Starting phenix.real_space_refine on Mon Feb 19 19:02:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqh_21870/02_2024/6wqh_21870_updated.pdb" } resolution = 3.6 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= 0.009 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 S 99 5.16 5 B 6 2.79 5 C 16078 2.51 5 N 4448 2.21 5 O 4827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ASP 434": "OD1" <-> "OD2" Residue "B GLU 441": "OE1" <-> "OE2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B GLU 655": "OE1" <-> "OE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C GLU 533": "OE1" <-> "OE2" Residue "C ARG 536": "NH1" <-> "NH2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F GLU 331": "OE1" <-> "OE2" Residue "F ARG 432": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ARG 584": "NH1" <-> "NH2" Residue "F GLU 631": "OE1" <-> "OE2" Residue "F ARG 709": "NH1" <-> "NH2" Residue "F GLU 745": "OE1" <-> "OE2" Residue "F GLU 760": "OE1" <-> "OE2" Residue "F GLU 764": "OE1" <-> "OE2" Residue "F GLU 773": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 432": "NH1" <-> "NH2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 536": "NH1" <-> "NH2" Residue "D GLU 537": "OE1" <-> "OE2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D GLU 613": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D GLU 744": "OE1" <-> "OE2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E ARG 432": "NH1" <-> "NH2" Residue "E GLU 489": "OE1" <-> "OE2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E GLU 533": "OE1" <-> "OE2" Residue "E ARG 536": "NH1" <-> "NH2" Residue "E ARG 584": "NH1" <-> "NH2" Residue "E GLU 591": "OE1" <-> "OE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E GLU 655": "OE1" <-> "OE2" Residue "E GLU 744": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25471 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 3, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 1 Chain: "B" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 2, 'PTRANS': 34, 'TRANS': 500} Chain breaks: 1 Chain: "C" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4188 Classifications: {'peptide': 538} Link IDs: {'CIS': 2, 'PTRANS': 34, 'TRANS': 501} Chain breaks: 1 Chain: "F" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 3, 'PTRANS': 34, 'TRANS': 499} Chain: "D" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 3, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 1 Chain: "E" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 3, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 1 Chain: "S" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'4KZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.32, per 1000 atoms: 0.52 Number of scatterers: 25471 At special positions: 0 Unit cell: (131.3, 148.85, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 99 16.00 P 13 15.00 O 4827 8.00 N 4448 7.00 C 16078 6.00 B 6 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 Atom "HETATM25162 O3B AGS A 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.61 Conformation dependent library (CDL) restraints added in 4.6 seconds 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 25 sheets defined 39.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.18 Creating SS restraints... Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.635A pdb=" N ARG A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 removed outlier: 4.842A pdb=" N LYS A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ARG A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 4.642A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 323 through 337 removed outlier: 3.644A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 removed outlier: 3.645A pdb=" N ARG A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 368 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 370 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 436 through 443 removed outlier: 4.293A pdb=" N LEU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.785A pdb=" N ALA A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.840A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.722A pdb=" N GLU A 546 " --> pdb=" O GLY A 542 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 Proline residue: A 575 - end of helix removed outlier: 4.252A pdb=" N LEU A 578 " --> pdb=" O PRO A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 719 through 727 removed outlier: 3.527A pdb=" N LEU A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 724 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 740 Processing helix chain 'A' and resid 742 through 745 removed outlier: 3.542A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 745' Processing helix chain 'A' and resid 748 through 751 No H-bonds generated for 'chain 'A' and resid 748 through 751' Processing helix chain 'A' and resid 762 through 769 removed outlier: 3.788A pdb=" N TYR A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.862A pdb=" N LEU B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 283 through 293 removed outlier: 4.489A pdb=" N TYR B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.675A pdb=" N MET B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.523A pdb=" N ARG B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.619A pdb=" N GLU B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 533 removed outlier: 4.118A pdb=" N VAL B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 560 removed outlier: 3.657A pdb=" N LYS B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 Proline residue: B 575 - end of helix No H-bonds generated for 'chain 'B' and resid 571 through 577' Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.687A pdb=" N ALA B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 660 No H-bonds generated for 'chain 'B' and resid 657 through 660' Processing helix chain 'B' and resid 680 through 691 Processing helix chain 'B' and resid 719 through 728 Processing helix chain 'B' and resid 737 through 745 removed outlier: 4.602A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 743 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.604A pdb=" N GLU B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 753' Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 260 through 274 removed outlier: 4.488A pdb=" N GLU C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 removed outlier: 4.225A pdb=" N THR C 288 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU C 295 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.532A pdb=" N GLN C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 337 removed outlier: 3.688A pdb=" N TYR C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 372 removed outlier: 4.219A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.651A pdb=" N MET C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 442 removed outlier: 4.222A pdb=" N LEU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 5.918A pdb=" N ASN C 449 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 506 through 513 Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.862A pdb=" N LEU C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 529 " --> pdb=" O ALA C 525 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 530 " --> pdb=" O ALA C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 560 removed outlier: 3.961A pdb=" N ARG C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLU C 546 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.699A pdb=" N ILE C 574 " --> pdb=" O ALA C 571 " (cutoff:3.500A) Proline residue: C 575 - end of helix removed outlier: 4.276A pdb=" N LEU C 578 " --> pdb=" O PRO C 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 571 through 578' Processing helix chain 'C' and resid 631 through 647 removed outlier: 3.561A pdb=" N HIS C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 680 through 692 removed outlier: 3.645A pdb=" N THR C 685 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 737 through 745 removed outlier: 4.471A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 4.026A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'F' and resid 245 through 253 removed outlier: 4.802A pdb=" N ARG F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 264 through 267 No H-bonds generated for 'chain 'F' and resid 264 through 267' Processing helix chain 'F' and resid 269 through 272 No H-bonds generated for 'chain 'F' and resid 269 through 272' Processing helix chain 'F' and resid 287 through 293 removed outlier: 4.608A pdb=" N TRP F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 315 removed outlier: 4.164A pdb=" N VAL F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 363 through 372 removed outlier: 3.686A pdb=" N MET F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 411 removed outlier: 3.567A pdb=" N ALA F 408 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 443 removed outlier: 3.857A pdb=" N GLU F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 484 removed outlier: 5.280A pdb=" N ARG F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 504 removed outlier: 3.787A pdb=" N ALA F 502 " --> pdb=" O LYS F 498 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN F 504 " --> pdb=" O ALA F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 514 removed outlier: 4.731A pdb=" N GLU F 513 " --> pdb=" O LYS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 532 removed outlier: 3.624A pdb=" N LEU F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG F 529 " --> pdb=" O ALA F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 560 removed outlier: 4.331A pdb=" N ARG F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU F 546 " --> pdb=" O GLY F 542 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 547 " --> pdb=" O LEU F 543 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP F 558 " --> pdb=" O GLY F 554 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 559 " --> pdb=" O ALA F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 578 removed outlier: 3.921A pdb=" N LEU F 578 " --> pdb=" O PRO F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 647 removed outlier: 3.558A pdb=" N GLN F 638 " --> pdb=" O LYS F 634 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 660 No H-bonds generated for 'chain 'F' and resid 657 through 660' Processing helix chain 'F' and resid 677 through 692 removed outlier: 3.582A pdb=" N GLY F 680 " --> pdb=" O PRO F 677 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE F 681 " --> pdb=" O SER F 678 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE F 687 " --> pdb=" O ALA F 684 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA F 690 " --> pdb=" O ILE F 687 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU F 691 " --> pdb=" O ALA F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 738 through 745 removed outlier: 3.578A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 753 Processing helix chain 'F' and resid 762 through 769 removed outlier: 3.695A pdb=" N GLU F 767 " --> pdb=" O GLY F 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 253 Processing helix chain 'D' and resid 260 through 275 removed outlier: 3.579A pdb=" N GLU D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 removed outlier: 3.560A pdb=" N TRP D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.132A pdb=" N ASP D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 336 removed outlier: 3.553A pdb=" N TYR D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 372 removed outlier: 3.690A pdb=" N ALA D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG D 370 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 436 through 442 removed outlier: 3.727A pdb=" N LEU D 440 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU D 441 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 442 " --> pdb=" O MET D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 479 through 483 removed outlier: 3.643A pdb=" N ASP D 483 " --> pdb=" O ARG D 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 479 through 483' Processing helix chain 'D' and resid 495 through 504 removed outlier: 4.350A pdb=" N ARG D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 514 removed outlier: 3.992A pdb=" N ARG D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 541 through 559 removed outlier: 3.955A pdb=" N GLU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 549 " --> pdb=" O ARG D 545 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 556 " --> pdb=" O ARG D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 578 Proline residue: D 575 - end of helix Processing helix chain 'D' and resid 631 through 646 Processing helix chain 'D' and resid 655 through 659 removed outlier: 4.139A pdb=" N TYR D 658 " --> pdb=" O GLU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 737 through 745 removed outlier: 4.399A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.623A pdb=" N GLU D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.702A pdb=" N GLU D 767 " --> pdb=" O GLY D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 249 removed outlier: 3.991A pdb=" N LEU E 249 " --> pdb=" O LEU E 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 246 through 249' Processing helix chain 'E' and resid 263 through 266 No H-bonds generated for 'chain 'E' and resid 263 through 266' Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 285 through 294 removed outlier: 3.715A pdb=" N TYR E 289 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU E 290 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP E 292 " --> pdb=" O TYR E 289 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 293 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 removed outlier: 4.653A pdb=" N GLN E 313 " --> pdb=" O ASN E 309 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 315 " --> pdb=" O THR E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 330 Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.548A pdb=" N GLN E 337 " --> pdb=" O ALA E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 372 removed outlier: 4.013A pdb=" N ARG E 366 " --> pdb=" O SER E 363 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA E 369 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARG E 370 " --> pdb=" O SER E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 424 through 426 No H-bonds generated for 'chain 'E' and resid 424 through 426' Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.618A pdb=" N MET E 439 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 479 through 481 No H-bonds generated for 'chain 'E' and resid 479 through 481' Processing helix chain 'E' and resid 495 through 504 removed outlier: 3.540A pdb=" N GLN E 499 " --> pdb=" O ASN E 495 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA E 500 " --> pdb=" O MET E 496 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 501 " --> pdb=" O GLU E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 514 removed outlier: 3.903A pdb=" N VAL E 511 " --> pdb=" O TRP E 507 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG E 512 " --> pdb=" O PRO E 508 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU E 513 " --> pdb=" O LYS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 532 removed outlier: 3.768A pdb=" N LEU E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG E 529 " --> pdb=" O ALA E 525 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL E 530 " --> pdb=" O ALA E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 543 No H-bonds generated for 'chain 'E' and resid 541 through 543' Processing helix chain 'E' and resid 548 through 560 removed outlier: 4.162A pdb=" N ALA E 555 " --> pdb=" O ALA E 551 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS E 556 " --> pdb=" O ARG E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 577 Proline residue: E 575 - end of helix Processing helix chain 'E' and resid 631 through 645 removed outlier: 3.738A pdb=" N SER E 636 " --> pdb=" O VAL E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 727 Processing helix chain 'E' and resid 737 through 739 No H-bonds generated for 'chain 'E' and resid 737 through 739' Processing helix chain 'E' and resid 741 through 745 removed outlier: 3.515A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 Processing helix chain 'E' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'A' and resid 468 through 471 removed outlier: 6.624A pdb=" N LEU A 351 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA A 471 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU A 486 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 354 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 488 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 376 through 378 removed outlier: 6.119A pdb=" N VAL A 418 " --> pdb=" O HIS A 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.193A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 596 through 603 removed outlier: 3.593A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 617 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.600A pdb=" N LYS A 732 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS A 757 " --> pdb=" O LEU A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 486 through 490 removed outlier: 3.622A pdb=" N THR B 470 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 520 through 522 removed outlier: 5.822A pdb=" N ARG B 567 " --> pdb=" O GLU B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 596 through 603 Processing sheet with id= I, first strand: chain 'B' and resid 700 through 702 removed outlier: 6.454A pdb=" N LYS B 732 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 468 through 471 removed outlier: 6.555A pdb=" N LEU C 351 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA C 471 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLU C 486 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 354 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE C 488 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 596 through 603 removed outlier: 6.545A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.368A pdb=" N LYS C 732 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU C 755 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU C 735 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS C 757 " --> pdb=" O LEU C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 485 through 489 removed outlier: 6.178A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR F 469 " --> pdb=" O LEU F 353 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 416 through 420 removed outlier: 6.886A pdb=" N LYS F 464 " --> pdb=" O PRO F 417 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE F 419 " --> pdb=" O LYS F 464 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE F 466 " --> pdb=" O ILE F 419 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.326A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 596 through 603 removed outlier: 3.539A pdb=" N VAL F 617 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER F 624 " --> pdb=" O LEU F 663 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 667 " --> pdb=" O THR F 626 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 732 through 736 removed outlier: 6.182A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 486 through 489 removed outlier: 3.657A pdb=" N VAL D 352 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU D 351 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR D 470 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU D 421 " --> pdb=" O THR D 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.107A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 596 through 601 Processing sheet with id= U, first strand: chain 'D' and resid 700 through 702 removed outlier: 6.174A pdb=" N LYS D 732 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 352 through 354 Processing sheet with id= W, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.395A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 596 through 603 Processing sheet with id= Y, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.495A pdb=" N LYS E 732 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y 667 hydrogen bonds defined for protein. 1806 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: 7.93 Time building geometry restraints manager: 12.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.43: 10285 1.43 - 1.82: 15672 1.82 - 2.20: 3 2.20 - 2.59: 0 2.59 - 2.98: 1 Bond restraints: 25961 Sorted by residual: bond pdb=" C GLU F 589 " pdb=" N THR F 590 " ideal model delta sigma weight residual 1.332 2.975 -1.643 1.40e-02 5.10e+03 1.38e+04 bond pdb=" C GLY F 676 " pdb=" N PRO F 677 " ideal model delta sigma weight residual 1.332 1.769 -0.437 8.90e-03 1.26e+04 2.41e+03 bond pdb=" C GLY D 676 " pdb=" N PRO D 677 " ideal model delta sigma weight residual 1.333 1.711 -0.378 7.80e-03 1.64e+04 2.34e+03 bond pdb=" C GLY A 676 " pdb=" N PRO A 677 " ideal model delta sigma weight residual 1.331 1.649 -0.318 7.90e-03 1.60e+04 1.62e+03 bond pdb=" C GLY B 676 " pdb=" N PRO B 677 " ideal model delta sigma weight residual 1.333 1.159 0.174 7.80e-03 1.64e+04 4.99e+02 ... (remaining 25956 not shown) Histogram of bond angle deviations from ideal: 48.18 - 65.98: 1 65.98 - 83.79: 0 83.79 - 101.59: 101 101.59 - 119.40: 22301 119.40 - 137.20: 12816 Bond angle restraints: 35219 Sorted by residual: angle pdb=" O GLU F 589 " pdb=" C GLU F 589 " pdb=" N THR F 590 " ideal model delta sigma weight residual 122.11 48.18 73.93 1.18e+00 7.18e-01 3.93e+03 angle pdb=" O GLY A 676 " pdb=" C GLY A 676 " pdb=" N PRO A 677 " ideal model delta sigma weight residual 121.77 105.57 16.20 1.00e+00 1.00e+00 2.62e+02 angle pdb=" C GLY A 676 " pdb=" N PRO A 677 " pdb=" CA PRO A 677 " ideal model delta sigma weight residual 121.00 137.20 -16.20 1.16e+00 7.43e-01 1.95e+02 angle pdb=" C GLY D 676 " pdb=" N PRO D 677 " pdb=" CA PRO D 677 " ideal model delta sigma weight residual 120.94 136.21 -15.27 1.14e+00 7.69e-01 1.79e+02 angle pdb=" O GLY D 676 " pdb=" C GLY D 676 " pdb=" N PRO D 677 " ideal model delta sigma weight residual 121.77 110.81 10.96 1.00e+00 1.00e+00 1.20e+02 ... (remaining 35214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.20: 15320 31.20 - 62.40: 515 62.40 - 93.59: 63 93.59 - 124.79: 1 124.79 - 155.99: 2 Dihedral angle restraints: 15901 sinusoidal: 6649 harmonic: 9252 Sorted by residual: dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 163.55 136.46 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" C5' ADP F 801 " pdb=" O5' ADP F 801 " pdb=" PA ADP F 801 " pdb=" O2A ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 -179.77 119.77 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" CA GLN C 278 " pdb=" C GLN C 278 " pdb=" N GLY C 279 " pdb=" CA GLY C 279 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 15898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3820 0.101 - 0.203: 169 0.203 - 0.304: 7 0.304 - 0.406: 1 0.406 - 0.507: 1 Chirality restraints: 3998 Sorted by residual: chirality pdb=" CA ARG B 432 " pdb=" N ARG B 432 " pdb=" C ARG B 432 " pdb=" CB ARG B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CA THR D 682 " pdb=" N THR D 682 " pdb=" C THR D 682 " pdb=" CB THR D 682 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ASP C 675 " pdb=" N ASP C 675 " pdb=" C ASP C 675 " pdb=" CB ASP C 675 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3995 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 589 " -0.189 2.00e-02 2.50e+03 2.74e-01 7.52e+02 pdb=" C GLU F 589 " 0.446 2.00e-02 2.50e+03 pdb=" O GLU F 589 " -0.256 2.00e-02 2.50e+03 pdb=" N THR F 590 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ D 802 " 0.206 2.00e-02 2.50e+03 2.22e-01 6.19e+02 pdb=" C18 4KZ D 802 " -0.138 2.00e-02 2.50e+03 pdb=" C21 4KZ D 802 " 0.264 2.00e-02 2.50e+03 pdb=" N20 4KZ D 802 " -0.341 2.00e-02 2.50e+03 pdb=" O19 4KZ D 802 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ B 802 " -0.200 2.00e-02 2.50e+03 2.15e-01 5.76e+02 pdb=" C18 4KZ B 802 " 0.127 2.00e-02 2.50e+03 pdb=" C21 4KZ B 802 " -0.257 2.00e-02 2.50e+03 pdb=" N20 4KZ B 802 " 0.329 2.00e-02 2.50e+03 pdb=" O19 4KZ B 802 " 0.001 2.00e-02 2.50e+03 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 17 1.97 - 2.70: 1293 2.70 - 3.44: 38410 3.44 - 4.17: 60082 4.17 - 4.90: 105787 Nonbonded interactions: 205589 Sorted by model distance: nonbonded pdb=" NH1 ARG A 385 " pdb=" O GLY B 433 " model vdw 1.240 2.520 nonbonded pdb=" CZ ARG A 385 " pdb=" CA GLY B 433 " model vdw 1.414 3.670 nonbonded pdb=" O VAL C 667 " pdb=" NZ LYS C 674 " model vdw 1.463 2.520 nonbonded pdb=" NH1 ARG A 385 " pdb=" C GLY B 433 " model vdw 1.502 3.350 nonbonded pdb=" CB VAL B 352 " pdb=" CE MET B 485 " model vdw 1.586 3.890 ... (remaining 205584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 244 through 780) selection = (chain 'B' and resid 244 through 780) selection = (chain 'C' and resid 244 through 780) selection = (chain 'D' and resid 244 through 780) selection = (chain 'E' and resid 244 through 780) selection = (chain 'F' and resid 244 through 780) } 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: 2.020 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: 9.270 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 70.060 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.110 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.013 1.643 25961 Z= 0.943 Angle : 0.980 73.933 35219 Z= 0.611 Chirality : 0.049 0.507 3998 Planarity : 0.009 0.274 4542 Dihedral : 15.553 155.990 9961 Min Nonbonded Distance : 1.240 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.97 % Favored : 91.87 % Rotamer: Outliers : 0.56 % Allowed : 7.33 % Favored : 92.12 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.13), residues: 3199 helix: -3.27 (0.11), residues: 1190 sheet: -1.70 (0.24), residues: 428 loop : -2.54 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 431 HIS 0.004 0.001 HIS C 454 PHE 0.017 0.002 PHE C 657 TYR 0.019 0.001 TYR E 455 ARG 0.005 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 437 time to evaluate : 3.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 TRP cc_start: 0.7201 (t60) cc_final: 0.6936 (t60) REVERT: A 439 MET cc_start: 0.9353 (mmm) cc_final: 0.8706 (mmm) REVERT: B 439 MET cc_start: 0.9349 (mmm) cc_final: 0.8951 (mmm) REVERT: B 472 ASN cc_start: 0.8709 (p0) cc_final: 0.8425 (p0) REVERT: B 495 ASN cc_start: 0.9164 (m-40) cc_final: 0.8880 (m-40) REVERT: B 659 ASN cc_start: 0.8927 (t0) cc_final: 0.8640 (t0) REVERT: B 662 ASP cc_start: 0.7891 (m-30) cc_final: 0.7546 (m-30) REVERT: B 675 ASP cc_start: 0.8246 (t0) cc_final: 0.7968 (t0) REVERT: C 317 GLU cc_start: 0.7935 (pt0) cc_final: 0.7580 (pt0) REVERT: C 546 GLU cc_start: 0.8437 (mp0) cc_final: 0.8058 (mp0) REVERT: C 584 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7364 (ttm110) REVERT: F 376 PHE cc_start: 0.5342 (t80) cc_final: 0.4636 (t80) REVERT: F 698 MET cc_start: 0.7925 (mmm) cc_final: 0.7202 (mmm) REVERT: D 265 LYS cc_start: 0.8399 (tptp) cc_final: 0.8121 (tppt) REVERT: D 276 MET cc_start: 0.6174 (tmm) cc_final: 0.5930 (tmm) REVERT: D 479 ARG cc_start: 0.8400 (mmt-90) cc_final: 0.8199 (mmm160) REVERT: D 596 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8915 (m) REVERT: D 683 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8358 (mpt) REVERT: D 738 ASP cc_start: 0.8330 (t0) cc_final: 0.7198 (t0) REVERT: D 776 MET cc_start: 0.3785 (mtp) cc_final: 0.3443 (mpp) REVERT: E 368 ILE cc_start: 0.8765 (mm) cc_final: 0.8427 (mm) REVERT: E 409 MET cc_start: 0.7482 (mmt) cc_final: 0.7192 (mmm) REVERT: E 497 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8371 (mt-10) REVERT: E 516 MET cc_start: 0.8382 (mmm) cc_final: 0.7332 (mtp) outliers start: 15 outliers final: 5 residues processed: 449 average time/residue: 0.4111 time to fit residues: 276.6917 Evaluate side-chains 308 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 301 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 683 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 134 optimal weight: 0.0170 chunk 82 optimal weight: 0.9980 chunk 163 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 186 optimal weight: 0.0870 chunk 289 optimal weight: 7.9990 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 340 GLN B 393 HIS B 510 GLN B 638 GLN C 739 ASN F 278 GLN F 310 HIS F 340 GLN F 495 ASN F 504 GLN F 739 ASN D 373 ASN D 411 GLN D 447 GLN D 454 HIS D 495 ASN D 504 GLN D 510 GLN D 628 GLN E 277 GLN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN E 447 GLN E 504 GLN E 510 GLN E 593 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25961 Z= 0.203 Angle : 0.641 8.667 35219 Z= 0.318 Chirality : 0.045 0.161 3998 Planarity : 0.005 0.054 4542 Dihedral : 9.265 143.917 3672 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.56 % Rotamer: Outliers : 2.19 % Allowed : 13.31 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.65 (0.14), residues: 3201 helix: -1.78 (0.14), residues: 1219 sheet: -0.98 (0.25), residues: 433 loop : -1.91 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 602 HIS 0.003 0.001 HIS D 664 PHE 0.019 0.002 PHE D 376 TYR 0.019 0.001 TYR E 455 ARG 0.012 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 380 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.4341 (tmm) cc_final: 0.3187 (mmt) REVERT: A 331 GLU cc_start: 0.8799 (pt0) cc_final: 0.8580 (pt0) REVERT: A 439 MET cc_start: 0.9293 (mmm) cc_final: 0.8659 (mmm) REVERT: A 633 MET cc_start: 0.8857 (ttp) cc_final: 0.8643 (ttp) REVERT: B 252 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8815 (tptt) REVERT: B 331 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8174 (mt-10) REVERT: B 439 MET cc_start: 0.9194 (mmm) cc_final: 0.8816 (mmm) REVERT: B 495 ASN cc_start: 0.8974 (m-40) cc_final: 0.8731 (m-40) REVERT: B 602 TRP cc_start: 0.8615 (t60) cc_final: 0.8412 (t60) REVERT: B 659 ASN cc_start: 0.8824 (t0) cc_final: 0.8498 (t0) REVERT: B 662 ASP cc_start: 0.7779 (m-30) cc_final: 0.7523 (m-30) REVERT: B 675 ASP cc_start: 0.8167 (t0) cc_final: 0.7957 (t0) REVERT: C 533 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7872 (mt-10) REVERT: C 546 GLU cc_start: 0.8264 (mp0) cc_final: 0.7914 (mp0) REVERT: C 626 THR cc_start: 0.8810 (p) cc_final: 0.8510 (p) REVERT: F 376 PHE cc_start: 0.5408 (t80) cc_final: 0.4888 (t80) REVERT: F 378 ARG cc_start: 0.9213 (ptp-170) cc_final: 0.8491 (mpt180) REVERT: F 598 GLN cc_start: 0.7622 (mm110) cc_final: 0.7365 (mm110) REVERT: F 633 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: F 698 MET cc_start: 0.7882 (mmm) cc_final: 0.7180 (mmm) REVERT: F 713 MET cc_start: 0.8741 (mmm) cc_final: 0.8530 (mmm) REVERT: D 265 LYS cc_start: 0.8242 (tptp) cc_final: 0.7962 (tppt) REVERT: D 391 ARG cc_start: 0.8409 (mtm180) cc_final: 0.7972 (mtm180) REVERT: D 444 ASP cc_start: 0.8720 (t0) cc_final: 0.8300 (t0) REVERT: D 495 ASN cc_start: 0.9257 (m110) cc_final: 0.9011 (m110) REVERT: D 496 MET cc_start: 0.8982 (pmm) cc_final: 0.8644 (tpt) REVERT: D 596 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8919 (m) REVERT: D 683 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7908 (mpt) REVERT: D 738 ASP cc_start: 0.8282 (t0) cc_final: 0.7950 (t0) REVERT: D 751 LEU cc_start: 0.8655 (mt) cc_final: 0.8386 (mm) REVERT: D 776 MET cc_start: 0.3801 (mtp) cc_final: 0.3465 (mpp) REVERT: E 409 MET cc_start: 0.7486 (mmt) cc_final: 0.7193 (mmm) REVERT: E 485 MET cc_start: 0.7456 (ppp) cc_final: 0.7196 (tmm) REVERT: E 516 MET cc_start: 0.8238 (mmm) cc_final: 0.7203 (mtp) REVERT: E 703 THR cc_start: 0.9249 (p) cc_final: 0.9034 (p) outliers start: 59 outliers final: 34 residues processed: 411 average time/residue: 0.3769 time to fit residues: 242.0570 Evaluate side-chains 349 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 312 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 718 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 241 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 313 optimal weight: 20.0000 chunk 258 optimal weight: 4.9990 chunk 287 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN C 659 ASN C 666 HIS C 731 HIS C 739 ASN F 407 HIS F 495 ASN F 727 GLN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25961 Z= 0.324 Angle : 0.669 8.320 35219 Z= 0.325 Chirality : 0.044 0.156 3998 Planarity : 0.005 0.050 4542 Dihedral : 9.042 151.228 3663 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.53 % Allowed : 15.28 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 3201 helix: -1.39 (0.14), residues: 1238 sheet: -0.76 (0.26), residues: 424 loop : -1.77 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 602 HIS 0.006 0.001 HIS C 726 PHE 0.015 0.002 PHE D 376 TYR 0.019 0.002 TYR E 455 ARG 0.007 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 316 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.3777 (tmm) cc_final: 0.2978 (mmm) REVERT: A 439 MET cc_start: 0.9327 (mmm) cc_final: 0.8541 (mmm) REVERT: A 485 MET cc_start: 0.7628 (mtm) cc_final: 0.7426 (mtm) REVERT: A 626 THR cc_start: 0.9155 (p) cc_final: 0.8846 (t) REVERT: B 252 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8812 (tptt) REVERT: B 389 GLU cc_start: 0.8860 (tp30) cc_final: 0.8516 (tp30) REVERT: B 439 MET cc_start: 0.9277 (mmm) cc_final: 0.8852 (mmm) REVERT: B 495 ASN cc_start: 0.9098 (m-40) cc_final: 0.8829 (m-40) REVERT: B 659 ASN cc_start: 0.8927 (t0) cc_final: 0.8562 (t0) REVERT: B 662 ASP cc_start: 0.7844 (m-30) cc_final: 0.7531 (m-30) REVERT: C 533 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7917 (mt-10) REVERT: C 546 GLU cc_start: 0.8446 (mp0) cc_final: 0.7877 (mp0) REVERT: F 376 PHE cc_start: 0.5461 (t80) cc_final: 0.4759 (t80) REVERT: F 598 GLN cc_start: 0.7719 (mm110) cc_final: 0.7323 (mm110) REVERT: F 683 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8774 (mtt) REVERT: F 698 MET cc_start: 0.7902 (mmm) cc_final: 0.7301 (mmm) REVERT: F 713 MET cc_start: 0.8878 (mmm) cc_final: 0.8666 (mmm) REVERT: D 265 LYS cc_start: 0.8303 (tptp) cc_final: 0.7946 (tppt) REVERT: D 391 ARG cc_start: 0.8451 (mtm180) cc_final: 0.8046 (mtm180) REVERT: D 444 ASP cc_start: 0.8432 (t0) cc_final: 0.8200 (t0) REVERT: D 495 ASN cc_start: 0.9282 (m110) cc_final: 0.8937 (m110) REVERT: D 496 MET cc_start: 0.8960 (pmm) cc_final: 0.8702 (tpt) REVERT: D 596 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8971 (m) REVERT: D 776 MET cc_start: 0.3941 (mtp) cc_final: 0.3704 (mpp) REVERT: E 409 MET cc_start: 0.7579 (mmt) cc_final: 0.7248 (mmm) REVERT: E 416 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6780 (p0) REVERT: E 485 MET cc_start: 0.7535 (ppp) cc_final: 0.7261 (tmm) REVERT: E 516 MET cc_start: 0.8293 (mmm) cc_final: 0.7321 (mtp) REVERT: E 703 THR cc_start: 0.9318 (p) cc_final: 0.9053 (p) outliers start: 95 outliers final: 62 residues processed: 375 average time/residue: 0.3526 time to fit residues: 211.8891 Evaluate side-chains 352 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 287 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 683 MET Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 718 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 0.0050 chunk 138 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 308 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN F 504 GLN D 731 HIS ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25961 Z= 0.300 Angle : 0.644 8.147 35219 Z= 0.313 Chirality : 0.044 0.152 3998 Planarity : 0.005 0.051 4542 Dihedral : 8.864 151.570 3660 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.46 % Allowed : 17.55 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 3201 helix: -1.11 (0.14), residues: 1246 sheet: -0.69 (0.26), residues: 424 loop : -1.68 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 602 HIS 0.005 0.001 HIS C 726 PHE 0.016 0.002 PHE D 376 TYR 0.015 0.001 TYR E 455 ARG 0.005 0.000 ARG C 584 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 316 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.3726 (tmm) cc_final: 0.3404 (mmm) REVERT: A 439 MET cc_start: 0.9324 (mmm) cc_final: 0.8548 (mmm) REVERT: B 252 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8813 (tptt) REVERT: B 389 GLU cc_start: 0.8877 (tp30) cc_final: 0.8506 (tp30) REVERT: B 439 MET cc_start: 0.9272 (mmm) cc_final: 0.8944 (mmm) REVERT: B 495 ASN cc_start: 0.9064 (m-40) cc_final: 0.8772 (m-40) REVERT: B 659 ASN cc_start: 0.8917 (t0) cc_final: 0.8555 (t0) REVERT: B 662 ASP cc_start: 0.7832 (m-30) cc_final: 0.7492 (m-30) REVERT: B 675 ASP cc_start: 0.8294 (t0) cc_final: 0.8042 (t0) REVERT: B 698 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7742 (mtp) REVERT: C 533 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7930 (mt-10) REVERT: C 546 GLU cc_start: 0.8442 (mp0) cc_final: 0.7854 (mp0) REVERT: C 675 ASP cc_start: 0.7941 (t0) cc_final: 0.7358 (m-30) REVERT: F 376 PHE cc_start: 0.5453 (t80) cc_final: 0.4847 (t80) REVERT: F 427 MET cc_start: 0.2617 (tpp) cc_final: 0.2009 (tpp) REVERT: F 598 GLN cc_start: 0.7715 (mm110) cc_final: 0.7434 (mm110) REVERT: F 698 MET cc_start: 0.7847 (mmm) cc_final: 0.7215 (mmm) REVERT: D 265 LYS cc_start: 0.8263 (tptp) cc_final: 0.7918 (tppt) REVERT: D 276 MET cc_start: 0.6654 (tmm) cc_final: 0.6323 (tmm) REVERT: D 391 ARG cc_start: 0.8421 (mtm180) cc_final: 0.8019 (mtm180) REVERT: D 444 ASP cc_start: 0.8455 (t0) cc_final: 0.8191 (t0) REVERT: D 495 ASN cc_start: 0.9302 (m110) cc_final: 0.8771 (t0) REVERT: D 496 MET cc_start: 0.8946 (pmm) cc_final: 0.8734 (tpt) REVERT: D 596 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.8992 (m) REVERT: D 751 LEU cc_start: 0.8659 (mt) cc_final: 0.8420 (mm) REVERT: D 776 MET cc_start: 0.3979 (mtp) cc_final: 0.3621 (mpp) REVERT: E 409 MET cc_start: 0.7616 (mmt) cc_final: 0.7289 (mmm) REVERT: E 416 ASN cc_start: 0.6950 (OUTLIER) cc_final: 0.6729 (p0) REVERT: E 485 MET cc_start: 0.7516 (ppp) cc_final: 0.7290 (tmm) REVERT: E 498 LYS cc_start: 0.7665 (tptt) cc_final: 0.6948 (mmmt) REVERT: E 516 MET cc_start: 0.8297 (mmm) cc_final: 0.7378 (mtp) REVERT: E 703 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9105 (p) outliers start: 93 outliers final: 60 residues processed: 382 average time/residue: 0.3650 time to fit residues: 222.3258 Evaluate side-chains 356 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 292 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 718 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 157 optimal weight: 10.0000 chunk 276 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25961 Z= 0.251 Angle : 0.616 8.336 35219 Z= 0.299 Chirality : 0.043 0.164 3998 Planarity : 0.004 0.048 4542 Dihedral : 8.701 152.597 3660 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.13 % Allowed : 18.82 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.15), residues: 3201 helix: -0.82 (0.15), residues: 1241 sheet: -0.59 (0.26), residues: 417 loop : -1.56 (0.17), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 602 HIS 0.005 0.001 HIS C 726 PHE 0.018 0.002 PHE D 376 TYR 0.012 0.001 TYR E 289 ARG 0.005 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 327 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 MET cc_start: 0.9308 (mmm) cc_final: 0.8546 (mmm) REVERT: B 252 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8807 (tptt) REVERT: B 387 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8824 (mm-30) REVERT: B 389 GLU cc_start: 0.8859 (tp30) cc_final: 0.8473 (tp30) REVERT: B 439 MET cc_start: 0.9252 (mmm) cc_final: 0.8701 (mmm) REVERT: B 495 ASN cc_start: 0.9061 (m-40) cc_final: 0.8775 (m-40) REVERT: B 659 ASN cc_start: 0.8893 (t0) cc_final: 0.8540 (t0) REVERT: B 662 ASP cc_start: 0.7799 (m-30) cc_final: 0.7505 (m-30) REVERT: B 698 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7675 (mtp) REVERT: C 533 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7922 (mt-10) REVERT: C 546 GLU cc_start: 0.8441 (mp0) cc_final: 0.7840 (mp0) REVERT: C 675 ASP cc_start: 0.7950 (t0) cc_final: 0.7631 (p0) REVERT: C 705 GLU cc_start: 0.7620 (tt0) cc_final: 0.7414 (tt0) REVERT: F 273 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7065 (tt) REVERT: F 276 MET cc_start: -0.1419 (tpt) cc_final: -0.3788 (ttm) REVERT: F 376 PHE cc_start: 0.5554 (t80) cc_final: 0.4877 (t80) REVERT: F 598 GLN cc_start: 0.7728 (mm110) cc_final: 0.7436 (mm110) REVERT: F 698 MET cc_start: 0.7802 (mmm) cc_final: 0.7181 (mmm) REVERT: D 265 LYS cc_start: 0.8208 (tptp) cc_final: 0.7864 (tppt) REVERT: D 391 ARG cc_start: 0.8438 (mtm180) cc_final: 0.8042 (mtm180) REVERT: D 444 ASP cc_start: 0.8431 (t0) cc_final: 0.8169 (t0) REVERT: D 495 ASN cc_start: 0.9322 (m110) cc_final: 0.8882 (t0) REVERT: D 596 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8974 (m) REVERT: D 751 LEU cc_start: 0.8659 (mt) cc_final: 0.8389 (mm) REVERT: D 776 MET cc_start: 0.3924 (mtp) cc_final: 0.3552 (mpp) REVERT: E 409 MET cc_start: 0.7583 (mmt) cc_final: 0.7257 (mmm) REVERT: E 416 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6740 (p0) REVERT: E 485 MET cc_start: 0.7503 (ppp) cc_final: 0.7167 (tmm) REVERT: E 498 LYS cc_start: 0.7644 (tptt) cc_final: 0.6968 (mmmt) REVERT: E 516 MET cc_start: 0.8286 (mmm) cc_final: 0.7377 (mtp) REVERT: E 703 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9111 (p) outliers start: 111 outliers final: 77 residues processed: 407 average time/residue: 0.3492 time to fit residues: 230.1188 Evaluate side-chains 382 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 300 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 718 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 6.9990 chunk 277 optimal weight: 0.0050 chunk 60 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 76 optimal weight: 0.3980 chunk 308 optimal weight: 8.9990 chunk 256 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25961 Z= 0.201 Angle : 0.600 8.771 35219 Z= 0.289 Chirality : 0.043 0.169 3998 Planarity : 0.004 0.051 4542 Dihedral : 8.496 153.225 3660 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.79 % Allowed : 20.01 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3201 helix: -0.59 (0.15), residues: 1245 sheet: -0.33 (0.27), residues: 407 loop : -1.52 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 602 HIS 0.004 0.001 HIS C 726 PHE 0.019 0.001 PHE D 376 TYR 0.034 0.001 TYR D 455 ARG 0.004 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 334 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ARG cc_start: 0.7487 (ppt170) cc_final: 0.7278 (ptt90) REVERT: A 439 MET cc_start: 0.9298 (mmm) cc_final: 0.8530 (mmm) REVERT: B 252 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8797 (tptt) REVERT: B 331 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 389 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8457 (tp30) REVERT: B 495 ASN cc_start: 0.9001 (m-40) cc_final: 0.8720 (m-40) REVERT: B 659 ASN cc_start: 0.8874 (t0) cc_final: 0.8523 (t0) REVERT: B 662 ASP cc_start: 0.7774 (m-30) cc_final: 0.7509 (m-30) REVERT: B 698 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7580 (mtp) REVERT: C 533 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7905 (mt-10) REVERT: C 546 GLU cc_start: 0.8414 (mp0) cc_final: 0.7814 (mp0) REVERT: C 626 THR cc_start: 0.8726 (p) cc_final: 0.8368 (p) REVERT: C 675 ASP cc_start: 0.7925 (t0) cc_final: 0.7628 (p0) REVERT: F 276 MET cc_start: -0.1374 (tpt) cc_final: -0.3810 (ttm) REVERT: F 376 PHE cc_start: 0.5540 (t80) cc_final: 0.4891 (t80) REVERT: F 427 MET cc_start: 0.2582 (tpp) cc_final: 0.2223 (tpp) REVERT: F 598 GLN cc_start: 0.7704 (mm110) cc_final: 0.7388 (mm110) REVERT: F 698 MET cc_start: 0.7766 (mmm) cc_final: 0.7163 (mmm) REVERT: D 265 LYS cc_start: 0.8106 (tptp) cc_final: 0.7763 (tppt) REVERT: D 391 ARG cc_start: 0.8443 (mtm180) cc_final: 0.8093 (mtm180) REVERT: D 444 ASP cc_start: 0.8427 (t0) cc_final: 0.8157 (t0) REVERT: D 495 ASN cc_start: 0.9306 (m110) cc_final: 0.8896 (t0) REVERT: D 596 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8951 (m) REVERT: D 751 LEU cc_start: 0.8644 (mt) cc_final: 0.8380 (mm) REVERT: D 776 MET cc_start: 0.3964 (mtp) cc_final: 0.3682 (mpp) REVERT: E 409 MET cc_start: 0.7596 (mmt) cc_final: 0.7166 (tpp) REVERT: E 516 MET cc_start: 0.8247 (mmm) cc_final: 0.7379 (mtp) outliers start: 102 outliers final: 76 residues processed: 402 average time/residue: 0.3633 time to fit residues: 235.7360 Evaluate side-chains 385 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 306 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 609 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 718 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 225 optimal weight: 0.8980 chunk 174 optimal weight: 50.0000 chunk 259 optimal weight: 9.9990 chunk 172 optimal weight: 0.2980 chunk 307 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25961 Z= 0.215 Angle : 0.611 10.936 35219 Z= 0.294 Chirality : 0.043 0.160 3998 Planarity : 0.004 0.050 4542 Dihedral : 8.424 154.856 3660 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.17 % Allowed : 20.45 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3201 helix: -0.39 (0.15), residues: 1240 sheet: -0.22 (0.26), residues: 412 loop : -1.45 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 602 HIS 0.004 0.001 HIS D 664 PHE 0.019 0.001 PHE D 376 TYR 0.013 0.001 TYR A 397 ARG 0.006 0.000 ARG E 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 321 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ARG cc_start: 0.7527 (ppt170) cc_final: 0.7066 (ptt90) REVERT: A 439 MET cc_start: 0.9319 (mmm) cc_final: 0.8523 (mmm) REVERT: A 485 MET cc_start: 0.7583 (mtm) cc_final: 0.7289 (mtm) REVERT: B 252 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8785 (tptt) REVERT: B 331 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8134 (mt-10) REVERT: B 332 TYR cc_start: 0.9232 (t80) cc_final: 0.9017 (t80) REVERT: B 385 ARG cc_start: 0.7144 (ptm-80) cc_final: 0.6895 (ptm-80) REVERT: B 389 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: B 495 ASN cc_start: 0.9023 (m-40) cc_final: 0.8742 (m-40) REVERT: B 659 ASN cc_start: 0.8875 (t0) cc_final: 0.8520 (t0) REVERT: B 662 ASP cc_start: 0.7754 (m-30) cc_final: 0.7499 (m-30) REVERT: B 698 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7536 (mtp) REVERT: C 533 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7911 (mt-10) REVERT: C 546 GLU cc_start: 0.8424 (mp0) cc_final: 0.7825 (mp0) REVERT: C 626 THR cc_start: 0.8698 (p) cc_final: 0.8450 (p) REVERT: C 675 ASP cc_start: 0.7941 (t0) cc_final: 0.7628 (p0) REVERT: C 713 MET cc_start: 0.8479 (mtt) cc_final: 0.8135 (mtt) REVERT: F 273 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7069 (tt) REVERT: F 276 MET cc_start: -0.1092 (tpt) cc_final: -0.3404 (ttm) REVERT: F 376 PHE cc_start: 0.5565 (t80) cc_final: 0.4900 (t80) REVERT: F 427 MET cc_start: 0.2605 (tpp) cc_final: 0.2246 (tpp) REVERT: F 598 GLN cc_start: 0.7711 (mm110) cc_final: 0.7396 (mm110) REVERT: F 698 MET cc_start: 0.7749 (mmm) cc_final: 0.7180 (mmm) REVERT: D 391 ARG cc_start: 0.8456 (mtm180) cc_final: 0.8085 (mtm180) REVERT: D 444 ASP cc_start: 0.8421 (t0) cc_final: 0.8148 (t0) REVERT: D 495 ASN cc_start: 0.9310 (m110) cc_final: 0.8889 (t0) REVERT: D 596 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8941 (m) REVERT: D 751 LEU cc_start: 0.8660 (mt) cc_final: 0.8388 (mm) REVERT: D 776 MET cc_start: 0.4023 (mtp) cc_final: 0.3728 (mpp) REVERT: E 409 MET cc_start: 0.7627 (mmt) cc_final: 0.7192 (tpp) REVERT: E 439 MET cc_start: 0.8421 (mpp) cc_final: 0.7886 (mpp) REVERT: E 516 MET cc_start: 0.8231 (mmm) cc_final: 0.7389 (mtp) outliers start: 112 outliers final: 86 residues processed: 397 average time/residue: 0.3761 time to fit residues: 240.2117 Evaluate side-chains 391 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 301 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 609 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 718 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 0.0020 chunk 195 optimal weight: 0.0370 chunk 209 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 overall best weight: 0.7668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25961 Z= 0.156 Angle : 0.590 10.335 35219 Z= 0.285 Chirality : 0.042 0.158 3998 Planarity : 0.004 0.052 4542 Dihedral : 8.248 154.859 3660 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.98 % Allowed : 21.79 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3201 helix: -0.19 (0.15), residues: 1234 sheet: -0.12 (0.26), residues: 429 loop : -1.21 (0.17), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 602 HIS 0.005 0.001 HIS D 664 PHE 0.020 0.001 PHE D 376 TYR 0.013 0.001 TYR D 455 ARG 0.010 0.000 ARG D 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 363 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ARG cc_start: 0.7466 (ppt170) cc_final: 0.7126 (ptt90) REVERT: A 439 MET cc_start: 0.9289 (mmm) cc_final: 0.8487 (mmm) REVERT: A 629 LEU cc_start: 0.9079 (mp) cc_final: 0.8874 (mt) REVERT: A 633 MET cc_start: 0.8841 (ttt) cc_final: 0.8423 (ttt) REVERT: B 252 LYS cc_start: 0.9072 (mtpt) cc_final: 0.8747 (tptt) REVERT: B 385 ARG cc_start: 0.7052 (ptm-80) cc_final: 0.6815 (ptm-80) REVERT: B 389 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: B 659 ASN cc_start: 0.8795 (t0) cc_final: 0.8471 (t0) REVERT: B 663 LEU cc_start: 0.9194 (tt) cc_final: 0.8947 (tt) REVERT: C 420 LEU cc_start: 0.9329 (tp) cc_final: 0.9076 (tt) REVERT: C 546 GLU cc_start: 0.8388 (mp0) cc_final: 0.7860 (mp0) REVERT: C 626 THR cc_start: 0.8538 (p) cc_final: 0.8300 (p) REVERT: C 675 ASP cc_start: 0.7832 (t0) cc_final: 0.7476 (p0) REVERT: F 273 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7130 (tt) REVERT: F 276 MET cc_start: -0.1135 (tpt) cc_final: -0.3415 (ttm) REVERT: F 376 PHE cc_start: 0.5574 (t80) cc_final: 0.4902 (t80) REVERT: F 427 MET cc_start: 0.2610 (tpp) cc_final: 0.1587 (tpp) REVERT: F 598 GLN cc_start: 0.7587 (mm110) cc_final: 0.7201 (mm110) REVERT: F 698 MET cc_start: 0.7620 (mmm) cc_final: 0.7044 (mmm) REVERT: D 274 GLU cc_start: 0.8359 (tp30) cc_final: 0.8016 (tt0) REVERT: D 372 MET cc_start: 0.8058 (tmm) cc_final: 0.7802 (tmm) REVERT: D 391 ARG cc_start: 0.8421 (mtm180) cc_final: 0.8099 (mtm180) REVERT: D 444 ASP cc_start: 0.8414 (t0) cc_final: 0.8156 (t0) REVERT: D 495 ASN cc_start: 0.9289 (m110) cc_final: 0.8860 (t0) REVERT: D 776 MET cc_start: 0.3986 (mtp) cc_final: 0.3643 (mpp) REVERT: E 516 MET cc_start: 0.8129 (mmm) cc_final: 0.7327 (mtp) REVERT: E 702 MET cc_start: 0.8694 (ptp) cc_final: 0.8266 (ptt) outliers start: 80 outliers final: 61 residues processed: 414 average time/residue: 0.3447 time to fit residues: 228.8000 Evaluate side-chains 392 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 329 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 622 LYS Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 672 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 4.9990 chunk 294 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 chunk 270 optimal weight: 0.3980 chunk 285 optimal weight: 10.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25961 Z= 0.275 Angle : 0.646 9.749 35219 Z= 0.308 Chirality : 0.044 0.204 3998 Planarity : 0.004 0.048 4542 Dihedral : 8.290 156.963 3659 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.09 % Allowed : 22.24 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3201 helix: -0.14 (0.15), residues: 1235 sheet: -0.10 (0.26), residues: 423 loop : -1.24 (0.17), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 602 HIS 0.005 0.001 HIS C 726 PHE 0.024 0.001 PHE D 376 TYR 0.012 0.001 TYR E 455 ARG 0.006 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 321 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ARG cc_start: 0.7526 (ppt170) cc_final: 0.7206 (ptt90) REVERT: A 439 MET cc_start: 0.9336 (mmm) cc_final: 0.8530 (mmm) REVERT: A 485 MET cc_start: 0.7661 (mtm) cc_final: 0.7286 (mtm) REVERT: B 252 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8786 (tptt) REVERT: B 331 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8154 (mt-10) REVERT: B 389 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8456 (tp30) REVERT: B 659 ASN cc_start: 0.8879 (t0) cc_final: 0.8515 (t0) REVERT: C 546 GLU cc_start: 0.8431 (mp0) cc_final: 0.7865 (mp0) REVERT: C 675 ASP cc_start: 0.7971 (t0) cc_final: 0.7657 (p0) REVERT: F 273 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7118 (tt) REVERT: F 276 MET cc_start: -0.1137 (tpt) cc_final: -0.3357 (ttm) REVERT: F 376 PHE cc_start: 0.5578 (t80) cc_final: 0.4890 (t80) REVERT: F 427 MET cc_start: 0.2598 (tpp) cc_final: 0.1552 (tpp) REVERT: F 598 GLN cc_start: 0.7736 (mm110) cc_final: 0.7394 (mm110) REVERT: F 698 MET cc_start: 0.7666 (mmm) cc_final: 0.7124 (mmm) REVERT: D 274 GLU cc_start: 0.8392 (tp30) cc_final: 0.7948 (tt0) REVERT: D 391 ARG cc_start: 0.8365 (mtm180) cc_final: 0.8079 (mtm180) REVERT: D 444 ASP cc_start: 0.8415 (t0) cc_final: 0.8148 (t0) REVERT: D 495 ASN cc_start: 0.9322 (m110) cc_final: 0.8880 (t0) REVERT: D 751 LEU cc_start: 0.8641 (mt) cc_final: 0.8375 (mm) REVERT: D 776 MET cc_start: 0.4088 (mtp) cc_final: 0.3665 (mpp) REVERT: E 409 MET cc_start: 0.7556 (mmt) cc_final: 0.7307 (mmm) REVERT: E 439 MET cc_start: 0.8563 (mpp) cc_final: 0.8079 (mpp) REVERT: E 516 MET cc_start: 0.8241 (mmm) cc_final: 0.7400 (mtp) outliers start: 83 outliers final: 70 residues processed: 378 average time/residue: 0.3540 time to fit residues: 215.7257 Evaluate side-chains 381 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 309 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 622 LYS Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 672 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 210 optimal weight: 0.0270 chunk 317 optimal weight: 0.0570 chunk 292 optimal weight: 20.0000 chunk 253 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 chunk 195 optimal weight: 0.0000 chunk 155 optimal weight: 0.9980 overall best weight: 0.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25961 Z= 0.160 Angle : 0.605 11.131 35219 Z= 0.289 Chirality : 0.042 0.162 3998 Planarity : 0.005 0.047 4542 Dihedral : 8.166 155.774 3659 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.38 % Allowed : 23.09 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3201 helix: 0.04 (0.15), residues: 1233 sheet: -0.09 (0.26), residues: 437 loop : -1.16 (0.17), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 602 HIS 0.005 0.001 HIS D 664 PHE 0.023 0.001 PHE D 376 TYR 0.015 0.001 TYR B 332 ARG 0.011 0.000 ARG C 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 351 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LYS cc_start: 0.7882 (tptp) cc_final: 0.7529 (tttt) REVERT: A 385 ARG cc_start: 0.7436 (ppt170) cc_final: 0.6847 (ptt-90) REVERT: A 439 MET cc_start: 0.9288 (mmm) cc_final: 0.8492 (mmm) REVERT: B 331 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8113 (mt-10) REVERT: B 389 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8292 (tp30) REVERT: B 659 ASN cc_start: 0.8738 (t0) cc_final: 0.8410 (t0) REVERT: C 546 GLU cc_start: 0.8361 (mp0) cc_final: 0.7852 (mp0) REVERT: C 626 THR cc_start: 0.8458 (p) cc_final: 0.8241 (p) REVERT: C 675 ASP cc_start: 0.7824 (t0) cc_final: 0.7460 (p0) REVERT: F 273 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7144 (tt) REVERT: F 276 MET cc_start: -0.1123 (tpt) cc_final: -0.3324 (ttm) REVERT: F 376 PHE cc_start: 0.5606 (t80) cc_final: 0.4919 (t80) REVERT: F 427 MET cc_start: 0.2669 (tpp) cc_final: 0.1626 (tpp) REVERT: F 598 GLN cc_start: 0.7538 (mm110) cc_final: 0.7096 (mm110) REVERT: F 698 MET cc_start: 0.7550 (mmm) cc_final: 0.7043 (mmm) REVERT: D 274 GLU cc_start: 0.8426 (tp30) cc_final: 0.7980 (tt0) REVERT: D 391 ARG cc_start: 0.8307 (mtm180) cc_final: 0.8029 (mtm180) REVERT: D 444 ASP cc_start: 0.8398 (t0) cc_final: 0.8136 (t0) REVERT: D 495 ASN cc_start: 0.9289 (m110) cc_final: 0.8845 (t0) REVERT: D 776 MET cc_start: 0.4006 (mtp) cc_final: 0.3652 (mpp) REVERT: E 409 MET cc_start: 0.7479 (mmt) cc_final: 0.7213 (mmm) REVERT: E 439 MET cc_start: 0.8584 (mpp) cc_final: 0.8122 (mpp) REVERT: E 503 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7856 (tmm-80) REVERT: E 516 MET cc_start: 0.8100 (mmm) cc_final: 0.7309 (mtp) outliers start: 64 outliers final: 53 residues processed: 388 average time/residue: 0.3476 time to fit residues: 216.2708 Evaluate side-chains 379 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 324 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 672 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 260 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN D 377 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.120076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095646 restraints weight = 66784.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.098180 restraints weight = 32338.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.099804 restraints weight = 19898.090| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25961 Z= 0.226 Angle : 0.630 12.121 35219 Z= 0.300 Chirality : 0.043 0.189 3998 Planarity : 0.004 0.046 4542 Dihedral : 8.180 158.166 3659 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.71 % Allowed : 22.98 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3201 helix: 0.10 (0.15), residues: 1237 sheet: -0.04 (0.26), residues: 416 loop : -1.07 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 602 HIS 0.005 0.001 HIS D 664 PHE 0.026 0.001 PHE D 376 TYR 0.011 0.001 TYR A 397 ARG 0.005 0.000 ARG C 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5832.29 seconds wall clock time: 106 minutes 50.94 seconds (6410.94 seconds total)