Starting phenix.real_space_refine on Mon Mar 18 12:58:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/03_2024/6pvm_20493.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/03_2024/6pvm_20493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/03_2024/6pvm_20493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/03_2024/6pvm_20493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/03_2024/6pvm_20493.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/03_2024/6pvm_20493.pdb" } resolution = 4.5 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= 0.011 sd= 0.247 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 13648 2.51 5 N 3480 2.21 5 O 3752 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 PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 712": "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 PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 696": "NH1" <-> "NH2" Residue "B ARG 712": "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 PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 696": "NH1" <-> "NH2" Residue "C ARG 712": "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 PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 696": "NH1" <-> "NH2" Residue "D ARG 712": "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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21006 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "B" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "C" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "D" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} 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: "C" 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: 10.88, per 1000 atoms: 0.52 Number of scatterers: 21006 At special positions: 0 Unit cell: (162.18, 162.18, 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 3752 8.00 N 3480 7.00 C 13648 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: 8.37 Conformation dependent library (CDL) restraints added in 3.7 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: 128 helices and 4 sheets defined 58.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.608A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.719A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.644A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.848A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.876A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.903A pdb=" N SER A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.599A pdb=" N GLU A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.649A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 420' Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.646A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 458 removed outlier: 3.536A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.777A pdb=" N HIS A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.507A pdb=" N HIS A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.540A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.617A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.609A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.720A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.848A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.660A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.877A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.903A pdb=" N SER B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.648A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 374' Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 420' Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 458 removed outlier: 3.536A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 540 removed outlier: 3.776A pdb=" N HIS B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 581 through 586 removed outlier: 4.506A pdb=" N HIS B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.617A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.609A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.720A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.847A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 removed outlier: 3.857A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.877A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.902A pdb=" N SER C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.648A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.998A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 374' Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.567A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 420' Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 458 removed outlier: 3.535A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 540 removed outlier: 3.776A pdb=" N HIS C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.628A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 581 through 586 removed outlier: 4.506A pdb=" N HIS C 585 " --> pdb=" O LYS C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 685 removed outlier: 3.638A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.616A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.608A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.719A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.847A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.876A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.901A pdb=" N SER D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.649A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.682A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 374' Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 458 removed outlier: 3.535A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 540 removed outlier: 3.777A pdb=" N HIS D 523 " --> pdb=" O ASP D 519 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 556 " --> pdb=" O VAL D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 581 through 586 removed outlier: 4.507A pdb=" N HIS D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 4.325A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 607 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.616A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (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 388 736 hydrogen bonds defined for protein. 2160 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: 6.19 Time building geometry restraints manager: 9.01 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: 6493 1.34 - 1.46: 4374 1.46 - 1.58: 10389 1.58 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21460 Sorted by residual: bond pdb=" C LEU A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.334 1.391 -0.058 2.34e-02 1.83e+03 6.04e+00 bond pdb=" C LEU B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.96e+00 bond pdb=" C LEU C 469 " pdb=" N PRO C 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.95e+00 bond pdb=" C LEU D 469 " pdb=" N PRO D 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.89e+00 bond pdb=" C ARG B 509 " pdb=" N PRO B 510 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.81e+00 ... (remaining 21455 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.50: 312 105.50 - 112.63: 10743 112.63 - 119.76: 7927 119.76 - 126.89: 9763 126.89 - 134.02: 287 Bond angle restraints: 29032 Sorted by residual: angle pdb=" C TRP B 739 " pdb=" N THR B 740 " pdb=" CA THR B 740 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" C TRP C 739 " pdb=" N THR C 740 " pdb=" CA THR C 740 " ideal model delta sigma weight residual 121.54 132.43 -10.89 1.91e+00 2.74e-01 3.25e+01 angle pdb=" C TRP A 739 " pdb=" N THR A 740 " pdb=" CA THR A 740 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C TRP D 739 " pdb=" N THR D 740 " pdb=" CA THR D 740 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" N ILE D 503 " pdb=" CA ILE D 503 " pdb=" C ILE D 503 " ideal model delta sigma weight residual 112.96 107.49 5.47 1.00e+00 1.00e+00 2.99e+01 ... (remaining 29027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 11556 14.98 - 29.97: 935 29.97 - 44.95: 309 44.95 - 59.93: 36 59.93 - 74.91: 20 Dihedral angle restraints: 12856 sinusoidal: 5252 harmonic: 7604 Sorted by residual: dihedral pdb=" CA HIS C 256 " pdb=" C HIS C 256 " pdb=" N GLU C 257 " pdb=" CA GLU C 257 " ideal model delta harmonic sigma weight residual -180.00 -135.43 -44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA HIS B 256 " pdb=" C HIS B 256 " pdb=" N GLU B 257 " pdb=" CA GLU B 257 " ideal model delta harmonic sigma weight residual -180.00 -135.43 -44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA HIS D 256 " pdb=" C HIS D 256 " pdb=" N GLU D 257 " pdb=" CA GLU D 257 " ideal model delta harmonic sigma weight residual -180.00 -135.49 -44.51 0 5.00e+00 4.00e-02 7.93e+01 ... (remaining 12853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2075 0.048 - 0.095: 908 0.095 - 0.143: 227 0.143 - 0.191: 81 0.191 - 0.238: 17 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CB ILE D 199 " pdb=" CA ILE D 199 " pdb=" CG1 ILE D 199 " pdb=" CG2 ILE D 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE B 199 " pdb=" CA ILE B 199 " pdb=" CG1 ILE B 199 " pdb=" CG2 ILE B 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 199 " pdb=" CA ILE A 199 " pdb=" CG1 ILE A 199 " pdb=" CG2 ILE A 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3305 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 754 " 0.052 5.00e-02 4.00e+02 7.82e-02 9.78e+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 " 0.043 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 7.79e-02 9.71e+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 B 754 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO B 755 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 755 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 755 " 0.042 5.00e-02 4.00e+02 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 636 2.70 - 3.25: 20772 3.25 - 3.80: 32076 3.80 - 4.35: 39228 4.35 - 4.90: 62291 Nonbonded interactions: 155003 Sorted by model distance: nonbonded pdb=" OE1 GLU A 751 " pdb=" OH TYR D 213 " model vdw 2.154 2.440 nonbonded pdb=" OH TYR C 213 " pdb=" OE1 GLU D 751 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR A 460 " pdb=" OG SER D 607 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR A 213 " pdb=" OE1 GLU B 751 " model vdw 2.254 2.440 nonbonded pdb=" OG SER A 607 " pdb=" OH TYR B 460 " model vdw 2.282 2.440 ... (remaining 154998 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' selection = (chain 'C' and resid 115 through 758) 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.880 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 54.630 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 0.060 21460 Z= 0.378 Angle : 1.184 14.755 29032 Z= 0.623 Chirality : 0.059 0.238 3308 Planarity : 0.007 0.078 3624 Dihedral : 12.600 74.915 7920 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.62 % Favored : 84.07 % Rotamer: Outliers : 0.87 % Allowed : 8.30 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -6.13 (0.11), residues: 2568 helix: -4.24 (0.07), residues: 1252 sheet: -4.71 (0.36), residues: 56 loop : -3.86 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 742 HIS 0.019 0.003 HIS D 471 PHE 0.019 0.003 PHE B 506 TYR 0.019 0.002 TYR C 382 ARG 0.014 0.001 ARG C 696 *********************** 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 1054 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1034 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8762 (mptt) REVERT: A 260 TYR cc_start: 0.8442 (t80) cc_final: 0.8200 (t80) REVERT: A 273 ASN cc_start: 0.8577 (t0) cc_final: 0.7620 (t0) REVERT: A 293 ASP cc_start: 0.7205 (m-30) cc_final: 0.6791 (m-30) REVERT: A 314 ASN cc_start: 0.7808 (t160) cc_final: 0.7151 (t0) REVERT: A 338 ASN cc_start: 0.7944 (p0) cc_final: 0.7605 (p0) REVERT: A 343 THR cc_start: 0.8524 (m) cc_final: 0.7646 (m) REVERT: A 355 GLU cc_start: 0.8470 (tp30) cc_final: 0.7864 (tp30) REVERT: A 376 LYS cc_start: 0.7677 (tptm) cc_final: 0.7091 (tptp) REVERT: A 409 TYR cc_start: 0.8676 (m-80) cc_final: 0.7195 (m-10) REVERT: A 439 TYR cc_start: 0.8277 (m-80) cc_final: 0.8076 (m-10) REVERT: A 440 MET cc_start: 0.7167 (mmt) cc_final: 0.6894 (tpp) REVERT: A 452 ASN cc_start: 0.9087 (m110) cc_final: 0.8871 (m110) REVERT: A 481 TRP cc_start: 0.5481 (t-100) cc_final: 0.4171 (t60) REVERT: A 539 LEU cc_start: 0.8638 (mt) cc_final: 0.8375 (mm) REVERT: A 542 PHE cc_start: 0.6804 (p90) cc_final: 0.6046 (p90) REVERT: A 574 MET cc_start: 0.8510 (mtp) cc_final: 0.8062 (ttm) REVERT: A 633 PHE cc_start: 0.8282 (t80) cc_final: 0.7424 (t80) REVERT: A 670 LEU cc_start: 0.9209 (mm) cc_final: 0.8757 (mm) REVERT: A 673 LEU cc_start: 0.9043 (tp) cc_final: 0.8833 (tp) REVERT: A 706 MET cc_start: 0.7200 (ttt) cc_final: 0.6596 (tpp) REVERT: B 121 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8741 (mptt) REVERT: B 260 TYR cc_start: 0.8456 (t80) cc_final: 0.8221 (t80) REVERT: B 273 ASN cc_start: 0.8566 (t0) cc_final: 0.7859 (t0) REVERT: B 293 ASP cc_start: 0.7226 (m-30) cc_final: 0.6827 (m-30) REVERT: B 314 ASN cc_start: 0.7666 (t160) cc_final: 0.7018 (t0) REVERT: B 338 ASN cc_start: 0.8050 (p0) cc_final: 0.7681 (p0) REVERT: B 343 THR cc_start: 0.8548 (m) cc_final: 0.7678 (m) REVERT: B 355 GLU cc_start: 0.8464 (tp30) cc_final: 0.7826 (tp30) REVERT: B 376 LYS cc_start: 0.7652 (tptm) cc_final: 0.7067 (tptp) REVERT: B 382 TYR cc_start: 0.5978 (t80) cc_final: 0.5768 (t80) REVERT: B 409 TYR cc_start: 0.8696 (m-80) cc_final: 0.7042 (m-10) REVERT: B 439 TYR cc_start: 0.8281 (m-80) cc_final: 0.8076 (m-10) REVERT: B 440 MET cc_start: 0.7164 (mmt) cc_final: 0.6844 (tpp) REVERT: B 452 ASN cc_start: 0.9053 (m110) cc_final: 0.8796 (m110) REVERT: B 481 TRP cc_start: 0.5429 (t-100) cc_final: 0.4094 (t60) REVERT: B 539 LEU cc_start: 0.8687 (mt) cc_final: 0.7912 (mt) REVERT: B 574 MET cc_start: 0.8531 (mtp) cc_final: 0.8019 (ttm) REVERT: B 633 PHE cc_start: 0.8232 (t80) cc_final: 0.7467 (t80) REVERT: B 670 LEU cc_start: 0.9223 (mm) cc_final: 0.8734 (mm) REVERT: B 673 LEU cc_start: 0.9055 (tp) cc_final: 0.8855 (tp) REVERT: B 703 PHE cc_start: 0.8839 (m-80) cc_final: 0.8636 (m-10) REVERT: B 758 ARG cc_start: 0.7358 (tpp80) cc_final: 0.6557 (ttt-90) REVERT: C 121 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8746 (mptt) REVERT: C 273 ASN cc_start: 0.8551 (t0) cc_final: 0.8179 (t0) REVERT: C 290 THR cc_start: 0.8548 (m) cc_final: 0.8340 (p) REVERT: C 293 ASP cc_start: 0.7309 (m-30) cc_final: 0.6913 (m-30) REVERT: C 314 ASN cc_start: 0.7627 (t160) cc_final: 0.7010 (t0) REVERT: C 338 ASN cc_start: 0.8020 (p0) cc_final: 0.7613 (p0) REVERT: C 343 THR cc_start: 0.8516 (m) cc_final: 0.7570 (m) REVERT: C 355 GLU cc_start: 0.8462 (tp30) cc_final: 0.7864 (tp30) REVERT: C 376 LYS cc_start: 0.7643 (tptm) cc_final: 0.7163 (tptp) REVERT: C 382 TYR cc_start: 0.6090 (t80) cc_final: 0.5804 (t80) REVERT: C 409 TYR cc_start: 0.8706 (m-80) cc_final: 0.7190 (m-10) REVERT: C 440 MET cc_start: 0.7139 (mmt) cc_final: 0.6841 (tpp) REVERT: C 452 ASN cc_start: 0.9069 (m110) cc_final: 0.8844 (m110) REVERT: C 481 TRP cc_start: 0.5410 (t-100) cc_final: 0.4216 (t60) REVERT: C 539 LEU cc_start: 0.8646 (mt) cc_final: 0.7934 (mt) REVERT: C 542 PHE cc_start: 0.6855 (p90) cc_final: 0.6168 (p90) REVERT: C 555 MET cc_start: 0.9113 (mtt) cc_final: 0.8909 (mtp) REVERT: C 574 MET cc_start: 0.8488 (mtp) cc_final: 0.8017 (ttm) REVERT: C 642 LEU cc_start: 0.7718 (pt) cc_final: 0.7494 (pt) REVERT: C 650 TYR cc_start: 0.5023 (m-10) cc_final: 0.4407 (t80) REVERT: C 673 LEU cc_start: 0.9053 (tp) cc_final: 0.8502 (tp) REVERT: C 684 VAL cc_start: 0.9184 (t) cc_final: 0.8911 (t) REVERT: C 706 MET cc_start: 0.7190 (ttt) cc_final: 0.6432 (tpp) REVERT: C 735 ASN cc_start: 0.8160 (m-40) cc_final: 0.7833 (p0) REVERT: C 758 ARG cc_start: 0.7457 (tpp80) cc_final: 0.6378 (ttt-90) REVERT: D 121 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8715 (mptt) REVERT: D 273 ASN cc_start: 0.8542 (t0) cc_final: 0.7441 (t0) REVERT: D 293 ASP cc_start: 0.7294 (m-30) cc_final: 0.6888 (m-30) REVERT: D 314 ASN cc_start: 0.7795 (t160) cc_final: 0.7133 (t0) REVERT: D 342 LEU cc_start: 0.8296 (pt) cc_final: 0.8063 (pp) REVERT: D 355 GLU cc_start: 0.8463 (tp30) cc_final: 0.7903 (tp30) REVERT: D 370 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (pp) REVERT: D 376 LYS cc_start: 0.7620 (tptm) cc_final: 0.6956 (tptp) REVERT: D 409 TYR cc_start: 0.8697 (m-80) cc_final: 0.7516 (m-10) REVERT: D 440 MET cc_start: 0.7203 (mmt) cc_final: 0.6900 (tpp) REVERT: D 452 ASN cc_start: 0.9046 (m110) cc_final: 0.8806 (m110) REVERT: D 481 TRP cc_start: 0.5303 (t-100) cc_final: 0.3682 (t60) REVERT: D 534 ILE cc_start: 0.9145 (tp) cc_final: 0.8875 (tp) REVERT: D 539 LEU cc_start: 0.8619 (mt) cc_final: 0.8336 (mm) REVERT: D 542 PHE cc_start: 0.6814 (p90) cc_final: 0.6061 (p90) REVERT: D 574 MET cc_start: 0.8506 (mtp) cc_final: 0.8071 (ttm) REVERT: D 633 PHE cc_start: 0.8068 (t80) cc_final: 0.7299 (t80) REVERT: D 650 TYR cc_start: 0.4870 (m-10) cc_final: 0.4411 (t80) REVERT: D 670 LEU cc_start: 0.9210 (mm) cc_final: 0.8729 (mm) REVERT: D 673 LEU cc_start: 0.9048 (tp) cc_final: 0.8546 (tp) REVERT: D 684 VAL cc_start: 0.9176 (t) cc_final: 0.8934 (t) REVERT: D 706 MET cc_start: 0.7213 (ttt) cc_final: 0.6589 (tpp) REVERT: D 735 ASN cc_start: 0.8174 (m-40) cc_final: 0.6766 (m-40) outliers start: 20 outliers final: 4 residues processed: 1049 average time/residue: 0.3075 time to fit residues: 493.5818 Evaluate side-chains 769 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 764 time to evaluate : 2.510 ------------------------------------------------------------------------------- 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: 4.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 232 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 452 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 452 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 313 GLN C 452 ASN C 647 ASN D 160 HIS D 313 GLN D 417 HIS D 452 ASN D 647 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21460 Z= 0.257 Angle : 0.819 10.777 29032 Z= 0.419 Chirality : 0.044 0.140 3308 Planarity : 0.006 0.068 3624 Dihedral : 7.287 35.693 2808 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.41 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.14), residues: 2568 helix: -2.15 (0.12), residues: 1280 sheet: -3.90 (0.41), residues: 76 loop : -3.62 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 742 HIS 0.010 0.002 HIS B 160 PHE 0.025 0.002 PHE B 249 TYR 0.017 0.002 TYR D 460 ARG 0.003 0.001 ARG C 295 *********************** 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 782 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 782 time to evaluate : 2.492 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 121 LYS cc_start: 0.9157 (mmmt) cc_final: 0.8787 (mptt) REVERT: A 122 ARG cc_start: 0.8682 (ttt90) cc_final: 0.8394 (ttp-110) REVERT: A 170 THR cc_start: 0.8938 (p) cc_final: 0.8329 (p) REVERT: A 260 TYR cc_start: 0.8692 (t80) cc_final: 0.8434 (t80) REVERT: A 282 MET cc_start: 0.8243 (tmm) cc_final: 0.8022 (tpp) REVERT: A 293 ASP cc_start: 0.6844 (m-30) cc_final: 0.6466 (m-30) REVERT: A 338 ASN cc_start: 0.8247 (p0) cc_final: 0.7947 (p0) REVERT: A 342 LEU cc_start: 0.8384 (pt) cc_final: 0.7740 (pp) REVERT: A 355 GLU cc_start: 0.8458 (tp30) cc_final: 0.7969 (tp30) REVERT: A 409 TYR cc_start: 0.8072 (m-80) cc_final: 0.7274 (m-80) REVERT: A 544 TYR cc_start: 0.5435 (t80) cc_final: 0.4802 (t80) REVERT: A 546 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 555 MET cc_start: 0.9359 (mtt) cc_final: 0.8963 (mtt) REVERT: A 574 MET cc_start: 0.8579 (mtp) cc_final: 0.8097 (ttm) REVERT: A 576 SER cc_start: 0.9224 (t) cc_final: 0.8770 (p) REVERT: A 578 MET cc_start: 0.8568 (tpp) cc_final: 0.8161 (mmt) REVERT: A 650 TYR cc_start: 0.5003 (m-10) cc_final: 0.4440 (t80) REVERT: A 663 ILE cc_start: 0.9049 (tp) cc_final: 0.8844 (tp) REVERT: A 669 LEU cc_start: 0.9394 (mt) cc_final: 0.9184 (mt) REVERT: A 681 VAL cc_start: 0.8429 (t) cc_final: 0.7895 (t) REVERT: A 699 THR cc_start: 0.9172 (t) cc_final: 0.8966 (m) REVERT: A 702 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7939 (mm-30) REVERT: A 705 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8432 (mttt) REVERT: A 706 MET cc_start: 0.7511 (ttt) cc_final: 0.6937 (tpp) REVERT: A 717 MET cc_start: 0.8252 (mtp) cc_final: 0.7621 (mtp) REVERT: A 732 LEU cc_start: 0.8956 (mt) cc_final: 0.8741 (mt) REVERT: A 735 ASN cc_start: 0.8210 (m110) cc_final: 0.7485 (m-40) REVERT: B 121 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8783 (mptt) REVERT: B 122 ARG cc_start: 0.8675 (ttt90) cc_final: 0.8381 (ttp-110) REVERT: B 170 THR cc_start: 0.8956 (p) cc_final: 0.8348 (p) REVERT: B 260 TYR cc_start: 0.8687 (t80) cc_final: 0.8449 (t80) REVERT: B 293 ASP cc_start: 0.6944 (m-30) cc_final: 0.6586 (m-30) REVERT: B 338 ASN cc_start: 0.8329 (p0) cc_final: 0.7988 (p0) REVERT: B 342 LEU cc_start: 0.8395 (pt) cc_final: 0.7693 (pp) REVERT: B 355 GLU cc_start: 0.8453 (tp30) cc_final: 0.7983 (tp30) REVERT: B 409 TYR cc_start: 0.8024 (m-80) cc_final: 0.7688 (m-80) REVERT: B 555 MET cc_start: 0.9343 (mtt) cc_final: 0.8945 (mtt) REVERT: B 574 MET cc_start: 0.8587 (mtp) cc_final: 0.8016 (ttm) REVERT: B 576 SER cc_start: 0.9217 (t) cc_final: 0.8779 (p) REVERT: B 650 TYR cc_start: 0.4855 (m-10) cc_final: 0.4339 (t80) REVERT: B 669 LEU cc_start: 0.9382 (mt) cc_final: 0.9157 (mt) REVERT: B 681 VAL cc_start: 0.8334 (t) cc_final: 0.8116 (t) REVERT: B 702 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8209 (mm-30) REVERT: B 705 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8473 (mttt) REVERT: B 706 MET cc_start: 0.8124 (tpt) cc_final: 0.7176 (tpp) REVERT: C 121 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8776 (mptt) REVERT: C 170 THR cc_start: 0.8992 (p) cc_final: 0.8352 (p) REVERT: C 260 TYR cc_start: 0.8701 (t80) cc_final: 0.8484 (t80) REVERT: C 282 MET cc_start: 0.8229 (tmm) cc_final: 0.7780 (tpp) REVERT: C 293 ASP cc_start: 0.7254 (m-30) cc_final: 0.6867 (m-30) REVERT: C 355 GLU cc_start: 0.8437 (tp30) cc_final: 0.7999 (tp30) REVERT: C 373 LEU cc_start: 0.8703 (mp) cc_final: 0.8437 (mp) REVERT: C 409 TYR cc_start: 0.8074 (m-80) cc_final: 0.7272 (m-80) REVERT: C 443 LEU cc_start: 0.8863 (tt) cc_final: 0.8647 (mm) REVERT: C 544 TYR cc_start: 0.4964 (t80) cc_final: 0.4410 (t80) REVERT: C 555 MET cc_start: 0.9307 (mtt) cc_final: 0.8900 (mtt) REVERT: C 574 MET cc_start: 0.8585 (mtp) cc_final: 0.7955 (ttm) REVERT: C 650 TYR cc_start: 0.4879 (m-10) cc_final: 0.4464 (t80) REVERT: C 695 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8915 (mm-40) REVERT: C 699 THR cc_start: 0.9147 (t) cc_final: 0.8893 (m) REVERT: C 702 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7904 (mm-30) REVERT: C 705 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8425 (mttt) REVERT: C 706 MET cc_start: 0.7505 (ttt) cc_final: 0.6899 (tpp) REVERT: C 735 ASN cc_start: 0.8119 (m-40) cc_final: 0.7881 (m-40) REVERT: D 121 LYS cc_start: 0.9124 (mmmt) cc_final: 0.8760 (mptt) REVERT: D 170 THR cc_start: 0.8975 (p) cc_final: 0.8356 (p) REVERT: D 260 TYR cc_start: 0.8717 (t80) cc_final: 0.8505 (t80) REVERT: D 293 ASP cc_start: 0.7106 (m-30) cc_final: 0.6737 (m-30) REVERT: D 355 GLU cc_start: 0.8449 (tp30) cc_final: 0.8016 (tp30) REVERT: D 373 LEU cc_start: 0.8703 (mp) cc_final: 0.8428 (mp) REVERT: D 376 LYS cc_start: 0.7647 (tptm) cc_final: 0.7426 (tptp) REVERT: D 405 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7912 (tm-30) REVERT: D 409 TYR cc_start: 0.8068 (m-80) cc_final: 0.7114 (m-80) REVERT: D 481 TRP cc_start: 0.5037 (t-100) cc_final: 0.3393 (t60) REVERT: D 544 TYR cc_start: 0.5334 (t80) cc_final: 0.4695 (t80) REVERT: D 546 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7430 (mt-10) REVERT: D 555 MET cc_start: 0.9333 (mtt) cc_final: 0.8881 (mtt) REVERT: D 574 MET cc_start: 0.8597 (mtp) cc_final: 0.8370 (mtp) REVERT: D 650 TYR cc_start: 0.4875 (m-10) cc_final: 0.4492 (t80) REVERT: D 663 ILE cc_start: 0.9084 (tp) cc_final: 0.8884 (tp) REVERT: D 669 LEU cc_start: 0.9390 (mt) cc_final: 0.9184 (mt) REVERT: D 681 VAL cc_start: 0.8377 (p) cc_final: 0.8066 (p) REVERT: D 695 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8918 (mm-40) REVERT: D 699 THR cc_start: 0.9172 (t) cc_final: 0.8917 (m) REVERT: D 702 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7906 (mm-30) REVERT: D 705 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8415 (mttt) REVERT: D 706 MET cc_start: 0.7577 (ttt) cc_final: 0.7096 (tpp) REVERT: D 735 ASN cc_start: 0.8100 (m-40) cc_final: 0.7867 (m-40) outliers start: 0 outliers final: 0 residues processed: 782 average time/residue: 0.2890 time to fit residues: 356.8179 Evaluate side-chains 679 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 679 time to evaluate : 2.465 ------------------------------------------------------------------------------- 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: 8.9990 chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 232 optimal weight: 30.0000 chunk 251 optimal weight: 0.0670 chunk 207 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 overall best weight: 4.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 695 GLN B 647 ASN B 695 GLN C 279 GLN C 417 HIS ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21460 Z= 0.236 Angle : 0.763 10.153 29032 Z= 0.389 Chirality : 0.043 0.148 3308 Planarity : 0.005 0.066 3624 Dihedral : 6.994 37.024 2808 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.45 % Favored : 85.24 % Rotamer: Outliers : 0.17 % Allowed : 4.57 % Favored : 95.26 % 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: -3.35 (0.16), residues: 2568 helix: -1.20 (0.14), residues: 1312 sheet: -4.10 (0.41), residues: 76 loop : -3.35 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 742 HIS 0.009 0.001 HIS A 471 PHE 0.024 0.002 PHE D 633 TYR 0.016 0.001 TYR C 382 ARG 0.004 0.000 ARG A 733 *********************** 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 766 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 762 time to evaluate : 2.556 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 121 LYS cc_start: 0.9168 (mmmt) cc_final: 0.8799 (mptt) REVERT: A 122 ARG cc_start: 0.8666 (ttt90) cc_final: 0.8329 (ttp-110) REVERT: A 338 ASN cc_start: 0.8290 (p0) cc_final: 0.7936 (p0) REVERT: A 342 LEU cc_start: 0.8495 (pt) cc_final: 0.7681 (pp) REVERT: A 355 GLU cc_start: 0.8497 (tp30) cc_final: 0.8057 (tp30) REVERT: A 391 ASP cc_start: 0.8062 (t70) cc_final: 0.7829 (t70) REVERT: A 409 TYR cc_start: 0.7959 (m-80) cc_final: 0.7299 (m-80) REVERT: A 481 TRP cc_start: 0.6235 (m100) cc_final: 0.5313 (t-100) REVERT: A 555 MET cc_start: 0.9382 (mtt) cc_final: 0.8999 (mtt) REVERT: A 567 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.8048 (ptp-110) REVERT: A 574 MET cc_start: 0.8521 (mtp) cc_final: 0.8008 (ttm) REVERT: A 576 SER cc_start: 0.9136 (t) cc_final: 0.8640 (p) REVERT: A 630 LEU cc_start: 0.9368 (mm) cc_final: 0.9153 (mm) REVERT: A 650 TYR cc_start: 0.4693 (m-10) cc_final: 0.4255 (t80) REVERT: A 695 GLN cc_start: 0.8779 (tp40) cc_final: 0.8022 (mm-40) REVERT: A 699 THR cc_start: 0.9229 (t) cc_final: 0.8986 (m) REVERT: A 702 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 705 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8460 (mttt) REVERT: A 706 MET cc_start: 0.7901 (ttt) cc_final: 0.7112 (tpp) REVERT: A 717 MET cc_start: 0.8285 (mtp) cc_final: 0.7704 (mtp) REVERT: A 722 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7386 (mtmt) REVERT: B 121 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8801 (mptt) REVERT: B 122 ARG cc_start: 0.8659 (ttt90) cc_final: 0.8393 (ttp-110) REVERT: B 132 VAL cc_start: 0.7906 (t) cc_final: 0.7697 (t) REVERT: B 338 ASN cc_start: 0.8265 (p0) cc_final: 0.7916 (p0) REVERT: B 342 LEU cc_start: 0.8510 (pt) cc_final: 0.8100 (pp) REVERT: B 355 GLU cc_start: 0.8453 (tp30) cc_final: 0.8038 (tp30) REVERT: B 409 TYR cc_start: 0.8043 (m-80) cc_final: 0.7541 (m-80) REVERT: B 440 MET cc_start: 0.7384 (mmt) cc_final: 0.7094 (tpp) REVERT: B 481 TRP cc_start: 0.6132 (m100) cc_final: 0.5224 (t-100) REVERT: B 555 MET cc_start: 0.9365 (mtt) cc_final: 0.8967 (mtt) REVERT: B 562 MET cc_start: 0.8687 (ppp) cc_final: 0.7911 (ppp) REVERT: B 567 ARG cc_start: 0.8693 (mtt-85) cc_final: 0.8059 (ptp-110) REVERT: B 576 SER cc_start: 0.9114 (t) cc_final: 0.8616 (p) REVERT: B 650 TYR cc_start: 0.4715 (m-10) cc_final: 0.4248 (t80) REVERT: B 674 ILE cc_start: 0.9266 (mm) cc_final: 0.9037 (mm) REVERT: B 676 LEU cc_start: 0.9092 (tt) cc_final: 0.8803 (tt) REVERT: B 695 GLN cc_start: 0.8821 (tp40) cc_final: 0.8045 (mm-40) REVERT: B 702 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8294 (mm-30) REVERT: B 722 LYS cc_start: 0.8270 (mtmt) cc_final: 0.7561 (mtmt) REVERT: C 121 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8746 (mptt) REVERT: C 260 TYR cc_start: 0.8662 (t80) cc_final: 0.8456 (t80) REVERT: C 327 ARG cc_start: 0.7570 (tpp-160) cc_final: 0.7209 (tpp-160) REVERT: C 338 ASN cc_start: 0.7954 (p0) cc_final: 0.7725 (p0) REVERT: C 355 GLU cc_start: 0.8475 (tp30) cc_final: 0.8028 (tp30) REVERT: C 391 ASP cc_start: 0.8144 (t70) cc_final: 0.7876 (t70) REVERT: C 409 TYR cc_start: 0.7959 (m-80) cc_final: 0.7280 (m-80) REVERT: C 544 TYR cc_start: 0.5359 (t80) cc_final: 0.4697 (t80) REVERT: C 555 MET cc_start: 0.9320 (mtt) cc_final: 0.8975 (mtt) REVERT: C 574 MET cc_start: 0.8518 (mtp) cc_final: 0.8055 (ttm) REVERT: C 576 SER cc_start: 0.9139 (t) cc_final: 0.8672 (p) REVERT: C 676 LEU cc_start: 0.8964 (tt) cc_final: 0.8763 (tt) REVERT: C 695 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8872 (mm-40) REVERT: C 699 THR cc_start: 0.9137 (t) cc_final: 0.8905 (m) REVERT: C 702 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8103 (mm-30) REVERT: C 705 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8362 (mttt) REVERT: C 706 MET cc_start: 0.7852 (ttt) cc_final: 0.7056 (tpp) REVERT: D 121 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8749 (mptt) REVERT: D 293 ASP cc_start: 0.7189 (m-30) cc_final: 0.6670 (m-30) REVERT: D 342 LEU cc_start: 0.8234 (pt) cc_final: 0.7855 (pp) REVERT: D 346 GLN cc_start: 0.9161 (mp10) cc_final: 0.8867 (mt0) REVERT: D 355 GLU cc_start: 0.8447 (tp30) cc_final: 0.8060 (tp30) REVERT: D 376 LYS cc_start: 0.7757 (tptm) cc_final: 0.7313 (tptp) REVERT: D 391 ASP cc_start: 0.8170 (t70) cc_final: 0.7850 (t70) REVERT: D 409 TYR cc_start: 0.8004 (m-80) cc_final: 0.7261 (m-80) REVERT: D 481 TRP cc_start: 0.5211 (t-100) cc_final: 0.3595 (t60) REVERT: D 544 TYR cc_start: 0.5615 (t80) cc_final: 0.4955 (t80) REVERT: D 546 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7618 (mt-10) REVERT: D 555 MET cc_start: 0.9363 (mtt) cc_final: 0.9026 (mtt) REVERT: D 574 MET cc_start: 0.8514 (mtp) cc_final: 0.8006 (ttm) REVERT: D 576 SER cc_start: 0.9157 (t) cc_final: 0.8692 (p) REVERT: D 650 TYR cc_start: 0.4649 (m-10) cc_final: 0.4448 (t80) REVERT: D 672 MET cc_start: 0.8797 (mmp) cc_final: 0.8503 (mmt) REVERT: D 676 LEU cc_start: 0.8840 (tt) cc_final: 0.8632 (tt) REVERT: D 695 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8879 (mm-40) REVERT: D 702 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7976 (mm-30) REVERT: D 705 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8427 (mttt) REVERT: D 706 MET cc_start: 0.7855 (ttt) cc_final: 0.7132 (tpp) outliers start: 4 outliers final: 4 residues processed: 766 average time/residue: 0.2837 time to fit residues: 344.0757 Evaluate side-chains 641 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 637 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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: 5.9990 chunk 175 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 221 optimal weight: 0.0060 chunk 66 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 292 GLN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 314 ASN C 417 HIS C 647 ASN D 160 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 417 HIS D 647 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21460 Z= 0.193 Angle : 0.734 10.046 29032 Z= 0.370 Chirality : 0.043 0.150 3308 Planarity : 0.005 0.064 3624 Dihedral : 6.672 34.931 2808 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.52 % Favored : 85.16 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.01 (0.16), residues: 2568 helix: -0.82 (0.14), residues: 1320 sheet: -4.17 (0.42), residues: 76 loop : -3.32 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 742 HIS 0.010 0.001 HIS C 160 PHE 0.020 0.002 PHE D 625 TYR 0.014 0.001 TYR D 382 ARG 0.004 0.000 ARG B 327 *********************** 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 743 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 743 time to evaluate : 2.514 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 121 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8817 (mptt) REVERT: A 122 ARG cc_start: 0.8689 (ttt90) cc_final: 0.8376 (ttp-110) REVERT: A 135 LEU cc_start: 0.8760 (tp) cc_final: 0.8498 (tp) REVERT: A 263 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6616 (mt-10) REVERT: A 338 ASN cc_start: 0.8198 (p0) cc_final: 0.7588 (p0) REVERT: A 342 LEU cc_start: 0.8014 (pt) cc_final: 0.7668 (pp) REVERT: A 347 LEU cc_start: 0.9300 (tp) cc_final: 0.9098 (tp) REVERT: A 355 GLU cc_start: 0.8432 (tp30) cc_final: 0.8013 (tp30) REVERT: A 391 ASP cc_start: 0.7964 (t70) cc_final: 0.7749 (t70) REVERT: A 405 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7973 (tm-30) REVERT: A 409 TYR cc_start: 0.7953 (m-80) cc_final: 0.7008 (m-80) REVERT: A 481 TRP cc_start: 0.6028 (m100) cc_final: 0.5121 (t-100) REVERT: A 542 PHE cc_start: 0.6894 (p90) cc_final: 0.6284 (p90) REVERT: A 555 MET cc_start: 0.9349 (mtt) cc_final: 0.9024 (mtt) REVERT: A 569 PHE cc_start: 0.7560 (m-10) cc_final: 0.7291 (m-10) REVERT: A 574 MET cc_start: 0.8432 (mtp) cc_final: 0.7995 (ttm) REVERT: A 576 SER cc_start: 0.9088 (t) cc_final: 0.8572 (p) REVERT: A 650 TYR cc_start: 0.4636 (m-10) cc_final: 0.4332 (t80) REVERT: A 672 MET cc_start: 0.8638 (mmp) cc_final: 0.8412 (mmp) REVERT: A 695 GLN cc_start: 0.8846 (tp40) cc_final: 0.8125 (mm-40) REVERT: A 699 THR cc_start: 0.9201 (t) cc_final: 0.8951 (m) REVERT: A 702 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 705 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8440 (mttt) REVERT: A 706 MET cc_start: 0.7811 (ttt) cc_final: 0.7168 (tpp) REVERT: A 722 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7387 (mtmt) REVERT: B 121 LYS cc_start: 0.9157 (mmmt) cc_final: 0.8800 (mptt) REVERT: B 263 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6613 (mt-10) REVERT: B 338 ASN cc_start: 0.7714 (p0) cc_final: 0.7498 (p0) REVERT: B 342 LEU cc_start: 0.8027 (pt) cc_final: 0.7665 (pp) REVERT: B 355 GLU cc_start: 0.8409 (tp30) cc_final: 0.7979 (tp30) REVERT: B 359 TYR cc_start: 0.8250 (t80) cc_final: 0.7482 (t80) REVERT: B 391 ASP cc_start: 0.7977 (t70) cc_final: 0.7705 (t70) REVERT: B 405 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 409 TYR cc_start: 0.8029 (m-80) cc_final: 0.7334 (m-80) REVERT: B 440 MET cc_start: 0.7503 (mmt) cc_final: 0.7164 (tpp) REVERT: B 481 TRP cc_start: 0.6064 (m100) cc_final: 0.5161 (t-100) REVERT: B 555 MET cc_start: 0.9339 (mtt) cc_final: 0.9019 (mtt) REVERT: B 574 MET cc_start: 0.8426 (mtp) cc_final: 0.7736 (tpp) REVERT: B 576 SER cc_start: 0.9083 (t) cc_final: 0.8588 (p) REVERT: B 630 LEU cc_start: 0.9333 (mm) cc_final: 0.9123 (mm) REVERT: B 650 TYR cc_start: 0.4707 (m-10) cc_final: 0.4421 (t80) REVERT: B 702 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8181 (mm-30) REVERT: B 722 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7273 (mtmt) REVERT: C 121 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8722 (mptt) REVERT: C 135 LEU cc_start: 0.8719 (tp) cc_final: 0.8502 (tp) REVERT: C 338 ASN cc_start: 0.7927 (p0) cc_final: 0.7659 (p0) REVERT: C 343 THR cc_start: 0.8128 (m) cc_final: 0.7577 (m) REVERT: C 355 GLU cc_start: 0.8408 (tp30) cc_final: 0.7977 (tp30) REVERT: C 391 ASP cc_start: 0.8091 (t70) cc_final: 0.7783 (t70) REVERT: C 405 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 409 TYR cc_start: 0.7971 (m-80) cc_final: 0.7044 (m-80) REVERT: C 555 MET cc_start: 0.9329 (mtt) cc_final: 0.9061 (mtt) REVERT: C 567 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.8054 (ptp-110) REVERT: C 574 MET cc_start: 0.8487 (mtp) cc_final: 0.7903 (ttm) REVERT: C 576 SER cc_start: 0.9133 (t) cc_final: 0.8647 (p) REVERT: C 625 PHE cc_start: 0.6872 (t80) cc_final: 0.6242 (t80) REVERT: C 634 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7600 (ttmt) REVERT: C 677 MET cc_start: 0.9164 (mmm) cc_final: 0.8961 (mmm) REVERT: C 699 THR cc_start: 0.9175 (t) cc_final: 0.8975 (p) REVERT: C 702 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8008 (mm-30) REVERT: C 705 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8422 (mttt) REVERT: C 706 MET cc_start: 0.7766 (ttt) cc_final: 0.7135 (tpp) REVERT: C 722 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7204 (mtmt) REVERT: C 732 LEU cc_start: 0.8631 (mt) cc_final: 0.8336 (mt) REVERT: C 733 ARG cc_start: 0.6728 (mtp-110) cc_final: 0.6346 (ptm160) REVERT: D 121 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8771 (mptt) REVERT: D 273 ASN cc_start: 0.8601 (t0) cc_final: 0.7795 (t0) REVERT: D 293 ASP cc_start: 0.6987 (m-30) cc_final: 0.6688 (m-30) REVERT: D 342 LEU cc_start: 0.7954 (pt) cc_final: 0.7753 (pp) REVERT: D 343 THR cc_start: 0.8023 (m) cc_final: 0.7653 (m) REVERT: D 355 GLU cc_start: 0.8400 (tp30) cc_final: 0.8030 (tp30) REVERT: D 376 LYS cc_start: 0.7694 (tptm) cc_final: 0.7364 (tptp) REVERT: D 391 ASP cc_start: 0.8140 (t70) cc_final: 0.7935 (t70) REVERT: D 409 TYR cc_start: 0.7948 (m-80) cc_final: 0.7036 (m-10) REVERT: D 481 TRP cc_start: 0.5320 (t-100) cc_final: 0.3633 (t60) REVERT: D 555 MET cc_start: 0.9374 (mtt) cc_final: 0.9121 (mtt) REVERT: D 567 ARG cc_start: 0.8562 (mtt-85) cc_final: 0.8004 (ptp-110) REVERT: D 625 PHE cc_start: 0.6922 (t80) cc_final: 0.6356 (t80) REVERT: D 634 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7821 (mtmt) REVERT: D 677 MET cc_start: 0.9134 (mmm) cc_final: 0.8915 (mmm) REVERT: D 699 THR cc_start: 0.9144 (t) cc_final: 0.8920 (p) REVERT: D 702 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7959 (mm-30) REVERT: D 705 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8458 (mttt) REVERT: D 706 MET cc_start: 0.7778 (ttt) cc_final: 0.7210 (tpp) REVERT: D 722 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7282 (mtmt) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 0.2944 time to fit residues: 343.7901 Evaluate side-chains 650 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 650 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 222 optimal weight: 0.0770 chunk 62 optimal weight: 8.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 417 HIS A 471 HIS ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 417 HIS B 647 ASN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 417 HIS C 647 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 647 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21460 Z= 0.223 Angle : 0.754 9.886 29032 Z= 0.377 Chirality : 0.044 0.153 3308 Planarity : 0.005 0.063 3624 Dihedral : 6.605 35.056 2808 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.07 % Favored : 84.62 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.95 (0.17), residues: 2568 helix: -0.72 (0.14), residues: 1352 sheet: -4.06 (0.43), residues: 72 loop : -3.44 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 742 HIS 0.013 0.001 HIS A 471 PHE 0.019 0.002 PHE A 625 TYR 0.016 0.001 TYR C 650 ARG 0.013 0.000 ARG A 733 *********************** 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 737 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 737 time to evaluate : 2.743 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 121 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8812 (mptt) REVERT: A 122 ARG cc_start: 0.8609 (ttt90) cc_final: 0.8288 (ttp-110) REVERT: A 135 LEU cc_start: 0.8876 (tp) cc_final: 0.8540 (tp) REVERT: A 338 ASN cc_start: 0.8214 (p0) cc_final: 0.7712 (p0) REVERT: A 342 LEU cc_start: 0.7862 (pt) cc_final: 0.7603 (pp) REVERT: A 355 GLU cc_start: 0.8508 (tp30) cc_final: 0.8209 (tp30) REVERT: A 356 ILE cc_start: 0.9634 (tt) cc_final: 0.9429 (mm) REVERT: A 376 LYS cc_start: 0.7468 (tptm) cc_final: 0.7101 (tptp) REVERT: A 481 TRP cc_start: 0.6003 (m100) cc_final: 0.5131 (t-100) REVERT: A 555 MET cc_start: 0.9348 (mtt) cc_final: 0.9097 (mtt) REVERT: A 569 PHE cc_start: 0.7537 (m-10) cc_final: 0.7170 (m-10) REVERT: A 574 MET cc_start: 0.8479 (mtp) cc_final: 0.8172 (ttm) REVERT: A 677 MET cc_start: 0.9251 (mmm) cc_final: 0.9048 (mmm) REVERT: A 699 THR cc_start: 0.9157 (t) cc_final: 0.8872 (m) REVERT: A 702 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8419 (mm-30) REVERT: A 705 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8463 (mttt) REVERT: A 706 MET cc_start: 0.7767 (ttt) cc_final: 0.6805 (tpp) REVERT: A 722 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7165 (mtmt) REVERT: A 730 LEU cc_start: 0.8452 (mp) cc_final: 0.8094 (mp) REVERT: B 121 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8809 (mptt) REVERT: B 132 VAL cc_start: 0.8029 (t) cc_final: 0.7794 (t) REVERT: B 327 ARG cc_start: 0.7497 (tpp-160) cc_final: 0.7275 (tpp-160) REVERT: B 338 ASN cc_start: 0.8131 (p0) cc_final: 0.7704 (p0) REVERT: B 342 LEU cc_start: 0.7942 (pt) cc_final: 0.7643 (pp) REVERT: B 355 GLU cc_start: 0.8498 (tp30) cc_final: 0.8206 (tp30) REVERT: B 356 ILE cc_start: 0.9633 (tt) cc_final: 0.9426 (mm) REVERT: B 376 LYS cc_start: 0.7517 (tptm) cc_final: 0.7180 (tptp) REVERT: B 391 ASP cc_start: 0.7982 (t70) cc_final: 0.7704 (t70) REVERT: B 409 TYR cc_start: 0.8003 (m-80) cc_final: 0.7180 (m-80) REVERT: B 440 MET cc_start: 0.7357 (mmt) cc_final: 0.7034 (tpp) REVERT: B 481 TRP cc_start: 0.5935 (m100) cc_final: 0.5096 (t-100) REVERT: B 552 VAL cc_start: 0.9583 (p) cc_final: 0.9374 (p) REVERT: B 555 MET cc_start: 0.9349 (mtt) cc_final: 0.9020 (mtt) REVERT: B 574 MET cc_start: 0.8521 (mtp) cc_final: 0.7681 (tpp) REVERT: B 625 PHE cc_start: 0.6954 (t80) cc_final: 0.6301 (t80) REVERT: B 650 TYR cc_start: 0.4580 (m-10) cc_final: 0.4377 (t80) REVERT: B 695 GLN cc_start: 0.9000 (tp40) cc_final: 0.8587 (mm-40) REVERT: B 702 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8043 (mm-30) REVERT: B 730 LEU cc_start: 0.8764 (mp) cc_final: 0.8472 (mp) REVERT: C 121 LYS cc_start: 0.9102 (mmmt) cc_final: 0.8757 (mptt) REVERT: C 135 LEU cc_start: 0.8760 (tp) cc_final: 0.8548 (tp) REVERT: C 338 ASN cc_start: 0.8002 (p0) cc_final: 0.7685 (p0) REVERT: C 355 GLU cc_start: 0.8451 (tp30) cc_final: 0.8070 (tp30) REVERT: C 409 TYR cc_start: 0.7956 (m-80) cc_final: 0.7183 (m-80) REVERT: C 481 TRP cc_start: 0.4570 (m-90) cc_final: 0.4235 (t-100) REVERT: C 555 MET cc_start: 0.9340 (mtt) cc_final: 0.9088 (mtt) REVERT: C 567 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8111 (ptp-110) REVERT: C 574 MET cc_start: 0.8427 (mtp) cc_final: 0.7882 (ttm) REVERT: C 625 PHE cc_start: 0.6714 (t80) cc_final: 0.6073 (t80) REVERT: C 634 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7871 (ttmt) REVERT: C 642 LEU cc_start: 0.6903 (pt) cc_final: 0.6669 (pt) REVERT: C 677 MET cc_start: 0.9146 (mmm) cc_final: 0.8906 (mmm) REVERT: C 702 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8212 (mm-30) REVERT: C 705 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8470 (mttt) REVERT: C 706 MET cc_start: 0.7748 (ttt) cc_final: 0.6790 (tpp) REVERT: C 722 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7292 (mtmt) REVERT: C 730 LEU cc_start: 0.8592 (mp) cc_final: 0.8310 (mp) REVERT: D 121 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8761 (mptt) REVERT: D 135 LEU cc_start: 0.8739 (tp) cc_final: 0.8534 (tp) REVERT: D 273 ASN cc_start: 0.8842 (t0) cc_final: 0.8065 (t0) REVERT: D 279 GLN cc_start: 0.8778 (tp40) cc_final: 0.8044 (mm110) REVERT: D 283 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8075 (mp0) REVERT: D 293 ASP cc_start: 0.6970 (m-30) cc_final: 0.6507 (m-30) REVERT: D 327 ARG cc_start: 0.7362 (tpp-160) cc_final: 0.7076 (tpp-160) REVERT: D 355 GLU cc_start: 0.8506 (tp30) cc_final: 0.8224 (tp30) REVERT: D 391 ASP cc_start: 0.8092 (t70) cc_final: 0.7725 (t70) REVERT: D 409 TYR cc_start: 0.7933 (m-80) cc_final: 0.6970 (m-10) REVERT: D 440 MET cc_start: 0.7624 (tpp) cc_final: 0.7365 (tpp) REVERT: D 481 TRP cc_start: 0.5385 (t-100) cc_final: 0.3897 (t60) REVERT: D 555 MET cc_start: 0.9374 (mtt) cc_final: 0.9131 (mtt) REVERT: D 567 ARG cc_start: 0.8590 (mtt-85) cc_final: 0.8099 (ptp-110) REVERT: D 574 MET cc_start: 0.8411 (mtp) cc_final: 0.7609 (tpp) REVERT: D 578 MET cc_start: 0.8579 (tpp) cc_final: 0.8376 (mmt) REVERT: D 625 PHE cc_start: 0.6957 (t80) cc_final: 0.6229 (t80) REVERT: D 634 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7897 (mtmt) REVERT: D 699 THR cc_start: 0.9166 (t) cc_final: 0.8958 (p) REVERT: D 702 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8016 (mm-30) REVERT: D 705 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8446 (mttt) REVERT: D 706 MET cc_start: 0.7980 (ttt) cc_final: 0.6967 (tpp) REVERT: D 730 LEU cc_start: 0.8620 (mp) cc_final: 0.8339 (mp) outliers start: 0 outliers final: 0 residues processed: 737 average time/residue: 0.2854 time to fit residues: 331.7705 Evaluate side-chains 631 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 631 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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: 0.1980 chunk 222 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 145 optimal weight: 0.0870 chunk 61 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 114 optimal weight: 0.0000 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 overall best weight: 1.6566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN B 314 ASN B 417 HIS ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 417 HIS ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 417 HIS D 647 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21460 Z= 0.175 Angle : 0.727 10.037 29032 Z= 0.361 Chirality : 0.042 0.154 3308 Planarity : 0.005 0.060 3624 Dihedral : 6.349 33.828 2808 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.63 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.75 (0.17), residues: 2568 helix: -0.49 (0.14), residues: 1352 sheet: -4.27 (0.39), residues: 76 loop : -3.40 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 742 HIS 0.004 0.001 HIS A 301 PHE 0.020 0.001 PHE A 625 TYR 0.015 0.001 TYR A 321 ARG 0.006 0.000 ARG B 733 *********************** 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 748 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 748 time to evaluate : 2.507 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 121 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8792 (mptt) REVERT: A 122 ARG cc_start: 0.8630 (ttt90) cc_final: 0.8287 (ttp-110) REVERT: A 132 VAL cc_start: 0.8119 (t) cc_final: 0.7656 (t) REVERT: A 135 LEU cc_start: 0.8763 (tp) cc_final: 0.8441 (tp) REVERT: A 261 PHE cc_start: 0.8811 (p90) cc_final: 0.8282 (p90) REVERT: A 282 MET cc_start: 0.8035 (tmm) cc_final: 0.7815 (tmm) REVERT: A 283 GLU cc_start: 0.8664 (mm-30) cc_final: 0.7999 (mp0) REVERT: A 338 ASN cc_start: 0.8163 (p0) cc_final: 0.7498 (p0) REVERT: A 355 GLU cc_start: 0.8503 (tp30) cc_final: 0.7898 (tp30) REVERT: A 356 ILE cc_start: 0.9573 (tt) cc_final: 0.9370 (mm) REVERT: A 376 LYS cc_start: 0.7366 (tptm) cc_final: 0.7085 (tptp) REVERT: A 391 ASP cc_start: 0.7815 (t70) cc_final: 0.7450 (t70) REVERT: A 409 TYR cc_start: 0.7772 (m-80) cc_final: 0.6492 (m-10) REVERT: A 481 TRP cc_start: 0.5984 (m100) cc_final: 0.5157 (t-100) REVERT: A 555 MET cc_start: 0.9332 (mtt) cc_final: 0.9092 (mtt) REVERT: A 562 MET cc_start: 0.9025 (ppp) cc_final: 0.7906 (ppp) REVERT: A 569 PHE cc_start: 0.7324 (m-10) cc_final: 0.6937 (m-80) REVERT: A 574 MET cc_start: 0.8393 (mtp) cc_final: 0.8049 (ttm) REVERT: A 625 PHE cc_start: 0.6820 (t80) cc_final: 0.6309 (t80) REVERT: A 630 LEU cc_start: 0.9307 (mm) cc_final: 0.9095 (mm) REVERT: A 701 LEU cc_start: 0.9108 (mt) cc_final: 0.8874 (mt) REVERT: A 702 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 705 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8446 (mttt) REVERT: A 706 MET cc_start: 0.7668 (ttt) cc_final: 0.6907 (tpp) REVERT: A 732 LEU cc_start: 0.8198 (mt) cc_final: 0.7982 (mt) REVERT: B 121 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8808 (mptt) REVERT: B 261 PHE cc_start: 0.8736 (p90) cc_final: 0.8223 (p90) REVERT: B 283 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8034 (mp0) REVERT: B 338 ASN cc_start: 0.8178 (p0) cc_final: 0.7644 (p0) REVERT: B 355 GLU cc_start: 0.8477 (tp30) cc_final: 0.7944 (tp30) REVERT: B 356 ILE cc_start: 0.9606 (tt) cc_final: 0.9386 (mm) REVERT: B 376 LYS cc_start: 0.7362 (tptm) cc_final: 0.7087 (tptp) REVERT: B 391 ASP cc_start: 0.7875 (t70) cc_final: 0.7635 (t70) REVERT: B 409 TYR cc_start: 0.8001 (m-80) cc_final: 0.7158 (m-10) REVERT: B 440 MET cc_start: 0.7514 (mmt) cc_final: 0.7197 (tpp) REVERT: B 481 TRP cc_start: 0.6016 (m100) cc_final: 0.5194 (t-100) REVERT: B 555 MET cc_start: 0.9327 (mtt) cc_final: 0.9081 (mtt) REVERT: B 567 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8320 (mtm-85) REVERT: B 569 PHE cc_start: 0.7323 (m-10) cc_final: 0.6952 (m-10) REVERT: B 574 MET cc_start: 0.8422 (mtp) cc_final: 0.7522 (tpp) REVERT: B 625 PHE cc_start: 0.6902 (t80) cc_final: 0.5993 (t80) REVERT: B 630 LEU cc_start: 0.9320 (mm) cc_final: 0.9096 (mm) REVERT: B 702 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7984 (mm-30) REVERT: B 730 LEU cc_start: 0.8672 (mp) cc_final: 0.8384 (mp) REVERT: C 121 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8729 (mptt) REVERT: C 135 LEU cc_start: 0.8675 (tp) cc_final: 0.8472 (tp) REVERT: C 261 PHE cc_start: 0.8717 (p90) cc_final: 0.8349 (p90) REVERT: C 280 LEU cc_start: 0.8907 (tp) cc_final: 0.8662 (mm) REVERT: C 283 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7899 (mp0) REVERT: C 284 ASN cc_start: 0.9165 (t0) cc_final: 0.8915 (t0) REVERT: C 293 ASP cc_start: 0.7248 (m-30) cc_final: 0.6146 (m-30) REVERT: C 343 THR cc_start: 0.8203 (m) cc_final: 0.7805 (m) REVERT: C 355 GLU cc_start: 0.8487 (tp30) cc_final: 0.7925 (tp30) REVERT: C 387 SER cc_start: 0.8519 (t) cc_final: 0.8182 (p) REVERT: C 409 TYR cc_start: 0.7914 (m-80) cc_final: 0.6757 (m-10) REVERT: C 481 TRP cc_start: 0.4616 (m-90) cc_final: 0.4284 (t-100) REVERT: C 501 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7998 (mm-30) REVERT: C 555 MET cc_start: 0.9340 (mtt) cc_final: 0.9077 (mtt) REVERT: C 567 ARG cc_start: 0.8418 (mtt-85) cc_final: 0.8179 (ptp-110) REVERT: C 574 MET cc_start: 0.8365 (mtp) cc_final: 0.7710 (ttm) REVERT: C 625 PHE cc_start: 0.6640 (t80) cc_final: 0.6035 (t80) REVERT: C 642 LEU cc_start: 0.7010 (pt) cc_final: 0.6791 (pt) REVERT: C 677 MET cc_start: 0.9135 (mmm) cc_final: 0.8932 (mmm) REVERT: C 702 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 705 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8397 (mttt) REVERT: C 706 MET cc_start: 0.7637 (ttt) cc_final: 0.6854 (tpp) REVERT: C 730 LEU cc_start: 0.8459 (mp) cc_final: 0.8195 (mp) REVERT: C 732 LEU cc_start: 0.8432 (mt) cc_final: 0.8155 (mt) REVERT: C 733 ARG cc_start: 0.6540 (mtp-110) cc_final: 0.5618 (ptm160) REVERT: D 121 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8720 (mptt) REVERT: D 135 LEU cc_start: 0.8696 (tp) cc_final: 0.8486 (tp) REVERT: D 273 ASN cc_start: 0.8487 (t0) cc_final: 0.7783 (t0) REVERT: D 293 ASP cc_start: 0.6825 (m-30) cc_final: 0.6272 (m-30) REVERT: D 343 THR cc_start: 0.8101 (m) cc_final: 0.7709 (m) REVERT: D 355 GLU cc_start: 0.8374 (tp30) cc_final: 0.7778 (tp30) REVERT: D 391 ASP cc_start: 0.7873 (t70) cc_final: 0.7591 (t70) REVERT: D 409 TYR cc_start: 0.7883 (m-80) cc_final: 0.6323 (m-10) REVERT: D 481 TRP cc_start: 0.5434 (t-100) cc_final: 0.3807 (t60) REVERT: D 501 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7981 (mm-30) REVERT: D 555 MET cc_start: 0.9364 (mtt) cc_final: 0.9133 (mtt) REVERT: D 567 ARG cc_start: 0.8472 (mtt-85) cc_final: 0.7801 (ptp-110) REVERT: D 574 MET cc_start: 0.8356 (mtp) cc_final: 0.7307 (tpp) REVERT: D 625 PHE cc_start: 0.6765 (t80) cc_final: 0.5903 (t80) REVERT: D 634 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7839 (mtmt) REVERT: D 672 MET cc_start: 0.8588 (mmp) cc_final: 0.8221 (mmt) REVERT: D 695 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8621 (mm-40) REVERT: D 702 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7941 (mm-30) REVERT: D 705 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8504 (mttt) REVERT: D 706 MET cc_start: 0.7728 (ttt) cc_final: 0.6934 (tpp) REVERT: D 730 LEU cc_start: 0.8492 (mp) cc_final: 0.8193 (mp) outliers start: 0 outliers final: 0 residues processed: 748 average time/residue: 0.2913 time to fit residues: 340.8712 Evaluate side-chains 638 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 638 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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: 0.4980 chunk 27 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 647 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 417 HIS D 647 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21460 Z= 0.180 Angle : 0.733 10.348 29032 Z= 0.364 Chirality : 0.042 0.187 3308 Planarity : 0.005 0.070 3624 Dihedral : 6.260 33.601 2808 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.25 % Favored : 85.44 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -2.62 (0.17), residues: 2568 helix: -0.37 (0.14), residues: 1348 sheet: -4.29 (0.39), residues: 76 loop : -3.34 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 742 HIS 0.005 0.001 HIS B 417 PHE 0.023 0.001 PHE C 633 TYR 0.027 0.001 TYR A 650 ARG 0.008 0.000 ARG B 696 *********************** 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 730 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 730 time to evaluate : 2.374 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 121 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8767 (mptt) REVERT: A 122 ARG cc_start: 0.8660 (ttt90) cc_final: 0.8336 (ttp-110) REVERT: A 135 LEU cc_start: 0.8729 (tp) cc_final: 0.8372 (tp) REVERT: A 261 PHE cc_start: 0.8710 (p90) cc_final: 0.8177 (p90) REVERT: A 283 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8472 (mm-30) REVERT: A 338 ASN cc_start: 0.8148 (p0) cc_final: 0.7881 (p0) REVERT: A 355 GLU cc_start: 0.8458 (tp30) cc_final: 0.8071 (tp30) REVERT: A 356 ILE cc_start: 0.9550 (tt) cc_final: 0.9305 (mm) REVERT: A 376 LYS cc_start: 0.7253 (tptm) cc_final: 0.7014 (tptp) REVERT: A 391 ASP cc_start: 0.7714 (t70) cc_final: 0.7398 (t70) REVERT: A 409 TYR cc_start: 0.7752 (m-80) cc_final: 0.6619 (m-10) REVERT: A 481 TRP cc_start: 0.6035 (m100) cc_final: 0.5240 (t-100) REVERT: A 555 MET cc_start: 0.9336 (mtt) cc_final: 0.9112 (mtt) REVERT: A 569 PHE cc_start: 0.7144 (m-10) cc_final: 0.6731 (m-80) REVERT: A 574 MET cc_start: 0.8343 (mtp) cc_final: 0.8043 (ttm) REVERT: A 625 PHE cc_start: 0.6782 (t80) cc_final: 0.6094 (t80) REVERT: A 630 LEU cc_start: 0.9289 (mm) cc_final: 0.9087 (mm) REVERT: A 702 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 705 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8432 (mttt) REVERT: A 706 MET cc_start: 0.7648 (ttt) cc_final: 0.6815 (tpp) REVERT: B 121 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8800 (mptt) REVERT: B 261 PHE cc_start: 0.8839 (p90) cc_final: 0.8428 (p90) REVERT: B 283 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8438 (mm-30) REVERT: B 338 ASN cc_start: 0.7940 (p0) cc_final: 0.7646 (p0) REVERT: B 355 GLU cc_start: 0.8463 (tp30) cc_final: 0.7824 (tp30) REVERT: B 356 ILE cc_start: 0.9597 (tt) cc_final: 0.9360 (mm) REVERT: B 375 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.7186 (ttm170) REVERT: B 391 ASP cc_start: 0.7837 (t70) cc_final: 0.7260 (t70) REVERT: B 481 TRP cc_start: 0.6090 (m100) cc_final: 0.5276 (t-100) REVERT: B 555 MET cc_start: 0.9339 (mtt) cc_final: 0.9121 (mtt) REVERT: B 569 PHE cc_start: 0.7257 (m-10) cc_final: 0.6881 (m-80) REVERT: B 574 MET cc_start: 0.8304 (mtp) cc_final: 0.7535 (ttm) REVERT: B 625 PHE cc_start: 0.6974 (t80) cc_final: 0.6121 (t80) REVERT: B 630 LEU cc_start: 0.9283 (mm) cc_final: 0.9057 (mm) REVERT: B 677 MET cc_start: 0.9231 (mmm) cc_final: 0.9024 (mmm) REVERT: B 689 GLU cc_start: 0.7727 (tp30) cc_final: 0.7378 (tp30) REVERT: B 730 LEU cc_start: 0.8646 (mp) cc_final: 0.8343 (mp) REVERT: C 121 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8744 (mptt) REVERT: C 135 LEU cc_start: 0.8715 (tp) cc_final: 0.8435 (tp) REVERT: C 280 LEU cc_start: 0.8949 (tp) cc_final: 0.8659 (mm) REVERT: C 283 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7965 (mp0) REVERT: C 284 ASN cc_start: 0.9154 (t0) cc_final: 0.8941 (t0) REVERT: C 355 GLU cc_start: 0.8461 (tp30) cc_final: 0.7783 (tp30) REVERT: C 387 SER cc_start: 0.8469 (t) cc_final: 0.8075 (p) REVERT: C 405 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7994 (tm-30) REVERT: C 409 TYR cc_start: 0.7851 (m-80) cc_final: 0.6591 (m-10) REVERT: C 479 MET cc_start: 0.5820 (ptp) cc_final: 0.5598 (ptp) REVERT: C 481 TRP cc_start: 0.4749 (m-90) cc_final: 0.4418 (t-100) REVERT: C 555 MET cc_start: 0.9348 (mtt) cc_final: 0.9066 (mtt) REVERT: C 567 ARG cc_start: 0.8407 (mtt-85) cc_final: 0.7882 (ptp-110) REVERT: C 574 MET cc_start: 0.8302 (mtp) cc_final: 0.7763 (ttm) REVERT: C 625 PHE cc_start: 0.6757 (t80) cc_final: 0.6092 (t80) REVERT: C 634 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7759 (ttmt) REVERT: C 642 LEU cc_start: 0.7229 (pt) cc_final: 0.6966 (pt) REVERT: C 695 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8705 (mm-40) REVERT: C 699 THR cc_start: 0.9191 (t) cc_final: 0.8983 (m) REVERT: C 702 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 705 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8410 (mttt) REVERT: C 706 MET cc_start: 0.7691 (ttt) cc_final: 0.6840 (tpp) REVERT: D 121 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8734 (mptt) REVERT: D 135 LEU cc_start: 0.8745 (tp) cc_final: 0.8474 (tp) REVERT: D 273 ASN cc_start: 0.8629 (t0) cc_final: 0.7785 (t0) REVERT: D 293 ASP cc_start: 0.6674 (m-30) cc_final: 0.6075 (m-30) REVERT: D 343 THR cc_start: 0.8079 (m) cc_final: 0.7664 (m) REVERT: D 355 GLU cc_start: 0.8437 (tp30) cc_final: 0.7872 (tp30) REVERT: D 356 ILE cc_start: 0.9568 (tt) cc_final: 0.9340 (mm) REVERT: D 391 ASP cc_start: 0.7961 (t70) cc_final: 0.7391 (t70) REVERT: D 405 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7912 (tm-30) REVERT: D 409 TYR cc_start: 0.7960 (m-80) cc_final: 0.6273 (m-10) REVERT: D 439 TYR cc_start: 0.7876 (m-80) cc_final: 0.7635 (m-10) REVERT: D 481 TRP cc_start: 0.5389 (t-100) cc_final: 0.3733 (t60) REVERT: D 488 MET cc_start: 0.6605 (mmm) cc_final: 0.6145 (mtp) REVERT: D 555 MET cc_start: 0.9364 (mtt) cc_final: 0.9147 (mtt) REVERT: D 574 MET cc_start: 0.8251 (mtp) cc_final: 0.7230 (tpp) REVERT: D 625 PHE cc_start: 0.6876 (t80) cc_final: 0.6110 (t80) REVERT: D 634 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7834 (mtmt) REVERT: D 672 MET cc_start: 0.8621 (mmp) cc_final: 0.8332 (mmt) REVERT: D 676 LEU cc_start: 0.8839 (tt) cc_final: 0.8639 (tt) REVERT: D 677 MET cc_start: 0.9188 (mmm) cc_final: 0.8961 (mmm) REVERT: D 702 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7837 (mm-30) REVERT: D 705 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8465 (mttt) REVERT: D 706 MET cc_start: 0.7779 (ttt) cc_final: 0.6926 (tpp) REVERT: D 730 LEU cc_start: 0.8490 (mp) cc_final: 0.8197 (mp) outliers start: 0 outliers final: 0 residues processed: 730 average time/residue: 0.2874 time to fit residues: 330.3544 Evaluate side-chains 644 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 644 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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: 0.2980 chunk 147 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS B 417 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B 695 GLN C 314 ASN C 417 HIS C 647 ASN ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21460 Z= 0.270 Angle : 0.800 9.821 29032 Z= 0.401 Chirality : 0.045 0.162 3308 Planarity : 0.005 0.069 3624 Dihedral : 6.491 33.917 2808 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.43 % Favored : 83.41 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -2.47 (0.17), residues: 2568 helix: -0.26 (0.14), residues: 1324 sheet: -4.19 (0.44), residues: 76 loop : -3.20 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 742 HIS 0.005 0.001 HIS A 471 PHE 0.023 0.002 PHE B 526 TYR 0.020 0.002 TYR D 382 ARG 0.008 0.001 ARG A 733 *********************** 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 700 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8758 (mptt) REVERT: A 261 PHE cc_start: 0.8982 (p90) cc_final: 0.8557 (p90) REVERT: A 338 ASN cc_start: 0.8501 (p0) cc_final: 0.8212 (p0) REVERT: A 355 GLU cc_start: 0.8562 (tp30) cc_final: 0.8109 (tp30) REVERT: A 356 ILE cc_start: 0.9608 (tt) cc_final: 0.9392 (mm) REVERT: A 376 LYS cc_start: 0.7429 (tptm) cc_final: 0.6975 (tptp) REVERT: A 391 ASP cc_start: 0.8238 (t70) cc_final: 0.7993 (t70) REVERT: A 479 MET cc_start: 0.5588 (ptp) cc_final: 0.5329 (ptp) REVERT: A 481 TRP cc_start: 0.6020 (m100) cc_final: 0.5214 (t-100) REVERT: A 555 MET cc_start: 0.9337 (mtt) cc_final: 0.9082 (mtt) REVERT: A 569 PHE cc_start: 0.7272 (m-10) cc_final: 0.6873 (m-80) REVERT: A 574 MET cc_start: 0.8372 (mtp) cc_final: 0.8080 (ttm) REVERT: A 625 PHE cc_start: 0.7011 (t80) cc_final: 0.6319 (t80) REVERT: A 705 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8493 (mttt) REVERT: A 706 MET cc_start: 0.7958 (ttt) cc_final: 0.6898 (tpp) REVERT: B 121 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8801 (mptt) REVERT: B 263 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6843 (mt-10) REVERT: B 283 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8100 (mp0) REVERT: B 355 GLU cc_start: 0.8547 (tp30) cc_final: 0.7963 (tp30) REVERT: B 356 ILE cc_start: 0.9609 (tt) cc_final: 0.9403 (mm) REVERT: B 391 ASP cc_start: 0.7860 (t70) cc_final: 0.7594 (t70) REVERT: B 479 MET cc_start: 0.5581 (ptp) cc_final: 0.5318 (ptp) REVERT: B 481 TRP cc_start: 0.5944 (m100) cc_final: 0.5169 (t-100) REVERT: B 555 MET cc_start: 0.9337 (mtt) cc_final: 0.9073 (mtt) REVERT: B 569 PHE cc_start: 0.7425 (m-10) cc_final: 0.7084 (m-10) REVERT: B 574 MET cc_start: 0.8119 (mtp) cc_final: 0.7497 (ttm) REVERT: B 625 PHE cc_start: 0.6948 (t80) cc_final: 0.6173 (t80) REVERT: B 630 LEU cc_start: 0.9247 (mm) cc_final: 0.9044 (mm) REVERT: B 677 MET cc_start: 0.9296 (mmm) cc_final: 0.9049 (mmm) REVERT: B 701 LEU cc_start: 0.9154 (mt) cc_final: 0.8859 (mt) REVERT: B 702 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 717 MET cc_start: 0.8305 (mtp) cc_final: 0.7709 (mtp) REVERT: B 732 LEU cc_start: 0.8620 (mt) cc_final: 0.8309 (mt) REVERT: C 121 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8793 (mptt) REVERT: C 135 LEU cc_start: 0.8819 (tp) cc_final: 0.8526 (tp) REVERT: C 280 LEU cc_start: 0.8991 (tp) cc_final: 0.8729 (mm) REVERT: C 281 LEU cc_start: 0.8991 (mp) cc_final: 0.8781 (mp) REVERT: C 283 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8091 (mp0) REVERT: C 284 ASN cc_start: 0.9188 (t0) cc_final: 0.8985 (t0) REVERT: C 355 GLU cc_start: 0.8569 (tp30) cc_final: 0.7902 (tp30) REVERT: C 391 ASP cc_start: 0.8293 (t70) cc_final: 0.7998 (t70) REVERT: C 409 TYR cc_start: 0.7858 (m-80) cc_final: 0.6953 (m-10) REVERT: C 479 MET cc_start: 0.6174 (ptp) cc_final: 0.5970 (ptp) REVERT: C 481 TRP cc_start: 0.4658 (m-90) cc_final: 0.4435 (t-100) REVERT: C 555 MET cc_start: 0.9353 (mtt) cc_final: 0.9055 (mtt) REVERT: C 567 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.7708 (ptp-110) REVERT: C 625 PHE cc_start: 0.6839 (t80) cc_final: 0.6196 (t80) REVERT: C 634 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7579 (tttt) REVERT: C 642 LEU cc_start: 0.7526 (pt) cc_final: 0.7281 (pt) REVERT: C 683 ASN cc_start: 0.8766 (t0) cc_final: 0.8538 (t0) REVERT: C 695 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8547 (mm-40) REVERT: C 699 THR cc_start: 0.9203 (t) cc_final: 0.8976 (m) REVERT: C 702 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 705 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8521 (mttt) REVERT: C 706 MET cc_start: 0.7873 (ttt) cc_final: 0.6902 (tpp) REVERT: C 717 MET cc_start: 0.8290 (mtp) cc_final: 0.7653 (mtp) REVERT: D 121 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8785 (mptt) REVERT: D 261 PHE cc_start: 0.8731 (p90) cc_final: 0.8292 (p90) REVERT: D 293 ASP cc_start: 0.6927 (m-30) cc_final: 0.6343 (m-30) REVERT: D 343 THR cc_start: 0.8360 (m) cc_final: 0.7910 (m) REVERT: D 355 GLU cc_start: 0.8517 (tp30) cc_final: 0.7958 (tp30) REVERT: D 356 ILE cc_start: 0.9614 (tt) cc_final: 0.9408 (mm) REVERT: D 391 ASP cc_start: 0.8307 (t70) cc_final: 0.7899 (t70) REVERT: D 481 TRP cc_start: 0.5615 (t-100) cc_final: 0.3876 (t60) REVERT: D 488 MET cc_start: 0.6657 (mmm) cc_final: 0.6176 (mtp) REVERT: D 555 MET cc_start: 0.9367 (mtt) cc_final: 0.9120 (mtt) REVERT: D 574 MET cc_start: 0.8425 (mtp) cc_final: 0.7673 (ttm) REVERT: D 625 PHE cc_start: 0.6830 (t80) cc_final: 0.6185 (t80) REVERT: D 634 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7910 (mtmt) REVERT: D 670 LEU cc_start: 0.9247 (mm) cc_final: 0.8961 (mm) REVERT: D 677 MET cc_start: 0.9195 (mmm) cc_final: 0.8914 (mmm) REVERT: D 695 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8731 (mm-40) REVERT: D 702 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8175 (mm-30) REVERT: D 705 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8631 (mttt) REVERT: D 706 MET cc_start: 0.7899 (ttt) cc_final: 0.7030 (tpp) REVERT: D 717 MET cc_start: 0.8397 (mtp) cc_final: 0.7788 (mtp) REVERT: D 732 LEU cc_start: 0.8616 (mt) cc_final: 0.8314 (mt) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 0.2826 time to fit residues: 313.9798 Evaluate side-chains 619 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 619 time to evaluate : 2.501 ------------------------------------------------------------------------------- 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: 7.9990 chunk 236 optimal weight: 1.9990 chunk 215 optimal weight: 0.3980 chunk 229 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN B 301 HIS B 417 HIS ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN C 314 ASN C 417 HIS C 647 ASN C 695 GLN D 279 GLN D 297 ASN D 301 HIS D 314 ASN D 417 HIS D 647 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21460 Z= 0.185 Angle : 0.773 10.026 29032 Z= 0.380 Chirality : 0.043 0.220 3308 Planarity : 0.005 0.059 3624 Dihedral : 6.216 33.417 2808 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.29 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -2.50 (0.17), residues: 2568 helix: -0.32 (0.14), residues: 1352 sheet: -4.15 (0.44), residues: 76 loop : -3.24 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 742 HIS 0.007 0.001 HIS B 301 PHE 0.039 0.001 PHE C 261 TYR 0.023 0.001 TYR C 260 ARG 0.007 0.000 ARG C 375 *********************** 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 711 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 711 time to evaluate : 2.485 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 121 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8738 (mptt) REVERT: A 135 LEU cc_start: 0.8730 (tp) cc_final: 0.8441 (tp) REVERT: A 261 PHE cc_start: 0.8662 (p90) cc_final: 0.8382 (p90) REVERT: A 338 ASN cc_start: 0.8507 (p0) cc_final: 0.8066 (p0) REVERT: A 355 GLU cc_start: 0.8489 (tp30) cc_final: 0.7845 (tp30) REVERT: A 356 ILE cc_start: 0.9528 (tt) cc_final: 0.9286 (mm) REVERT: A 376 LYS cc_start: 0.7187 (tptm) cc_final: 0.6922 (tptp) REVERT: A 391 ASP cc_start: 0.7980 (t70) cc_final: 0.7742 (t70) REVERT: A 479 MET cc_start: 0.5782 (ptp) cc_final: 0.5396 (ptp) REVERT: A 481 TRP cc_start: 0.5817 (m100) cc_final: 0.5128 (t-100) REVERT: A 555 MET cc_start: 0.9328 (mtt) cc_final: 0.9090 (mtt) REVERT: A 569 PHE cc_start: 0.6974 (m-10) cc_final: 0.6708 (m-80) REVERT: A 625 PHE cc_start: 0.6837 (t80) cc_final: 0.6062 (t80) REVERT: A 630 LEU cc_start: 0.9325 (mm) cc_final: 0.9092 (mm) REVERT: A 702 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 705 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8429 (mttt) REVERT: A 706 MET cc_start: 0.7762 (ttt) cc_final: 0.6777 (tpp) REVERT: B 121 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8807 (mptt) REVERT: B 261 PHE cc_start: 0.8880 (p90) cc_final: 0.8365 (p90) REVERT: B 338 ASN cc_start: 0.8369 (p0) cc_final: 0.7880 (p0) REVERT: B 355 GLU cc_start: 0.8477 (tp30) cc_final: 0.7819 (tp30) REVERT: B 356 ILE cc_start: 0.9557 (tt) cc_final: 0.9321 (mm) REVERT: B 391 ASP cc_start: 0.8108 (t70) cc_final: 0.7825 (t70) REVERT: B 479 MET cc_start: 0.5748 (ptp) cc_final: 0.5357 (ptp) REVERT: B 481 TRP cc_start: 0.5804 (m100) cc_final: 0.5066 (t-100) REVERT: B 555 MET cc_start: 0.9320 (mtt) cc_final: 0.9066 (mtt) REVERT: B 569 PHE cc_start: 0.7160 (m-10) cc_final: 0.6804 (m-80) REVERT: B 574 MET cc_start: 0.7902 (mtp) cc_final: 0.7153 (ttm) REVERT: B 625 PHE cc_start: 0.6975 (t80) cc_final: 0.6214 (t80) REVERT: B 630 LEU cc_start: 0.9205 (mm) cc_final: 0.8990 (mm) REVERT: B 677 MET cc_start: 0.9225 (mmm) cc_final: 0.9016 (mmm) REVERT: B 717 MET cc_start: 0.8276 (mtp) cc_final: 0.7678 (mtp) REVERT: C 121 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8768 (mptt) REVERT: C 135 LEU cc_start: 0.8721 (tp) cc_final: 0.8415 (tp) REVERT: C 159 MET cc_start: 0.7496 (mtp) cc_final: 0.7167 (mtp) REVERT: C 282 MET cc_start: 0.7844 (tmm) cc_final: 0.6756 (tmm) REVERT: C 283 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8207 (mm-30) REVERT: C 355 GLU cc_start: 0.8468 (tp30) cc_final: 0.7790 (tp30) REVERT: C 356 ILE cc_start: 0.9560 (tt) cc_final: 0.9306 (mm) REVERT: C 409 TYR cc_start: 0.7808 (m-80) cc_final: 0.6783 (m-10) REVERT: C 479 MET cc_start: 0.6356 (ptp) cc_final: 0.6076 (ptp) REVERT: C 555 MET cc_start: 0.9334 (mtt) cc_final: 0.9013 (mtt) REVERT: C 574 MET cc_start: 0.8306 (mtp) cc_final: 0.7958 (ttm) REVERT: C 625 PHE cc_start: 0.6592 (t80) cc_final: 0.5968 (t80) REVERT: C 634 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7492 (tttt) REVERT: C 651 PRO cc_start: 0.6771 (Cg_endo) cc_final: 0.6563 (Cg_exo) REVERT: C 699 THR cc_start: 0.9190 (t) cc_final: 0.8968 (m) REVERT: C 702 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7860 (mm-30) REVERT: C 705 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8416 (mttt) REVERT: C 706 MET cc_start: 0.7622 (ttt) cc_final: 0.6838 (tpp) REVERT: D 121 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8742 (mptt) REVERT: D 132 VAL cc_start: 0.8053 (t) cc_final: 0.7606 (t) REVERT: D 135 LEU cc_start: 0.8722 (tp) cc_final: 0.8463 (tp) REVERT: D 261 PHE cc_start: 0.8870 (p90) cc_final: 0.8618 (p90) REVERT: D 277 ILE cc_start: 0.8982 (tt) cc_final: 0.8776 (tt) REVERT: D 281 LEU cc_start: 0.8990 (mt) cc_final: 0.8746 (mp) REVERT: D 343 THR cc_start: 0.8231 (m) cc_final: 0.7755 (m) REVERT: D 355 GLU cc_start: 0.8478 (tp30) cc_final: 0.7819 (tp30) REVERT: D 356 ILE cc_start: 0.9544 (tt) cc_final: 0.9336 (mm) REVERT: D 391 ASP cc_start: 0.8200 (t70) cc_final: 0.7664 (t70) REVERT: D 479 MET cc_start: 0.5874 (ptp) cc_final: 0.5644 (ptp) REVERT: D 488 MET cc_start: 0.6519 (mmm) cc_final: 0.6030 (mtp) REVERT: D 527 PHE cc_start: 0.8723 (t80) cc_final: 0.8515 (t80) REVERT: D 555 MET cc_start: 0.9335 (mtt) cc_final: 0.9095 (mtt) REVERT: D 574 MET cc_start: 0.8269 (mtp) cc_final: 0.7441 (ttm) REVERT: D 625 PHE cc_start: 0.6857 (t80) cc_final: 0.6233 (t80) REVERT: D 634 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7891 (mtmt) REVERT: D 677 MET cc_start: 0.9112 (mmm) cc_final: 0.8901 (mmm) REVERT: D 695 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8749 (mm-40) REVERT: D 701 LEU cc_start: 0.9099 (mt) cc_final: 0.8834 (mt) REVERT: D 702 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7727 (mm-30) REVERT: D 705 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8590 (mttt) REVERT: D 706 MET cc_start: 0.7785 (ttt) cc_final: 0.6909 (tpp) REVERT: D 733 ARG cc_start: 0.5912 (ttp-170) cc_final: 0.5569 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 711 average time/residue: 0.2888 time to fit residues: 324.1448 Evaluate side-chains 616 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 616 time to evaluate : 2.517 ------------------------------------------------------------------------------- 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: 9.9990 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 234 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS B 580 GLN B 647 ASN C 417 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 647 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21460 Z= 0.233 Angle : 0.795 10.941 29032 Z= 0.392 Chirality : 0.045 0.189 3308 Planarity : 0.005 0.057 3624 Dihedral : 6.319 33.531 2808 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.04 % Favored : 83.80 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.55 (0.17), residues: 2568 helix: -0.34 (0.14), residues: 1372 sheet: -4.04 (0.46), residues: 76 loop : -3.36 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 742 HIS 0.005 0.001 HIS B 417 PHE 0.022 0.002 PHE D 259 TYR 0.031 0.002 TYR B 650 ARG 0.007 0.001 ARG A 733 ********************** 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 691 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 691 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8766 (mptt) REVERT: A 261 PHE cc_start: 0.8963 (p90) cc_final: 0.8586 (p90) REVERT: A 338 ASN cc_start: 0.8472 (p0) cc_final: 0.8177 (p0) REVERT: A 355 GLU cc_start: 0.8549 (tp30) cc_final: 0.7923 (tp30) REVERT: A 356 ILE cc_start: 0.9574 (tt) cc_final: 0.9339 (mm) REVERT: A 479 MET cc_start: 0.5745 (ptp) cc_final: 0.5437 (ptp) REVERT: A 481 TRP cc_start: 0.5786 (m100) cc_final: 0.5061 (t-100) REVERT: A 555 MET cc_start: 0.9348 (mtt) cc_final: 0.9102 (mtt) REVERT: A 569 PHE cc_start: 0.7044 (m-10) cc_final: 0.6674 (m-80) REVERT: A 574 MET cc_start: 0.8036 (ttm) cc_final: 0.7367 (ttm) REVERT: A 625 PHE cc_start: 0.7016 (t80) cc_final: 0.6256 (t80) REVERT: A 630 LEU cc_start: 0.9345 (mm) cc_final: 0.9125 (mm) REVERT: A 677 MET cc_start: 0.9300 (mmm) cc_final: 0.9090 (mmm) REVERT: A 701 LEU cc_start: 0.9130 (mt) cc_final: 0.8926 (mt) REVERT: A 702 GLU cc_start: 0.8810 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 705 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8457 (mttt) REVERT: A 706 MET cc_start: 0.7921 (ttt) cc_final: 0.6846 (tpp) REVERT: B 121 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8814 (mptt) REVERT: B 338 ASN cc_start: 0.8510 (p0) cc_final: 0.8275 (p0) REVERT: B 355 GLU cc_start: 0.8557 (tp30) cc_final: 0.7947 (tp30) REVERT: B 356 ILE cc_start: 0.9596 (tt) cc_final: 0.9372 (mm) REVERT: B 391 ASP cc_start: 0.8116 (t70) cc_final: 0.7786 (t70) REVERT: B 417 HIS cc_start: 0.7858 (p90) cc_final: 0.7650 (p90) REVERT: B 433 TRP cc_start: 0.8752 (t60) cc_final: 0.8550 (t60) REVERT: B 440 MET cc_start: 0.8119 (tpp) cc_final: 0.7856 (tpp) REVERT: B 479 MET cc_start: 0.5740 (ptp) cc_final: 0.5419 (ptp) REVERT: B 481 TRP cc_start: 0.5744 (m100) cc_final: 0.5031 (t-100) REVERT: B 555 MET cc_start: 0.9340 (mtt) cc_final: 0.9071 (mtt) REVERT: B 562 MET cc_start: 0.9150 (ppp) cc_final: 0.8941 (ppp) REVERT: B 569 PHE cc_start: 0.7245 (m-10) cc_final: 0.6837 (m-80) REVERT: B 575 TYR cc_start: 0.9316 (t80) cc_final: 0.8097 (t80) REVERT: B 625 PHE cc_start: 0.7055 (t80) cc_final: 0.6311 (t80) REVERT: B 630 LEU cc_start: 0.9190 (mm) cc_final: 0.8978 (mm) REVERT: B 677 MET cc_start: 0.9254 (mmm) cc_final: 0.9045 (mmm) REVERT: B 701 LEU cc_start: 0.9186 (mt) cc_final: 0.8974 (mt) REVERT: B 717 MET cc_start: 0.8322 (mtp) cc_final: 0.7832 (mtp) REVERT: C 121 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8789 (mptt) REVERT: C 135 LEU cc_start: 0.8758 (tp) cc_final: 0.8458 (tp) REVERT: C 282 MET cc_start: 0.7932 (tmm) cc_final: 0.6929 (tmm) REVERT: C 283 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8014 (mp0) REVERT: C 355 GLU cc_start: 0.8517 (tp30) cc_final: 0.7891 (tp30) REVERT: C 555 MET cc_start: 0.9349 (mtt) cc_final: 0.9062 (mtt) REVERT: C 574 MET cc_start: 0.8298 (mtp) cc_final: 0.7965 (ttm) REVERT: C 625 PHE cc_start: 0.6654 (t80) cc_final: 0.6008 (t80) REVERT: C 634 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7422 (tttt) REVERT: C 642 LEU cc_start: 0.7573 (pt) cc_final: 0.7324 (pt) REVERT: C 651 PRO cc_start: 0.6483 (Cg_endo) cc_final: 0.6193 (Cg_exo) REVERT: C 695 GLN cc_start: 0.9085 (mm110) cc_final: 0.8528 (mm-40) REVERT: C 705 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8499 (mttt) REVERT: C 706 MET cc_start: 0.7772 (ttt) cc_final: 0.6928 (tpp) REVERT: C 717 MET cc_start: 0.8175 (mtp) cc_final: 0.7634 (mtp) REVERT: D 121 LYS cc_start: 0.9157 (mmmt) cc_final: 0.8787 (mptt) REVERT: D 135 LEU cc_start: 0.8790 (tp) cc_final: 0.8514 (tp) REVERT: D 343 THR cc_start: 0.8259 (m) cc_final: 0.7833 (m) REVERT: D 355 GLU cc_start: 0.8540 (tp30) cc_final: 0.8034 (tp30) REVERT: D 356 ILE cc_start: 0.9569 (tt) cc_final: 0.9295 (mm) REVERT: D 391 ASP cc_start: 0.8163 (t70) cc_final: 0.7794 (t70) REVERT: D 479 MET cc_start: 0.5751 (ptp) cc_final: 0.5535 (ptp) REVERT: D 488 MET cc_start: 0.6532 (mmm) cc_final: 0.6030 (mtp) REVERT: D 555 MET cc_start: 0.9355 (mtt) cc_final: 0.9116 (mtt) REVERT: D 574 MET cc_start: 0.8318 (mtp) cc_final: 0.7523 (ttm) REVERT: D 625 PHE cc_start: 0.6901 (t80) cc_final: 0.6263 (t80) REVERT: D 634 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7964 (mtmt) REVERT: D 651 PRO cc_start: 0.6785 (Cg_endo) cc_final: 0.6446 (Cg_exo) REVERT: D 677 MET cc_start: 0.9151 (mmm) cc_final: 0.8937 (mmm) REVERT: D 695 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8751 (mm-40) REVERT: D 705 LYS cc_start: 0.8954 (ttpt) cc_final: 0.8572 (mttt) REVERT: D 706 MET cc_start: 0.7875 (ttt) cc_final: 0.6927 (tpp) REVERT: D 717 MET cc_start: 0.8386 (mtm) cc_final: 0.7955 (mmp) outliers start: 0 outliers final: 0 residues processed: 691 average time/residue: 0.2825 time to fit residues: 310.5791 Evaluate side-chains 600 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 600 time to evaluate : 2.500 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 208 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 244 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS C 417 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107940 restraints weight = 52333.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110924 restraints weight = 31319.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113074 restraints weight = 21224.193| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21460 Z= 0.221 Angle : 0.798 11.658 29032 Z= 0.393 Chirality : 0.044 0.170 3308 Planarity : 0.005 0.060 3624 Dihedral : 6.299 35.540 2808 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.50 % Favored : 84.35 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -2.53 (0.17), residues: 2568 helix: -0.31 (0.14), residues: 1372 sheet: -4.04 (0.45), residues: 76 loop : -3.36 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 742 HIS 0.006 0.001 HIS D 301 PHE 0.036 0.002 PHE C 261 TYR 0.025 0.002 TYR C 260 ARG 0.007 0.001 ARG A 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5711.63 seconds wall clock time: 102 minutes 53.25 seconds (6173.25 seconds total)