0.743 12.609 28872 Z= 0.374 Chirality : 0.044 0.293 3308 Planarity : 0.004 0.061 3608 Dihedral : 5.844 34.756 2804 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.29 % Favored : 85.55 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.38 (0.16), residues: 2568 helix: -0.00 (0.14), residues: 1468 sheet: -5.01 (0.43), residues: 20 loop : -3.93 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 493 HIS 0.003 0.001 HIS C 745 PHE 0.019 0.001 PHE A 249 TYR 0.024 0.002 TYR B 661 ARG 0.003 0.000 ARG A 729 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8785 (mm) cc_final: 0.8475 (mt) REVERT: A 138 LEU cc_start: 0.8637 (mp) cc_final: 0.8432 (mp) REVERT: A 139 LEU cc_start: 0.9079 (mm) cc_final: 0.8848 (tp) REVERT: A 163 THR cc_start: 0.8476 (m) cc_final: 0.8242 (p) REVERT: A 335 THR cc_start: 0.9299 (p) cc_final: 0.8927 (t) REVERT: A 540 TYR cc_start: 0.6588 (t80) cc_final: 0.6291 (t80) REVERT: A 605 LEU cc_start: 0.9241 (mt) cc_final: 0.8999 (mm) REVERT: B 119 LEU cc_start: 0.8665 (mm) cc_final: 0.8445 (mt) REVERT: B 159 MET cc_start: 0.7347 (tpp) cc_final: 0.6768 (tpp) REVERT: B 335 THR cc_start: 0.9304 (p) cc_final: 0.8884 (t) REVERT: B 371 ARG cc_start: 0.8607 (ttp-170) cc_final: 0.8381 (ttp-170) REVERT: B 562 MET cc_start: 0.8877 (ttt) cc_final: 0.8633 (ttt) REVERT: C 119 LEU cc_start: 0.8763 (mm) cc_final: 0.8531 (mt) REVERT: C 163 THR cc_start: 0.8482 (m) cc_final: 0.8270 (p) REVERT: C 335 THR cc_start: 0.9268 (p) cc_final: 0.8912 (t) REVERT: C 506 PHE cc_start: 0.7904 (t80) cc_final: 0.7691 (t80) REVERT: C 531 VAL cc_start: 0.9646 (m) cc_final: 0.9339 (p) REVERT: C 540 TYR cc_start: 0.6577 (t80) cc_final: 0.6266 (t80) REVERT: C 659 ILE cc_start: 0.9072 (pt) cc_final: 0.8724 (mm) REVERT: D 119 LEU cc_start: 0.8683 (mm) cc_final: 0.8453 (mt) REVERT: D 163 THR cc_start: 0.8457 (m) cc_final: 0.8246 (p) REVERT: D 335 THR cc_start: 0.9291 (p) cc_final: 0.8930 (t) REVERT: D 531 VAL cc_start: 0.9652 (m) cc_final: 0.9350 (p) REVERT: D 540 TYR cc_start: 0.6609 (t80) cc_final: 0.6309 (t80) REVERT: D 659 ILE cc_start: 0.9036 (pt) cc_final: 0.8697 (mm) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.2741 time to fit residues: 228.2001 Evaluate side-chains 401 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 229 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 180 optimal weight: 0.0060 chunk 70 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21324 Z= 0.183 Angle : 0.721 12.779 28872 Z= 0.365 Chirality : 0.045 0.455 3308 Planarity : 0.004 0.065 3608 Dihedral : 5.823 34.581 2804 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.67 % Favored : 86.18 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.18 (0.16), residues: 2568 helix: 0.20 (0.14), residues: 1448 sheet: -4.89 (0.45), residues: 20 loop : -3.85 (0.16), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 481 HIS 0.003 0.001 HIS B 301 PHE 0.026 0.001 PHE D 728 TYR 0.022 0.001 TYR B 382 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8509 (m) cc_final: 0.8264 (p) REVERT: A 335 THR cc_start: 0.9291 (p) cc_final: 0.8917 (t) REVERT: A 360 ILE cc_start: 0.9448 (tp) cc_final: 0.9230 (tt) REVERT: A 540 TYR cc_start: 0.6562 (t80) cc_final: 0.6264 (t80) REVERT: A 722 LYS cc_start: 0.6845 (tttt) cc_final: 0.6524 (tttt) REVERT: B 119 LEU cc_start: 0.8636 (mm) cc_final: 0.8422 (mt) REVERT: B 159 MET cc_start: 0.7333 (tpp) cc_final: 0.6735 (tpp) REVERT: B 335 THR cc_start: 0.9302 (p) cc_final: 0.8884 (t) REVERT: B 562 MET cc_start: 0.8846 (ttt) cc_final: 0.8621 (ttt) REVERT: B 728 PHE cc_start: 0.7226 (t80) cc_final: 0.6735 (p90) REVERT: C 163 THR cc_start: 0.8528 (m) cc_final: 0.8279 (p) REVERT: C 335 THR cc_start: 0.9240 (p) cc_final: 0.8885 (t) REVERT: C 488 MET cc_start: 0.7263 (mtt) cc_final: 0.6717 (mmm) REVERT: C 540 TYR cc_start: 0.6560 (t80) cc_final: 0.6269 (t80) REVERT: C 578 MET cc_start: 0.8739 (tpp) cc_final: 0.8450 (tpp) REVERT: C 659 ILE cc_start: 0.9042 (pt) cc_final: 0.8725 (mm) REVERT: D 163 THR cc_start: 0.8503 (m) cc_final: 0.8269 (p) REVERT: D 335 THR cc_start: 0.9265 (p) cc_final: 0.8922 (t) REVERT: D 540 TYR cc_start: 0.6582 (t80) cc_final: 0.6298 (t80) REVERT: D 659 ILE cc_start: 0.8997 (pt) cc_final: 0.8691 (mm) REVERT: D 722 LYS cc_start: 0.6595 (tttt) cc_final: 0.6236 (ttpt) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.2701 time to fit residues: 222.2017 Evaluate side-chains 391 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.9980 chunk 148 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 124 optimal weight: 0.0040 chunk 161 optimal weight: 5.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN B 645 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21324 Z= 0.201 Angle : 0.753 12.745 28872 Z= 0.375 Chirality : 0.045 0.426 3308 Planarity : 0.004 0.099 3608 Dihedral : 5.741 33.997 2804 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.28 % Favored : 86.57 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.09 (0.16), residues: 2568 helix: 0.25 (0.14), residues: 1444 sheet: -4.84 (0.46), residues: 20 loop : -3.75 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 739 HIS 0.002 0.001 HIS D 745 PHE 0.019 0.001 PHE C 506 TYR 0.023 0.002 TYR C 321 ARG 0.003 0.000 ARG D 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 494 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8521 (m) cc_final: 0.8292 (p) REVERT: A 335 THR cc_start: 0.9298 (p) cc_final: 0.8907 (t) REVERT: A 360 ILE cc_start: 0.9456 (tp) cc_final: 0.9245 (tt) REVERT: A 479 MET cc_start: -0.0550 (mmm) cc_final: -0.0902 (mmm) REVERT: A 482 LEU cc_start: 0.7703 (mm) cc_final: 0.7319 (mt) REVERT: A 540 TYR cc_start: 0.6512 (t80) cc_final: 0.6276 (t80) REVERT: A 569 PHE cc_start: 0.8172 (m-80) cc_final: 0.7965 (m-10) REVERT: A 659 ILE cc_start: 0.9039 (pt) cc_final: 0.8734 (mm) REVERT: A 722 LYS cc_start: 0.6887 (tttt) cc_final: 0.6658 (tttt) REVERT: B 119 LEU cc_start: 0.8625 (mm) cc_final: 0.8404 (mt) REVERT: B 159 MET cc_start: 0.7404 (tpp) cc_final: 0.6820 (tpp) REVERT: B 246 LYS cc_start: 0.8626 (mppt) cc_final: 0.8327 (mmtt) REVERT: B 290 THR cc_start: 0.8663 (m) cc_final: 0.8286 (t) REVERT: B 335 THR cc_start: 0.9322 (p) cc_final: 0.8873 (t) REVERT: B 410 ASN cc_start: 0.7283 (t0) cc_final: 0.6597 (t0) REVERT: B 555 MET cc_start: 0.8452 (ttm) cc_final: 0.8235 (ttm) REVERT: B 562 MET cc_start: 0.8852 (ttt) cc_final: 0.8639 (ttt) REVERT: B 679 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7563 (tp30) REVERT: B 728 PHE cc_start: 0.7258 (t80) cc_final: 0.6702 (p90) REVERT: C 163 THR cc_start: 0.8529 (m) cc_final: 0.8304 (p) REVERT: C 335 THR cc_start: 0.9259 (p) cc_final: 0.8905 (t) REVERT: C 488 MET cc_start: 0.7276 (mtt) cc_final: 0.6746 (mmm) REVERT: C 540 TYR cc_start: 0.6569 (t80) cc_final: 0.6287 (t80) REVERT: C 578 MET cc_start: 0.8646 (tpp) cc_final: 0.8358 (tpp) REVERT: C 659 ILE cc_start: 0.9084 (pt) cc_final: 0.8735 (mm) REVERT: C 722 LYS cc_start: 0.6920 (tttt) cc_final: 0.6713 (tttt) REVERT: D 335 THR cc_start: 0.9266 (p) cc_final: 0.8911 (t) REVERT: D 479 MET cc_start: -0.0383 (mmm) cc_final: -0.0750 (mmm) REVERT: D 482 LEU cc_start: 0.7660 (mm) cc_final: 0.7297 (mt) REVERT: D 540 TYR cc_start: 0.6549 (t80) cc_final: 0.6299 (t80) REVERT: D 569 PHE cc_start: 0.8134 (m-80) cc_final: 0.7924 (m-10) REVERT: D 659 ILE cc_start: 0.9008 (pt) cc_final: 0.8723 (mm) outliers start: 2 outliers final: 0 residues processed: 496 average time/residue: 0.2834 time to fit residues: 225.3279 Evaluate side-chains 390 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 187 optimal weight: 0.0020 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 25 optimal weight: 0.0030 chunk 37 optimal weight: 0.5980 chunk 178 optimal weight: 40.0000 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113473 restraints weight = 36375.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116027 restraints weight = 24172.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117386 restraints weight = 18674.524| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21324 Z= 0.175 Angle : 0.725 12.865 28872 Z= 0.364 Chirality : 0.043 0.345 3308 Planarity : 0.004 0.090 3608 Dihedral : 5.687 33.751 2804 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.28 % Favored : 86.57 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.00 (0.17), residues: 2568 helix: 0.33 (0.14), residues: 1448 sheet: -4.13 (0.43), residues: 60 loop : -3.70 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 739 HIS 0.003 0.001 HIS C 301 PHE 0.024 0.001 PHE A 506 TYR 0.022 0.001 TYR D 213 ARG 0.003 0.000 ARG C 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4888.12 seconds wall clock time: 88 minutes 30.17 seconds (5310.17 seconds total)