Starting phenix.real_space_refine on Sun Feb 18 05:27:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvz_8921/02_2024/6dvz_8921_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvz_8921/02_2024/6dvz_8921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvz_8921/02_2024/6dvz_8921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvz_8921/02_2024/6dvz_8921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvz_8921/02_2024/6dvz_8921_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvz_8921/02_2024/6dvz_8921_updated.pdb" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 B 12 2.79 5 C 13656 2.51 5 N 3452 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5193 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 625} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5193 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 625} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5193 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 625} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5193 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 625} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'FZ4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'FZ4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'FZ4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'FZ4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.27, per 1000 atoms: 0.54 Number of scatterers: 20976 At special positions: 0 Unit cell: (140.98, 140.98, 126.14, 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 O 3732 8.00 N 3452 7.00 C 13656 6.00 B 12 5.00 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.94 Conformation dependent library (CDL) restraints added in 3.8 seconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 0 sheets defined 50.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 132 through 146 Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.674A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.674A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 removed outlier: 4.358A pdb=" N LYS A 184 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 185 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 186 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 188 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.830A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.729A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.525A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.518A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.620A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.765A pdb=" N TYR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.584A pdb=" N GLU A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.767A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.359A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.723A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.516A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 460 removed outlier: 3.683A pdb=" N CYS A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 500 removed outlier: 3.502A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 542 removed outlier: 4.210A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 5.151A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 575 through 581 removed outlier: 3.739A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 606 removed outlier: 4.134A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 633 removed outlier: 3.867A pdb=" N VAL A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.941A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 685 removed outlier: 3.628A pdb=" N LEU A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 705 removed outlier: 3.740A pdb=" N ARG A 696 " --> pdb=" O TRP A 692 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.673A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.674A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 removed outlier: 4.358A pdb=" N LYS B 184 " --> pdb=" O PRO B 181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 185 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 186 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 188 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.830A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.729A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 224' Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.526A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.518A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.766A pdb=" N TYR B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.584A pdb=" N GLU B 334 " --> pdb=" O TRP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 removed outlier: 3.767A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.358A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.723A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.516A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 460 removed outlier: 3.683A pdb=" N CYS B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 500 removed outlier: 3.500A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 506 No H-bonds generated for 'chain 'B' and resid 503 through 506' Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 542 removed outlier: 4.209A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 5.151A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing helix chain 'B' and resid 575 through 581 removed outlier: 3.739A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 606 removed outlier: 4.134A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 633 removed outlier: 3.867A pdb=" N VAL B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 removed outlier: 3.941A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 685 removed outlier: 3.627A pdb=" N LEU B 676 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 705 removed outlier: 3.740A pdb=" N ARG B 696 " --> pdb=" O TRP B 692 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 132 through 146 Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.673A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.675A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 4.344A pdb=" N LYS C 184 " --> pdb=" O PRO C 181 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU C 185 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C 186 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 188 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 189 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 removed outlier: 3.830A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.729A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 229 through 236 removed outlier: 3.526A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.518A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 299 through 306 removed outlier: 3.620A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.765A pdb=" N TYR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 removed outlier: 3.584A pdb=" N GLU C 334 " --> pdb=" O TRP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 removed outlier: 3.767A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.359A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.722A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 435 removed outlier: 3.516A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 460 removed outlier: 3.683A pdb=" N CYS C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 500 removed outlier: 3.500A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 506 No H-bonds generated for 'chain 'C' and resid 503 through 506' Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 542 removed outlier: 4.209A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 5.151A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 573 No H-bonds generated for 'chain 'C' and resid 570 through 573' Processing helix chain 'C' and resid 575 through 581 removed outlier: 3.739A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 606 removed outlier: 4.134A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 633 removed outlier: 3.867A pdb=" N VAL C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 665 removed outlier: 3.941A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 685 removed outlier: 3.627A pdb=" N LEU C 676 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 705 removed outlier: 3.740A pdb=" N ARG C 696 " --> pdb=" O TRP C 692 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 714 No H-bonds generated for 'chain 'C' and resid 712 through 714' Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 132 through 146 Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.673A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 removed outlier: 3.674A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 4.359A pdb=" N LYS D 184 " --> pdb=" O PRO D 181 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU D 185 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE D 186 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 188 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.830A pdb=" N ASN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.729A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 224' Processing helix chain 'D' and resid 229 through 236 removed outlier: 3.525A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.516A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 299 through 306 removed outlier: 3.622A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.765A pdb=" N TYR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 removed outlier: 3.585A pdb=" N GLU D 334 " --> pdb=" O TRP D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 350 removed outlier: 3.767A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.358A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.723A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.516A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 460 removed outlier: 3.683A pdb=" N CYS D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 500 removed outlier: 3.501A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 542 removed outlier: 4.209A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 5.151A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 573 No H-bonds generated for 'chain 'D' and resid 570 through 573' Processing helix chain 'D' and resid 575 through 581 removed outlier: 3.739A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 606 removed outlier: 4.134A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 633 removed outlier: 3.867A pdb=" N VAL D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 665 removed outlier: 3.941A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 685 removed outlier: 3.627A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 705 removed outlier: 3.740A pdb=" N ARG D 696 " --> pdb=" O TRP D 692 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 714 No H-bonds generated for 'chain 'D' and resid 712 through 714' 535 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 9.35 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: 6504 1.34 - 1.46: 4755 1.46 - 1.58: 9957 1.58 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21420 Sorted by residual: bond pdb=" CA SER A 515 " pdb=" C SER A 515 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.34e-02 5.57e+03 7.48e+00 bond pdb=" CA SER C 515 " pdb=" C SER C 515 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.34e-02 5.57e+03 7.48e+00 bond pdb=" CA SER B 515 " pdb=" C SER B 515 " ideal model delta sigma weight residual 1.523 1.560 -0.036 1.34e-02 5.57e+03 7.41e+00 bond pdb=" CA SER D 515 " pdb=" C SER D 515 " ideal model delta sigma weight residual 1.523 1.559 -0.036 1.34e-02 5.57e+03 7.27e+00 bond pdb=" CB GLN D 346 " pdb=" CG GLN D 346 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.93e+00 ... (remaining 21415 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.56: 297 105.56 - 112.76: 11024 112.76 - 119.97: 8428 119.97 - 127.17: 8971 127.17 - 134.37: 228 Bond angle restraints: 28948 Sorted by residual: angle pdb=" N PRO D 756 " pdb=" CA PRO D 756 " pdb=" CB PRO D 756 " ideal model delta sigma weight residual 103.15 110.78 -7.63 9.70e-01 1.06e+00 6.19e+01 angle pdb=" N PRO B 756 " pdb=" CA PRO B 756 " pdb=" CB PRO B 756 " ideal model delta sigma weight residual 103.15 110.74 -7.59 9.70e-01 1.06e+00 6.13e+01 angle pdb=" N PRO C 756 " pdb=" CA PRO C 756 " pdb=" CB PRO C 756 " ideal model delta sigma weight residual 103.15 110.74 -7.59 9.70e-01 1.06e+00 6.13e+01 angle pdb=" N PRO A 756 " pdb=" CA PRO A 756 " pdb=" CB PRO A 756 " ideal model delta sigma weight residual 103.15 110.74 -7.59 9.70e-01 1.06e+00 6.13e+01 angle pdb=" N PRO C 758 " pdb=" CA PRO C 758 " pdb=" CB PRO C 758 " ideal model delta sigma weight residual 103.25 111.21 -7.96 1.05e+00 9.07e-01 5.75e+01 ... (remaining 28943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 12300 23.85 - 47.71: 412 47.71 - 71.56: 32 71.56 - 95.42: 20 95.42 - 119.27: 4 Dihedral angle restraints: 12768 sinusoidal: 5184 harmonic: 7584 Sorted by residual: dihedral pdb=" CA GLU A 423 " pdb=" C GLU A 423 " pdb=" N PRO A 424 " pdb=" CA PRO A 424 " ideal model delta harmonic sigma weight residual -180.00 -120.92 -59.08 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA GLU D 423 " pdb=" C GLU D 423 " pdb=" N PRO D 424 " pdb=" CA PRO D 424 " ideal model delta harmonic sigma weight residual -180.00 -120.92 -59.08 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA GLU C 423 " pdb=" C GLU C 423 " pdb=" N PRO C 424 " pdb=" CA PRO C 424 " ideal model delta harmonic sigma weight residual -180.00 -120.92 -59.08 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 12765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2857 0.080 - 0.161: 371 0.161 - 0.241: 45 0.241 - 0.321: 15 0.321 - 0.402: 4 Chirality restraints: 3292 Sorted by residual: chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE C 644 " pdb=" CA ILE C 644 " pdb=" CG1 ILE C 644 " pdb=" CG2 ILE C 644 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE B 644 " pdb=" CA ILE B 644 " pdb=" CG1 ILE B 644 " pdb=" CG2 ILE B 644 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 3289 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 423 " 0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO B 424 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 423 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO D 424 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 424 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 424 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 423 " 0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO A 424 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " 0.048 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5734 2.79 - 3.32: 19647 3.32 - 3.85: 32151 3.85 - 4.37: 36473 4.37 - 4.90: 59258 Nonbonded interactions: 153263 Sorted by model distance: nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.266 2.440 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.266 2.440 nonbonded pdb=" O THR B 167 " pdb=" OG1 THR B 209 " model vdw 2.270 2.440 ... (remaining 153258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 3.320 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 55.390 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.008 0.073 21420 Z= 0.546 Angle : 1.270 12.469 28948 Z= 0.678 Chirality : 0.062 0.402 3292 Planarity : 0.007 0.089 3600 Dihedral : 12.685 119.270 7840 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.78 % Allowed : 16.63 % Favored : 82.59 % Rotamer: Outliers : 0.18 % Allowed : 5.88 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % 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: -5.86 (0.12), residues: 2556 helix: -3.94 (0.08), residues: 1220 sheet: -5.15 (0.43), residues: 52 loop : -3.82 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 331 HIS 0.011 0.003 HIS D 477 PHE 0.035 0.004 PHE A 259 TYR 0.032 0.004 TYR C 661 ARG 0.020 0.002 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 704 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 150 ARG cc_start: 0.8019 (pmt-80) cc_final: 0.7359 (ptp-170) REVERT: A 230 ILE cc_start: 0.9304 (mt) cc_final: 0.8884 (mt) REVERT: A 309 ASP cc_start: 0.8374 (m-30) cc_final: 0.7941 (t0) REVERT: A 321 TYR cc_start: 0.8695 (t80) cc_final: 0.8423 (t80) REVERT: A 414 ASP cc_start: 0.7582 (m-30) cc_final: 0.6958 (t0) REVERT: A 440 MET cc_start: 0.8537 (mtt) cc_final: 0.8282 (mmt) REVERT: A 491 LEU cc_start: 0.9415 (mt) cc_final: 0.9168 (mt) REVERT: A 580 GLN cc_start: 0.8757 (tt0) cc_final: 0.8476 (tt0) REVERT: A 705 LYS cc_start: 0.9533 (ttmt) cc_final: 0.9043 (ttmm) REVERT: B 150 ARG cc_start: 0.8020 (pmt-80) cc_final: 0.7353 (ptp-170) REVERT: B 230 ILE cc_start: 0.9306 (mt) cc_final: 0.8888 (mt) REVERT: B 309 ASP cc_start: 0.8380 (m-30) cc_final: 0.7949 (t0) REVERT: B 321 TYR cc_start: 0.8694 (t80) cc_final: 0.8434 (t80) REVERT: B 414 ASP cc_start: 0.7551 (m-30) cc_final: 0.6929 (t0) REVERT: B 440 MET cc_start: 0.8528 (mtt) cc_final: 0.8283 (mmt) REVERT: B 491 LEU cc_start: 0.9418 (mt) cc_final: 0.9172 (mt) REVERT: B 538 PHE cc_start: 0.7209 (t80) cc_final: 0.6998 (t80) REVERT: B 580 GLN cc_start: 0.8752 (tt0) cc_final: 0.8459 (tt0) REVERT: B 705 LYS cc_start: 0.9532 (ttmt) cc_final: 0.9041 (ttmm) REVERT: C 150 ARG cc_start: 0.8014 (pmt-80) cc_final: 0.7353 (ptp-170) REVERT: C 230 ILE cc_start: 0.9309 (mt) cc_final: 0.8885 (mt) REVERT: C 309 ASP cc_start: 0.8399 (m-30) cc_final: 0.7949 (t0) REVERT: C 321 TYR cc_start: 0.8686 (t80) cc_final: 0.8427 (t80) REVERT: C 414 ASP cc_start: 0.7555 (m-30) cc_final: 0.6932 (t0) REVERT: C 440 MET cc_start: 0.8507 (mtt) cc_final: 0.8280 (mmt) REVERT: C 491 LEU cc_start: 0.9424 (mt) cc_final: 0.9177 (mt) REVERT: C 538 PHE cc_start: 0.7190 (t80) cc_final: 0.6980 (t80) REVERT: C 705 LYS cc_start: 0.9534 (ttmt) cc_final: 0.9042 (ttmm) REVERT: D 150 ARG cc_start: 0.8011 (pmt-80) cc_final: 0.7356 (ptp-170) REVERT: D 230 ILE cc_start: 0.9303 (mt) cc_final: 0.8885 (mt) REVERT: D 309 ASP cc_start: 0.8391 (m-30) cc_final: 0.7945 (t0) REVERT: D 321 TYR cc_start: 0.8690 (t80) cc_final: 0.8416 (t80) REVERT: D 414 ASP cc_start: 0.7566 (m-30) cc_final: 0.6931 (t0) REVERT: D 440 MET cc_start: 0.8505 (mtt) cc_final: 0.8271 (mmt) REVERT: D 491 LEU cc_start: 0.9422 (mt) cc_final: 0.9173 (mt) REVERT: D 538 PHE cc_start: 0.7225 (t80) cc_final: 0.7011 (t80) REVERT: D 580 GLN cc_start: 0.8748 (tt0) cc_final: 0.8464 (tt0) REVERT: D 599 LEU cc_start: 0.9210 (tp) cc_final: 0.9009 (tp) REVERT: D 679 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8149 (tm-30) REVERT: D 705 LYS cc_start: 0.9538 (ttmt) cc_final: 0.9045 (ttmm) outliers start: 4 outliers final: 0 residues processed: 708 average time/residue: 0.3391 time to fit residues: 369.8270 Evaluate side-chains 452 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 2.692 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 232 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 735 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 645 GLN D 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21420 Z= 0.195 Angle : 0.747 9.492 28948 Z= 0.381 Chirality : 0.043 0.172 3292 Planarity : 0.005 0.073 3600 Dihedral : 9.584 95.253 2860 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.24 % Favored : 85.29 % Rotamer: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.13), residues: 2556 helix: -2.51 (0.11), residues: 1324 sheet: -4.48 (0.59), residues: 52 loop : -3.71 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 481 HIS 0.006 0.001 HIS A 477 PHE 0.020 0.002 PHE A 538 TYR 0.018 0.002 TYR A 540 ARG 0.003 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 606 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8778 (ttt180) cc_final: 0.8544 (ptt-90) REVERT: A 150 ARG cc_start: 0.7958 (pmt-80) cc_final: 0.7382 (ptp-170) REVERT: A 309 ASP cc_start: 0.8296 (m-30) cc_final: 0.7812 (t0) REVERT: A 321 TYR cc_start: 0.8536 (t80) cc_final: 0.8243 (t80) REVERT: A 440 MET cc_start: 0.8778 (mtt) cc_final: 0.8320 (mmp) REVERT: A 663 ILE cc_start: 0.9662 (tp) cc_final: 0.9444 (tp) REVERT: A 680 THR cc_start: 0.9505 (t) cc_final: 0.9300 (m) REVERT: A 702 GLU cc_start: 0.8599 (tt0) cc_final: 0.8390 (tp30) REVERT: B 122 ARG cc_start: 0.8777 (ttt180) cc_final: 0.8545 (ptt-90) REVERT: B 150 ARG cc_start: 0.7961 (pmt-80) cc_final: 0.7384 (ptp-170) REVERT: B 309 ASP cc_start: 0.8325 (m-30) cc_final: 0.7808 (t0) REVERT: B 321 TYR cc_start: 0.8527 (t80) cc_final: 0.8228 (t80) REVERT: B 440 MET cc_start: 0.8770 (mtt) cc_final: 0.8313 (mmp) REVERT: B 538 PHE cc_start: 0.7293 (t80) cc_final: 0.7083 (t80) REVERT: B 663 ILE cc_start: 0.9670 (tp) cc_final: 0.9439 (tp) REVERT: B 702 GLU cc_start: 0.8589 (tt0) cc_final: 0.8388 (tp30) REVERT: C 122 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8543 (ptt-90) REVERT: C 150 ARG cc_start: 0.7956 (pmt-80) cc_final: 0.7375 (ptp-170) REVERT: C 309 ASP cc_start: 0.8324 (m-30) cc_final: 0.7824 (t0) REVERT: C 321 TYR cc_start: 0.8528 (t80) cc_final: 0.8225 (t80) REVERT: C 440 MET cc_start: 0.8763 (mtt) cc_final: 0.8305 (mmp) REVERT: C 538 PHE cc_start: 0.7296 (t80) cc_final: 0.7084 (t80) REVERT: C 663 ILE cc_start: 0.9665 (tp) cc_final: 0.9450 (tp) REVERT: C 702 GLU cc_start: 0.8589 (tt0) cc_final: 0.8375 (tp30) REVERT: D 122 ARG cc_start: 0.8768 (ttt180) cc_final: 0.8542 (ptt-90) REVERT: D 150 ARG cc_start: 0.7943 (pmt-80) cc_final: 0.7375 (ptp-170) REVERT: D 309 ASP cc_start: 0.8324 (m-30) cc_final: 0.7829 (t0) REVERT: D 321 TYR cc_start: 0.8533 (t80) cc_final: 0.8239 (t80) REVERT: D 440 MET cc_start: 0.8757 (mtt) cc_final: 0.8302 (mmp) REVERT: D 663 ILE cc_start: 0.9657 (tp) cc_final: 0.9439 (tp) REVERT: D 680 THR cc_start: 0.9555 (t) cc_final: 0.8934 (m) REVERT: D 702 GLU cc_start: 0.8582 (tt0) cc_final: 0.8372 (tp30) outliers start: 2 outliers final: 0 residues processed: 608 average time/residue: 0.3100 time to fit residues: 297.4528 Evaluate side-chains 444 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 158 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN A 671 ASN B 645 GLN B 671 ASN C 645 GLN C 671 ASN D 645 GLN D 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21420 Z= 0.197 Angle : 0.671 8.827 28948 Z= 0.344 Chirality : 0.041 0.173 3292 Planarity : 0.004 0.073 3600 Dihedral : 8.818 76.721 2860 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.63 % Allowed : 15.22 % Favored : 84.15 % Rotamer: Outliers : 0.22 % Allowed : 3.03 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.15), residues: 2556 helix: -1.57 (0.12), residues: 1344 sheet: -4.03 (0.70), residues: 52 loop : -3.38 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 481 HIS 0.006 0.001 HIS C 477 PHE 0.018 0.001 PHE B 259 TYR 0.017 0.002 TYR B 540 ARG 0.005 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 559 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8834 (ttt180) cc_final: 0.8577 (ptt-90) REVERT: A 129 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7456 (mp0) REVERT: A 150 ARG cc_start: 0.7991 (pmt-80) cc_final: 0.7429 (ptp-170) REVERT: A 309 ASP cc_start: 0.8322 (m-30) cc_final: 0.7803 (t0) REVERT: A 311 LYS cc_start: 0.8497 (mttt) cc_final: 0.7339 (tmtt) REVERT: A 440 MET cc_start: 0.8645 (mtt) cc_final: 0.8247 (mmp) REVERT: A 538 PHE cc_start: 0.7334 (t80) cc_final: 0.7060 (t80) REVERT: B 122 ARG cc_start: 0.8825 (ttt180) cc_final: 0.8588 (ptt-90) REVERT: B 150 ARG cc_start: 0.7999 (pmt-80) cc_final: 0.7433 (ptp-170) REVERT: B 309 ASP cc_start: 0.8356 (m-30) cc_final: 0.7853 (t0) REVERT: B 311 LYS cc_start: 0.8507 (mttt) cc_final: 0.7347 (tmtt) REVERT: B 440 MET cc_start: 0.8632 (mtt) cc_final: 0.8236 (mmp) REVERT: B 538 PHE cc_start: 0.7382 (t80) cc_final: 0.7159 (t80) REVERT: B 663 ILE cc_start: 0.9672 (tp) cc_final: 0.9463 (tp) REVERT: C 122 ARG cc_start: 0.8826 (ttt180) cc_final: 0.8591 (ptt-90) REVERT: C 150 ARG cc_start: 0.8009 (pmt-80) cc_final: 0.7424 (ptp-170) REVERT: C 309 ASP cc_start: 0.8347 (m-30) cc_final: 0.7823 (t0) REVERT: C 311 LYS cc_start: 0.8495 (mttt) cc_final: 0.7332 (tmtt) REVERT: C 440 MET cc_start: 0.8627 (mtt) cc_final: 0.8235 (mmp) REVERT: C 538 PHE cc_start: 0.7380 (t80) cc_final: 0.7158 (t80) REVERT: D 122 ARG cc_start: 0.8824 (ttt180) cc_final: 0.8577 (ptt-90) REVERT: D 129 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7455 (mp0) REVERT: D 150 ARG cc_start: 0.7997 (pmt-80) cc_final: 0.7421 (ptp-170) REVERT: D 309 ASP cc_start: 0.8338 (m-30) cc_final: 0.7815 (t0) REVERT: D 311 LYS cc_start: 0.8496 (mttt) cc_final: 0.7329 (tmtt) REVERT: D 440 MET cc_start: 0.8621 (mtt) cc_final: 0.8236 (mmp) REVERT: D 538 PHE cc_start: 0.7337 (t80) cc_final: 0.7057 (t80) outliers start: 5 outliers final: 1 residues processed: 564 average time/residue: 0.3043 time to fit residues: 273.2677 Evaluate side-chains 403 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 2.732 ------------------------------------------------------------------------------- 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: 7.9990 chunk 175 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 339 ASN A 645 GLN B 178 ASN B 339 ASN B 645 GLN C 178 ASN C 339 ASN C 645 GLN D 178 ASN D 339 ASN D 645 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21420 Z= 0.173 Angle : 0.640 7.578 28948 Z= 0.327 Chirality : 0.040 0.171 3292 Planarity : 0.004 0.071 3600 Dihedral : 8.257 57.258 2860 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.24 % Favored : 85.45 % Rotamer: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.16), residues: 2556 helix: -1.06 (0.13), residues: 1336 sheet: -3.86 (0.71), residues: 52 loop : -3.16 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 493 HIS 0.006 0.001 HIS A 477 PHE 0.019 0.001 PHE D 590 TYR 0.020 0.002 TYR D 359 ARG 0.003 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 548 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7642 (mp0) REVERT: A 150 ARG cc_start: 0.7601 (pmt-80) cc_final: 0.7389 (ptp-170) REVERT: A 309 ASP cc_start: 0.8337 (m-30) cc_final: 0.7976 (t0) REVERT: A 311 LYS cc_start: 0.8412 (mttt) cc_final: 0.7654 (tmtt) REVERT: A 414 ASP cc_start: 0.7686 (m-30) cc_final: 0.6965 (t0) REVERT: A 440 MET cc_start: 0.8562 (mtt) cc_final: 0.8160 (mmt) REVERT: A 594 TYR cc_start: 0.9133 (t80) cc_final: 0.8741 (t80) REVERT: A 598 LEU cc_start: 0.9094 (tt) cc_final: 0.8849 (tt) REVERT: A 663 ILE cc_start: 0.9675 (tp) cc_final: 0.9453 (tp) REVERT: A 702 GLU cc_start: 0.8460 (tp30) cc_final: 0.8095 (tm-30) REVERT: B 129 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7650 (mp0) REVERT: B 150 ARG cc_start: 0.7614 (pmt-80) cc_final: 0.7398 (ptp-170) REVERT: B 309 ASP cc_start: 0.8367 (m-30) cc_final: 0.7964 (t0) REVERT: B 311 LYS cc_start: 0.8360 (mttt) cc_final: 0.7611 (tmtt) REVERT: B 414 ASP cc_start: 0.7644 (m-30) cc_final: 0.6938 (t0) REVERT: B 440 MET cc_start: 0.8560 (mtt) cc_final: 0.8151 (mmt) REVERT: B 538 PHE cc_start: 0.7223 (t80) cc_final: 0.6989 (t80) REVERT: B 594 TYR cc_start: 0.9131 (t80) cc_final: 0.8733 (t80) REVERT: B 598 LEU cc_start: 0.9116 (tt) cc_final: 0.8875 (tt) REVERT: B 663 ILE cc_start: 0.9693 (tp) cc_final: 0.9470 (tp) REVERT: B 702 GLU cc_start: 0.8588 (tp30) cc_final: 0.8052 (tm-30) REVERT: C 129 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7653 (mp0) REVERT: C 150 ARG cc_start: 0.7595 (pmt-80) cc_final: 0.7392 (ptp-170) REVERT: C 309 ASP cc_start: 0.8366 (m-30) cc_final: 0.7976 (t0) REVERT: C 311 LYS cc_start: 0.8361 (mttt) cc_final: 0.7600 (tmtt) REVERT: C 414 ASP cc_start: 0.7659 (m-30) cc_final: 0.6940 (t0) REVERT: C 440 MET cc_start: 0.8558 (mtt) cc_final: 0.8170 (mmt) REVERT: C 521 TRP cc_start: 0.8554 (t-100) cc_final: 0.8136 (t60) REVERT: C 538 PHE cc_start: 0.7233 (t80) cc_final: 0.6990 (t80) REVERT: C 594 TYR cc_start: 0.9117 (t80) cc_final: 0.8726 (t80) REVERT: C 598 LEU cc_start: 0.9103 (tt) cc_final: 0.8870 (tt) REVERT: C 663 ILE cc_start: 0.9682 (tp) cc_final: 0.9442 (tp) REVERT: C 702 GLU cc_start: 0.8492 (tp30) cc_final: 0.8276 (tp30) REVERT: D 129 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7641 (mp0) REVERT: D 309 ASP cc_start: 0.8352 (m-30) cc_final: 0.7984 (t0) REVERT: D 311 LYS cc_start: 0.8406 (mttt) cc_final: 0.7651 (tmtt) REVERT: D 414 ASP cc_start: 0.7667 (m-30) cc_final: 0.6947 (t0) REVERT: D 440 MET cc_start: 0.8539 (mtt) cc_final: 0.8149 (mmt) REVERT: D 538 PHE cc_start: 0.7219 (t80) cc_final: 0.6973 (t80) REVERT: D 594 TYR cc_start: 0.9134 (t80) cc_final: 0.8742 (t80) REVERT: D 598 LEU cc_start: 0.9091 (tt) cc_final: 0.8849 (tt) REVERT: D 663 ILE cc_start: 0.9673 (tp) cc_final: 0.9445 (tp) REVERT: D 702 GLU cc_start: 0.8430 (tp30) cc_final: 0.8067 (tm-30) outliers start: 2 outliers final: 0 residues processed: 550 average time/residue: 0.2953 time to fit residues: 258.2622 Evaluate side-chains 399 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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: 10.0000 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 222 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 645 GLN C 645 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21420 Z= 0.243 Angle : 0.684 8.673 28948 Z= 0.347 Chirality : 0.042 0.172 3292 Planarity : 0.004 0.073 3600 Dihedral : 8.175 56.844 2860 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.38 % Favored : 84.31 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.16 % 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 (0.16), residues: 2556 helix: -0.77 (0.14), residues: 1360 sheet: -4.19 (0.64), residues: 52 loop : -3.09 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 521 HIS 0.007 0.001 HIS D 477 PHE 0.016 0.002 PHE D 261 TYR 0.017 0.002 TYR D 540 ARG 0.005 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7659 (mp0) REVERT: A 150 ARG cc_start: 0.7850 (pmt-80) cc_final: 0.7449 (ptp-170) REVERT: A 293 ASP cc_start: 0.8165 (m-30) cc_final: 0.7271 (m-30) REVERT: A 304 VAL cc_start: 0.9532 (t) cc_final: 0.9320 (p) REVERT: A 309 ASP cc_start: 0.8430 (m-30) cc_final: 0.8028 (t0) REVERT: A 414 ASP cc_start: 0.7774 (m-30) cc_final: 0.7005 (t0) REVERT: A 440 MET cc_start: 0.8584 (mtt) cc_final: 0.8218 (mmt) REVERT: A 538 PHE cc_start: 0.7324 (t80) cc_final: 0.7072 (t80) REVERT: A 574 MET cc_start: 0.8719 (ppp) cc_final: 0.8254 (ppp) REVERT: A 594 TYR cc_start: 0.9194 (t80) cc_final: 0.8749 (t80) REVERT: A 598 LEU cc_start: 0.9094 (tt) cc_final: 0.8841 (tt) REVERT: A 663 ILE cc_start: 0.9695 (tp) cc_final: 0.9489 (tp) REVERT: A 702 GLU cc_start: 0.8762 (tp30) cc_final: 0.8391 (tm-30) REVERT: B 129 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7663 (mp0) REVERT: B 150 ARG cc_start: 0.7836 (pmt-80) cc_final: 0.7436 (ptp-170) REVERT: B 309 ASP cc_start: 0.8464 (m-30) cc_final: 0.8045 (t0) REVERT: B 351 MET cc_start: 0.9264 (mmp) cc_final: 0.8878 (mmp) REVERT: B 414 ASP cc_start: 0.7718 (m-30) cc_final: 0.7021 (t0) REVERT: B 440 MET cc_start: 0.8582 (mtt) cc_final: 0.8220 (mmt) REVERT: B 578 MET cc_start: 0.8089 (mtm) cc_final: 0.7888 (mtm) REVERT: B 594 TYR cc_start: 0.9223 (t80) cc_final: 0.8750 (t80) REVERT: B 598 LEU cc_start: 0.9120 (tt) cc_final: 0.8851 (tt) REVERT: B 702 GLU cc_start: 0.8711 (tp30) cc_final: 0.8404 (tm-30) REVERT: C 129 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7666 (mp0) REVERT: C 150 ARG cc_start: 0.7848 (pmt-80) cc_final: 0.7449 (ptp-170) REVERT: C 309 ASP cc_start: 0.8463 (m-30) cc_final: 0.8042 (t0) REVERT: C 351 MET cc_start: 0.9255 (mmp) cc_final: 0.8875 (mmp) REVERT: C 414 ASP cc_start: 0.7733 (m-30) cc_final: 0.6974 (t0) REVERT: C 440 MET cc_start: 0.8567 (mtt) cc_final: 0.8217 (mmt) REVERT: C 574 MET cc_start: 0.8732 (ppp) cc_final: 0.8206 (ppp) REVERT: C 578 MET cc_start: 0.8095 (mtm) cc_final: 0.7693 (mtm) REVERT: C 594 TYR cc_start: 0.9200 (t80) cc_final: 0.8737 (t80) REVERT: C 598 LEU cc_start: 0.9122 (tt) cc_final: 0.8861 (tt) REVERT: D 129 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7661 (mp0) REVERT: D 304 VAL cc_start: 0.9532 (t) cc_final: 0.9311 (p) REVERT: D 309 ASP cc_start: 0.8448 (m-30) cc_final: 0.8032 (t0) REVERT: D 414 ASP cc_start: 0.7734 (m-30) cc_final: 0.6981 (t0) REVERT: D 440 MET cc_start: 0.8566 (mtt) cc_final: 0.8204 (mmt) REVERT: D 574 MET cc_start: 0.8732 (ppp) cc_final: 0.8250 (ppp) REVERT: D 578 MET cc_start: 0.7912 (mtm) cc_final: 0.7609 (mtm) REVERT: D 594 TYR cc_start: 0.9213 (t80) cc_final: 0.8709 (t80) REVERT: D 598 LEU cc_start: 0.9121 (tt) cc_final: 0.8861 (tt) REVERT: D 702 GLU cc_start: 0.8739 (tp30) cc_final: 0.8369 (tm-30) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.2832 time to fit residues: 234.6016 Evaluate side-chains 392 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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: 10.0000 chunk 222 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 205 optimal weight: 0.0670 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 452 ASN B 178 ASN B 339 ASN C 178 ASN D 178 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21420 Z= 0.167 Angle : 0.661 10.540 28948 Z= 0.328 Chirality : 0.040 0.171 3292 Planarity : 0.004 0.072 3600 Dihedral : 7.631 54.070 2860 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.30 % Favored : 86.38 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.16 % 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: -2.43 (0.17), residues: 2556 helix: -0.48 (0.14), residues: 1352 sheet: -3.91 (0.69), residues: 52 loop : -2.96 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 521 HIS 0.006 0.001 HIS C 477 PHE 0.021 0.001 PHE C 522 TYR 0.015 0.001 TYR A 359 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7531 (mp0) REVERT: A 148 ARG cc_start: 0.8515 (mmt90) cc_final: 0.7975 (mmm160) REVERT: A 263 GLU cc_start: 0.7096 (pt0) cc_final: 0.6833 (pt0) REVERT: A 309 ASP cc_start: 0.8379 (m-30) cc_final: 0.7941 (t0) REVERT: A 311 LYS cc_start: 0.8460 (mttt) cc_final: 0.7612 (tmtt) REVERT: A 321 TYR cc_start: 0.9018 (t80) cc_final: 0.8717 (t80) REVERT: A 414 ASP cc_start: 0.7693 (m-30) cc_final: 0.7074 (t0) REVERT: A 440 MET cc_start: 0.8590 (mtt) cc_final: 0.8180 (mmt) REVERT: A 515 SER cc_start: 0.8351 (m) cc_final: 0.7341 (t) REVERT: A 538 PHE cc_start: 0.7211 (t80) cc_final: 0.6927 (t80) REVERT: A 594 TYR cc_start: 0.9209 (t80) cc_final: 0.8599 (t80) REVERT: A 598 LEU cc_start: 0.9104 (tt) cc_final: 0.8865 (tt) REVERT: A 702 GLU cc_start: 0.8668 (tp30) cc_final: 0.8320 (tm-30) REVERT: B 129 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7545 (mp0) REVERT: B 148 ARG cc_start: 0.8541 (mmt90) cc_final: 0.7994 (mmm160) REVERT: B 293 ASP cc_start: 0.7880 (m-30) cc_final: 0.7138 (m-30) REVERT: B 309 ASP cc_start: 0.8394 (m-30) cc_final: 0.7959 (t0) REVERT: B 311 LYS cc_start: 0.8443 (mttt) cc_final: 0.7600 (tmtt) REVERT: B 406 ILE cc_start: 0.9531 (tp) cc_final: 0.9278 (mm) REVERT: B 414 ASP cc_start: 0.7677 (m-30) cc_final: 0.7064 (t0) REVERT: B 440 MET cc_start: 0.8581 (mtt) cc_final: 0.8174 (mmt) REVERT: B 515 SER cc_start: 0.8348 (m) cc_final: 0.7285 (t) REVERT: B 538 PHE cc_start: 0.7231 (t80) cc_final: 0.6939 (t80) REVERT: B 574 MET cc_start: 0.8631 (ppp) cc_final: 0.8082 (ppp) REVERT: B 578 MET cc_start: 0.8004 (mtm) cc_final: 0.7301 (mtm) REVERT: B 594 TYR cc_start: 0.9192 (t80) cc_final: 0.8700 (t80) REVERT: B 663 ILE cc_start: 0.9698 (tp) cc_final: 0.9482 (tp) REVERT: B 702 GLU cc_start: 0.8721 (tp30) cc_final: 0.8329 (tm-30) REVERT: C 129 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7545 (mp0) REVERT: C 148 ARG cc_start: 0.8540 (mmt90) cc_final: 0.7993 (mmm160) REVERT: C 293 ASP cc_start: 0.7825 (m-30) cc_final: 0.7320 (m-30) REVERT: C 309 ASP cc_start: 0.8403 (m-30) cc_final: 0.7955 (t0) REVERT: C 311 LYS cc_start: 0.8437 (mttt) cc_final: 0.7588 (tmtt) REVERT: C 351 MET cc_start: 0.9142 (mmp) cc_final: 0.8779 (mmp) REVERT: C 414 ASP cc_start: 0.7670 (m-30) cc_final: 0.7040 (t0) REVERT: C 440 MET cc_start: 0.8559 (mtt) cc_final: 0.8179 (mmt) REVERT: C 538 PHE cc_start: 0.7207 (t80) cc_final: 0.6916 (t80) REVERT: C 578 MET cc_start: 0.7955 (mtm) cc_final: 0.7634 (mtm) REVERT: C 594 TYR cc_start: 0.9195 (t80) cc_final: 0.8702 (t80) REVERT: C 663 ILE cc_start: 0.9685 (tp) cc_final: 0.9480 (tp) REVERT: D 129 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7537 (mp0) REVERT: D 224 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8084 (tp30) REVERT: D 293 ASP cc_start: 0.7873 (m-30) cc_final: 0.7119 (m-30) REVERT: D 309 ASP cc_start: 0.8402 (m-30) cc_final: 0.7942 (t0) REVERT: D 311 LYS cc_start: 0.8443 (mttt) cc_final: 0.7609 (tmtt) REVERT: D 321 TYR cc_start: 0.9017 (t80) cc_final: 0.8762 (t80) REVERT: D 414 ASP cc_start: 0.7662 (m-30) cc_final: 0.7045 (t0) REVERT: D 440 MET cc_start: 0.8573 (mtt) cc_final: 0.8170 (mmt) REVERT: D 515 SER cc_start: 0.8348 (m) cc_final: 0.7282 (t) REVERT: D 538 PHE cc_start: 0.7224 (t80) cc_final: 0.6940 (t80) REVERT: D 574 MET cc_start: 0.8634 (ppp) cc_final: 0.8026 (ppp) REVERT: D 578 MET cc_start: 0.7727 (mtm) cc_final: 0.7379 (mtm) REVERT: D 594 TYR cc_start: 0.9189 (t80) cc_final: 0.8652 (t80) REVERT: D 598 LEU cc_start: 0.9093 (tt) cc_final: 0.8878 (tt) REVERT: D 702 GLU cc_start: 0.8628 (tp30) cc_final: 0.8311 (tm-30) outliers start: 0 outliers final: 0 residues processed: 546 average time/residue: 0.2916 time to fit residues: 251.7436 Evaluate side-chains 401 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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: 3.9990 chunk 27 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 246 optimal weight: 0.3980 chunk 154 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN B 452 ASN B 580 GLN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21420 Z= 0.199 Angle : 0.690 9.302 28948 Z= 0.343 Chirality : 0.041 0.169 3292 Planarity : 0.004 0.073 3600 Dihedral : 7.722 56.079 2860 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.51 % Favored : 85.02 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.16 % 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: -2.35 (0.17), residues: 2556 helix: -0.32 (0.14), residues: 1368 sheet: -4.05 (0.66), residues: 52 loop : -3.08 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 521 HIS 0.006 0.001 HIS D 477 PHE 0.018 0.001 PHE C 261 TYR 0.022 0.002 TYR A 451 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.8379 (m-30) cc_final: 0.7959 (t0) REVERT: A 321 TYR cc_start: 0.9111 (t80) cc_final: 0.8860 (t80) REVERT: A 414 ASP cc_start: 0.7721 (m-30) cc_final: 0.7045 (t0) REVERT: A 440 MET cc_start: 0.8628 (mtt) cc_final: 0.8237 (mmt) REVERT: A 538 PHE cc_start: 0.7435 (t80) cc_final: 0.7150 (t80) REVERT: A 594 TYR cc_start: 0.9206 (t80) cc_final: 0.8658 (t80) REVERT: A 598 LEU cc_start: 0.9115 (tt) cc_final: 0.8875 (tt) REVERT: A 677 MET cc_start: 0.8614 (mmm) cc_final: 0.8370 (mmm) REVERT: A 702 GLU cc_start: 0.8763 (tp30) cc_final: 0.8366 (tm-30) REVERT: B 148 ARG cc_start: 0.8502 (mmt90) cc_final: 0.7994 (mmm160) REVERT: B 309 ASP cc_start: 0.8440 (m-30) cc_final: 0.8007 (t0) REVERT: B 414 ASP cc_start: 0.7695 (m-30) cc_final: 0.7000 (t0) REVERT: B 440 MET cc_start: 0.8604 (mtt) cc_final: 0.8211 (mmt) REVERT: B 538 PHE cc_start: 0.7350 (t80) cc_final: 0.7048 (t80) REVERT: B 594 TYR cc_start: 0.9231 (t80) cc_final: 0.8725 (t80) REVERT: B 702 GLU cc_start: 0.8761 (tp30) cc_final: 0.8383 (tm-30) REVERT: C 148 ARG cc_start: 0.8510 (mmt90) cc_final: 0.7990 (mmm160) REVERT: C 293 ASP cc_start: 0.7824 (m-30) cc_final: 0.7337 (m-30) REVERT: C 309 ASP cc_start: 0.8411 (m-30) cc_final: 0.7982 (t0) REVERT: C 414 ASP cc_start: 0.7703 (m-30) cc_final: 0.7031 (t0) REVERT: C 440 MET cc_start: 0.8591 (mtt) cc_final: 0.8210 (mmt) REVERT: C 538 PHE cc_start: 0.7306 (t80) cc_final: 0.7050 (t80) REVERT: C 594 TYR cc_start: 0.9242 (t80) cc_final: 0.8749 (t80) REVERT: D 304 VAL cc_start: 0.9498 (t) cc_final: 0.9289 (p) REVERT: D 309 ASP cc_start: 0.8404 (m-30) cc_final: 0.7963 (t0) REVERT: D 321 TYR cc_start: 0.9114 (t80) cc_final: 0.8781 (t80) REVERT: D 414 ASP cc_start: 0.7687 (m-30) cc_final: 0.7020 (t0) REVERT: D 440 MET cc_start: 0.8615 (mtt) cc_final: 0.8223 (mmt) REVERT: D 538 PHE cc_start: 0.7345 (t80) cc_final: 0.7050 (t80) REVERT: D 594 TYR cc_start: 0.9204 (t80) cc_final: 0.8691 (t80) REVERT: D 598 LEU cc_start: 0.9099 (tt) cc_final: 0.8883 (tt) REVERT: D 702 GLU cc_start: 0.8742 (tp30) cc_final: 0.8335 (tm-30) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.2845 time to fit residues: 230.8300 Evaluate side-chains 375 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 0.4980 chunk 147 optimal weight: 0.0010 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 0.0670 chunk 168 optimal weight: 0.3980 chunk 121 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 overall best weight: 0.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21420 Z= 0.167 Angle : 0.688 8.811 28948 Z= 0.336 Chirality : 0.040 0.172 3292 Planarity : 0.004 0.071 3600 Dihedral : 7.516 58.631 2860 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.48 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % 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: -2.46 (0.16), residues: 2556 helix: -0.42 (0.14), residues: 1404 sheet: -3.97 (0.69), residues: 52 loop : -3.22 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 521 HIS 0.006 0.001 HIS A 477 PHE 0.016 0.001 PHE A 261 TYR 0.014 0.001 TYR C 650 ARG 0.002 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7327 (mp0) REVERT: A 309 ASP cc_start: 0.8367 (m-30) cc_final: 0.7952 (t0) REVERT: A 311 LYS cc_start: 0.8414 (mttt) cc_final: 0.7640 (tmtt) REVERT: A 414 ASP cc_start: 0.7628 (m-30) cc_final: 0.7091 (t0) REVERT: A 440 MET cc_start: 0.8566 (mtt) cc_final: 0.8184 (mmp) REVERT: A 482 LEU cc_start: 0.6724 (mm) cc_final: 0.6489 (tt) REVERT: A 515 SER cc_start: 0.8339 (m) cc_final: 0.7395 (t) REVERT: A 538 PHE cc_start: 0.7099 (t80) cc_final: 0.6889 (t80) REVERT: A 594 TYR cc_start: 0.9126 (t80) cc_final: 0.8694 (t80) REVERT: A 624 SER cc_start: 0.7657 (p) cc_final: 0.7446 (m) REVERT: A 663 ILE cc_start: 0.9702 (tp) cc_final: 0.9500 (tp) REVERT: A 702 GLU cc_start: 0.8736 (tp30) cc_final: 0.8287 (tm-30) REVERT: B 129 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7344 (mp0) REVERT: B 148 ARG cc_start: 0.8494 (mmt90) cc_final: 0.7986 (mmm160) REVERT: B 309 ASP cc_start: 0.8385 (m-30) cc_final: 0.7932 (t0) REVERT: B 311 LYS cc_start: 0.8394 (mttt) cc_final: 0.7624 (tmtt) REVERT: B 406 ILE cc_start: 0.9501 (tp) cc_final: 0.9259 (mm) REVERT: B 414 ASP cc_start: 0.7574 (m-30) cc_final: 0.7064 (t0) REVERT: B 440 MET cc_start: 0.8564 (mtt) cc_final: 0.8185 (mmp) REVERT: B 482 LEU cc_start: 0.6734 (mm) cc_final: 0.6487 (tt) REVERT: B 515 SER cc_start: 0.8324 (m) cc_final: 0.7351 (t) REVERT: B 521 TRP cc_start: 0.8185 (t60) cc_final: 0.7872 (t60) REVERT: B 538 PHE cc_start: 0.7193 (t80) cc_final: 0.6910 (t80) REVERT: B 594 TYR cc_start: 0.9187 (t80) cc_final: 0.8675 (t80) REVERT: B 702 GLU cc_start: 0.8705 (tp30) cc_final: 0.8258 (tm-30) REVERT: C 129 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7347 (mp0) REVERT: C 148 ARG cc_start: 0.8493 (mmt90) cc_final: 0.7973 (mmm160) REVERT: C 293 ASP cc_start: 0.7750 (m-30) cc_final: 0.7206 (m-30) REVERT: C 309 ASP cc_start: 0.8342 (m-30) cc_final: 0.7932 (t0) REVERT: C 311 LYS cc_start: 0.8397 (mttt) cc_final: 0.7598 (tmtt) REVERT: C 414 ASP cc_start: 0.7571 (m-30) cc_final: 0.7041 (t0) REVERT: C 440 MET cc_start: 0.8553 (mtt) cc_final: 0.8181 (mmp) REVERT: C 482 LEU cc_start: 0.6741 (mm) cc_final: 0.6508 (tt) REVERT: C 515 SER cc_start: 0.8301 (m) cc_final: 0.7332 (t) REVERT: C 521 TRP cc_start: 0.8497 (t60) cc_final: 0.7641 (t60) REVERT: C 538 PHE cc_start: 0.7153 (t80) cc_final: 0.6857 (t80) REVERT: C 594 TYR cc_start: 0.9154 (t80) cc_final: 0.8728 (t80) REVERT: D 129 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7336 (mp0) REVERT: D 309 ASP cc_start: 0.8392 (m-30) cc_final: 0.7951 (t0) REVERT: D 311 LYS cc_start: 0.8398 (mttt) cc_final: 0.7626 (tmtt) REVERT: D 414 ASP cc_start: 0.7592 (m-30) cc_final: 0.7053 (t0) REVERT: D 440 MET cc_start: 0.8550 (mtt) cc_final: 0.8183 (mmp) REVERT: D 482 LEU cc_start: 0.6739 (mm) cc_final: 0.6497 (tt) REVERT: D 515 SER cc_start: 0.8351 (m) cc_final: 0.7314 (t) REVERT: D 538 PHE cc_start: 0.7185 (t80) cc_final: 0.6889 (t80) REVERT: D 594 TYR cc_start: 0.9150 (t80) cc_final: 0.8710 (t80) REVERT: D 702 GLU cc_start: 0.8717 (tp30) cc_final: 0.8499 (tp30) outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.2859 time to fit residues: 251.2765 Evaluate side-chains 391 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.483 ------------------------------------------------------------------------------- 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: 4.9990 chunk 236 optimal weight: 0.0870 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 217 optimal weight: 0.4980 chunk 150 optimal weight: 10.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21420 Z= 0.158 Angle : 0.683 8.459 28948 Z= 0.330 Chirality : 0.040 0.168 3292 Planarity : 0.004 0.072 3600 Dihedral : 7.327 58.026 2860 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.56 % Favored : 87.13 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.16), residues: 2556 helix: -0.38 (0.14), residues: 1384 sheet: -3.94 (0.68), residues: 52 loop : -3.02 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 521 HIS 0.005 0.001 HIS C 477 PHE 0.015 0.001 PHE B 261 TYR 0.012 0.001 TYR A 359 ARG 0.005 0.000 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7514 (mp0) REVERT: A 148 ARG cc_start: 0.8455 (mmt90) cc_final: 0.7954 (mmm160) REVERT: A 211 GLU cc_start: 0.8530 (tt0) cc_final: 0.8248 (tp30) REVERT: A 309 ASP cc_start: 0.8336 (m-30) cc_final: 0.7989 (t0) REVERT: A 311 LYS cc_start: 0.8370 (mttt) cc_final: 0.7629 (tmtt) REVERT: A 347 LEU cc_start: 0.9365 (tp) cc_final: 0.9055 (tt) REVERT: A 414 ASP cc_start: 0.7566 (m-30) cc_final: 0.7183 (t0) REVERT: A 440 MET cc_start: 0.8491 (mtt) cc_final: 0.8221 (mmp) REVERT: A 482 LEU cc_start: 0.6802 (mm) cc_final: 0.6535 (tt) REVERT: A 538 PHE cc_start: 0.7204 (t80) cc_final: 0.6893 (t80) REVERT: A 594 TYR cc_start: 0.9099 (t80) cc_final: 0.8646 (t80) REVERT: B 129 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7525 (mp0) REVERT: B 148 ARG cc_start: 0.8462 (mmt90) cc_final: 0.7977 (mmm160) REVERT: B 211 GLU cc_start: 0.8553 (tt0) cc_final: 0.8246 (tp30) REVERT: B 304 VAL cc_start: 0.9526 (t) cc_final: 0.9307 (p) REVERT: B 309 ASP cc_start: 0.8355 (m-30) cc_final: 0.7973 (t0) REVERT: B 311 LYS cc_start: 0.8296 (mttt) cc_final: 0.7534 (tmtt) REVERT: B 347 LEU cc_start: 0.9158 (tp) cc_final: 0.8921 (tt) REVERT: B 414 ASP cc_start: 0.7606 (m-30) cc_final: 0.7131 (t0) REVERT: B 440 MET cc_start: 0.8486 (mtt) cc_final: 0.8218 (mmp) REVERT: B 482 LEU cc_start: 0.6836 (mm) cc_final: 0.6543 (tt) REVERT: B 515 SER cc_start: 0.8333 (m) cc_final: 0.7356 (t) REVERT: B 538 PHE cc_start: 0.7209 (t80) cc_final: 0.6911 (t80) REVERT: B 578 MET cc_start: 0.7864 (mtm) cc_final: 0.7590 (mtm) REVERT: B 594 TYR cc_start: 0.9148 (t80) cc_final: 0.8676 (t80) REVERT: C 129 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7521 (mp0) REVERT: C 148 ARG cc_start: 0.8470 (mmt90) cc_final: 0.7964 (mmm160) REVERT: C 211 GLU cc_start: 0.8551 (tt0) cc_final: 0.8248 (tp30) REVERT: C 293 ASP cc_start: 0.7633 (m-30) cc_final: 0.7012 (m-30) REVERT: C 309 ASP cc_start: 0.8336 (m-30) cc_final: 0.7978 (t0) REVERT: C 311 LYS cc_start: 0.8371 (mttt) cc_final: 0.7619 (tmtt) REVERT: C 414 ASP cc_start: 0.7524 (m-30) cc_final: 0.7146 (t0) REVERT: C 440 MET cc_start: 0.8480 (mtt) cc_final: 0.8198 (mmp) REVERT: C 482 LEU cc_start: 0.6848 (mm) cc_final: 0.6546 (tt) REVERT: C 515 SER cc_start: 0.8345 (m) cc_final: 0.7395 (t) REVERT: C 521 TRP cc_start: 0.8508 (t60) cc_final: 0.7575 (t60) REVERT: C 538 PHE cc_start: 0.7136 (t80) cc_final: 0.6839 (t80) REVERT: C 574 MET cc_start: 0.8557 (ppp) cc_final: 0.7656 (ptt) REVERT: C 594 TYR cc_start: 0.9144 (t80) cc_final: 0.8705 (t80) REVERT: D 129 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7519 (mp0) REVERT: D 211 GLU cc_start: 0.8539 (tt0) cc_final: 0.8241 (tp30) REVERT: D 309 ASP cc_start: 0.8375 (m-30) cc_final: 0.7995 (t0) REVERT: D 311 LYS cc_start: 0.8360 (mttt) cc_final: 0.7620 (tmtt) REVERT: D 414 ASP cc_start: 0.7547 (m-30) cc_final: 0.7160 (t0) REVERT: D 440 MET cc_start: 0.8467 (mtt) cc_final: 0.8207 (mmp) REVERT: D 482 LEU cc_start: 0.6840 (mm) cc_final: 0.6543 (tt) REVERT: D 515 SER cc_start: 0.8319 (m) cc_final: 0.7352 (t) REVERT: D 538 PHE cc_start: 0.7193 (t80) cc_final: 0.6909 (t80) REVERT: D 594 TYR cc_start: 0.9150 (t80) cc_final: 0.8659 (t80) REVERT: D 672 MET cc_start: 0.8595 (mmm) cc_final: 0.8179 (tpt) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.2876 time to fit residues: 240.3641 Evaluate side-chains 394 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.691 ------------------------------------------------------------------------------- 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: 4.9990 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 chunk 255 optimal weight: 30.0000 chunk 234 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 156 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 178 ASN C 178 ASN D 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21420 Z= 0.227 Angle : 0.736 11.225 28948 Z= 0.359 Chirality : 0.042 0.180 3292 Planarity : 0.005 0.072 3600 Dihedral : 7.536 57.750 2860 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.08 % Favored : 85.60 % 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 : 5.88 % Twisted General : 0.08 % 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: -2.11 (0.17), residues: 2556 helix: -0.11 (0.14), residues: 1348 sheet: None (None), residues: 0 loop : -3.04 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 521 HIS 0.007 0.001 HIS D 477 PHE 0.034 0.001 PHE A 261 TYR 0.015 0.002 TYR D 359 ARG 0.006 0.000 ARG D 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7555 (mp0) REVERT: A 309 ASP cc_start: 0.8353 (m-30) cc_final: 0.8007 (t0) REVERT: A 311 LYS cc_start: 0.8407 (mttt) cc_final: 0.7535 (tmtt) REVERT: A 414 ASP cc_start: 0.7713 (m-30) cc_final: 0.7234 (t0) REVERT: A 440 MET cc_start: 0.8561 (mtt) cc_final: 0.8258 (mmp) REVERT: A 482 LEU cc_start: 0.6877 (mm) cc_final: 0.6592 (tt) REVERT: A 515 SER cc_start: 0.8266 (m) cc_final: 0.7258 (t) REVERT: A 594 TYR cc_start: 0.9113 (t80) cc_final: 0.8658 (t80) REVERT: B 129 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7563 (mp0) REVERT: B 148 ARG cc_start: 0.8538 (mmt90) cc_final: 0.8005 (mmm160) REVERT: B 309 ASP cc_start: 0.8377 (m-30) cc_final: 0.8023 (t0) REVERT: B 311 LYS cc_start: 0.8383 (mttt) cc_final: 0.7596 (tmtt) REVERT: B 347 LEU cc_start: 0.9212 (tp) cc_final: 0.8958 (tt) REVERT: B 414 ASP cc_start: 0.7783 (m-30) cc_final: 0.7193 (t0) REVERT: B 440 MET cc_start: 0.8578 (mtt) cc_final: 0.8243 (mmp) REVERT: B 515 SER cc_start: 0.8283 (m) cc_final: 0.7208 (t) REVERT: B 538 PHE cc_start: 0.7298 (t80) cc_final: 0.7020 (t80) REVERT: B 578 MET cc_start: 0.7945 (mtm) cc_final: 0.7668 (mtm) REVERT: C 148 ARG cc_start: 0.8536 (mmt90) cc_final: 0.7991 (mmm160) REVERT: C 309 ASP cc_start: 0.8363 (m-30) cc_final: 0.8008 (t0) REVERT: C 311 LYS cc_start: 0.8387 (mttt) cc_final: 0.7514 (tmtt) REVERT: C 414 ASP cc_start: 0.7668 (m-30) cc_final: 0.7179 (t0) REVERT: C 440 MET cc_start: 0.8573 (mtt) cc_final: 0.8259 (mmp) REVERT: C 515 SER cc_start: 0.8252 (m) cc_final: 0.7206 (t) REVERT: C 538 PHE cc_start: 0.7271 (t80) cc_final: 0.6986 (t80) REVERT: C 594 TYR cc_start: 0.9137 (t80) cc_final: 0.8663 (t80) REVERT: D 309 ASP cc_start: 0.8381 (m-30) cc_final: 0.8001 (t0) REVERT: D 311 LYS cc_start: 0.8383 (mttt) cc_final: 0.7550 (tmtt) REVERT: D 414 ASP cc_start: 0.7680 (m-30) cc_final: 0.7212 (t0) REVERT: D 440 MET cc_start: 0.8551 (mtt) cc_final: 0.8240 (mmp) REVERT: D 515 SER cc_start: 0.8283 (m) cc_final: 0.7162 (t) REVERT: D 538 PHE cc_start: 0.7300 (t80) cc_final: 0.7017 (t80) REVERT: D 574 MET cc_start: 0.8691 (ppp) cc_final: 0.7545 (ptt) REVERT: D 578 MET cc_start: 0.8199 (mtm) cc_final: 0.7881 (mtm) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.2848 time to fit residues: 224.9774 Evaluate side-chains 370 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.665 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 85 optimal weight: 0.0270 chunk 208 optimal weight: 0.0270 chunk 25 optimal weight: 0.0000 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 339 ASN B 178 ASN B 220 ASN C 339 ASN C 452 ASN D 178 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.117102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.098706 restraints weight = 55984.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101249 restraints weight = 32674.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102994 restraints weight = 22250.844| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21420 Z= 0.164 Angle : 0.697 11.609 28948 Z= 0.335 Chirality : 0.041 0.175 3292 Planarity : 0.004 0.073 3600 Dihedral : 7.364 59.809 2860 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.46 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.17), residues: 2556 helix: -0.06 (0.14), residues: 1352 sheet: None (None), residues: 0 loop : -2.96 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 521 HIS 0.006 0.001 HIS A 477 PHE 0.023 0.001 PHE A 538 TYR 0.013 0.001 TYR B 359 ARG 0.005 0.000 ARG C 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4815.64 seconds wall clock time: 88 minutes 0.66 seconds (5280.66 seconds total)