Starting phenix.real_space_refine on Fri Feb 16 13:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epb_31236/02_2024/7epb_31236_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epb_31236/02_2024/7epb_31236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epb_31236/02_2024/7epb_31236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epb_31236/02_2024/7epb_31236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epb_31236/02_2024/7epb_31236_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epb_31236/02_2024/7epb_31236_updated.pdb" } resolution = 3.1 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= 0.198 sd= 0.783 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2352 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8214 2.51 5 N 2344 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ARG 720": "NH1" <-> "NH2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 467": "NH1" <-> "NH2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "B ARG 720": "NH1" <-> "NH2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ASP 72": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5632 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 37, 'TRANS': 741} Chain breaks: 1 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 577 Unresolved non-hydrogen dihedrals: 382 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 13, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 253 Chain: "B" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5638 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 37, 'TRANS': 741} Chain breaks: 1 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 566 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 10, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 246 Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 902 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 906 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'40F': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'40F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.94, per 1000 atoms: 0.53 Number of scatterers: 13104 At special positions: 0 Unit cell: (105.04, 91.52, 189.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2462 8.00 N 2344 7.00 C 8214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.04 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 632 " - pdb=" SG CYS B 721 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.08 Conformation dependent library (CDL) restraints added in 2.4 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 14 sheets defined 37.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 59 through 73 Processing helix chain 'A' and resid 95 through 116 removed outlier: 4.995A pdb=" N ASP A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.919A pdb=" N ASN A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 376 through 399 removed outlier: 4.002A pdb=" N MET A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 399 " --> pdb=" O HIS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 569 through 592 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.659A pdb=" N ALA A 600 " --> pdb=" O PRO A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 596 through 600' Processing helix chain 'A' and resid 603 through 624 removed outlier: 3.818A pdb=" N TYR A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 658 removed outlier: 3.818A pdb=" N CYS A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 700 Processing helix chain 'A' and resid 725 through 748 removed outlier: 3.835A pdb=" N LYS A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 787 through 815 removed outlier: 3.768A pdb=" N THR A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR A 792 " --> pdb=" O ARG A 788 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET A 794 " --> pdb=" O GLN A 790 " (cutoff:3.500A) Proline residue: A 812 - end of helix Processing helix chain 'B' and resid 59 through 73 Processing helix chain 'B' and resid 95 through 116 removed outlier: 4.977A pdb=" N ASP B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 158 removed outlier: 3.843A pdb=" N ASN B 153 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 215 through 231 Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 378 through 397 Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 569 through 592 Processing helix chain 'B' and resid 596 through 600 removed outlier: 3.614A pdb=" N ALA B 600 " --> pdb=" O PRO B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 596 through 600' Processing helix chain 'B' and resid 603 through 625 removed outlier: 4.608A pdb=" N ILE B 624 " --> pdb=" O THR B 620 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 625 " --> pdb=" O PHE B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 656 removed outlier: 3.878A pdb=" N CYS B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 700 Processing helix chain 'B' and resid 726 through 749 removed outlier: 3.996A pdb=" N LYS B 748 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR B 749 " --> pdb=" O TYR B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 785 Proline residue: B 778 - end of helix removed outlier: 3.743A pdb=" N SER B 784 " --> pdb=" O PHE B 780 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER B 785 " --> pdb=" O TYR B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 815 removed outlier: 4.025A pdb=" N THR B 792 " --> pdb=" O ARG B 788 " (cutoff:3.500A) Proline residue: B 812 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.658A pdb=" N LEU A 32 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N HIS A 87 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 138 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N LEU A 37 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 140 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY A 141 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE A 163 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.634A pdb=" N SER A 208 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR A 290 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 268 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 292 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.082A pdb=" N GLY A 472 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 457 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS A 470 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 459 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A 468 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 427 through 429 Processing sheet with id= E, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.622A pdb=" N LEU B 32 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N HIS B 87 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 34 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 89 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 36 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 138 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N LEU B 37 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 140 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY B 141 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE B 163 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.752A pdb=" N SER B 208 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR B 290 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU B 268 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 292 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 315 through 319 removed outlier: 4.123A pdb=" N GLY B 472 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR B 457 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 470 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 459 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TYR B 468 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 427 through 429 Processing sheet with id= I, first strand: chain 'B' and resid 509 through 511 Processing sheet with id= J, first strand: chain 'C' and resid 4 through 7 Processing sheet with id= K, first strand: chain 'C' and resid 105 through 108 removed outlier: 3.723A pdb=" N THR C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 4 through 7 Processing sheet with id= M, first strand: chain 'D' and resid 10 through 12 Processing sheet with id= N, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.604A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET D 34 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP D 98 " --> pdb=" O ASN D 32 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET D 34 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS D 96 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP D 36 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR D 94 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG D 38 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL D 92 " --> pdb=" O ARG D 38 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1569 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: 3.87 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4456 1.35 - 1.46: 3173 1.46 - 1.58: 5641 1.58 - 1.70: 4 1.70 - 1.82: 108 Bond restraints: 13382 Sorted by residual: bond pdb=" C6 40F A 901 " pdb=" C7 40F A 901 " ideal model delta sigma weight residual 1.534 1.393 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C6 40F B 901 " pdb=" C7 40F B 901 " ideal model delta sigma weight residual 1.534 1.394 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C 40F B 901 " pdb=" C1 40F B 901 " ideal model delta sigma weight residual 1.554 1.415 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C 40F A 901 " pdb=" C1 40F A 901 " ideal model delta sigma weight residual 1.554 1.415 0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5 40F A 901 " pdb=" C6 40F A 901 " ideal model delta sigma weight residual 1.522 1.653 -0.131 2.00e-02 2.50e+03 4.32e+01 ... (remaining 13377 not shown) Histogram of bond angle deviations from ideal: 59.65 - 78.00: 6 78.00 - 96.35: 0 96.35 - 114.70: 8157 114.70 - 133.05: 10049 133.05 - 151.40: 28 Bond angle restraints: 18240 Sorted by residual: angle pdb=" C3 40F A 901 " pdb=" C5 40F A 901 " pdb=" C6 40F A 901 " ideal model delta sigma weight residual 116.92 151.40 -34.48 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C3 40F B 901 " pdb=" C5 40F B 901 " pdb=" C6 40F B 901 " ideal model delta sigma weight residual 116.92 151.33 -34.41 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C1 40F B 901 " pdb=" C2 40F B 901 " pdb=" C3 40F B 901 " ideal model delta sigma weight residual 118.97 130.97 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C1 40F A 901 " pdb=" C2 40F A 901 " pdb=" C3 40F A 901 " ideal model delta sigma weight residual 118.97 130.90 -11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N VAL D 48 " pdb=" CA VAL D 48 " pdb=" C VAL D 48 " ideal model delta sigma weight residual 113.53 109.76 3.77 9.80e-01 1.04e+00 1.48e+01 ... (remaining 18235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7286 17.89 - 35.78: 571 35.78 - 53.67: 134 53.67 - 71.55: 14 71.55 - 89.44: 21 Dihedral angle restraints: 8026 sinusoidal: 2861 harmonic: 5165 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual -86.00 -2.71 -83.29 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B 50 " pdb=" SG CYS B 50 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual -86.00 -3.94 -82.06 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 504 " pdb=" SG CYS A 504 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -166.26 80.26 1 1.00e+01 1.00e-02 7.98e+01 ... (remaining 8023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 2061 0.259 - 0.518: 2 0.518 - 0.777: 0 0.777 - 1.035: 0 1.035 - 1.294: 2 Chirality restraints: 2065 Sorted by residual: chirality pdb=" C5 40F A 901 " pdb=" C2 40F A 901 " pdb=" C3 40F A 901 " pdb=" C6 40F A 901 " both_signs ideal model delta sigma weight residual True 2.64 1.34 1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C5 40F B 901 " pdb=" C2 40F B 901 " pdb=" C3 40F B 901 " pdb=" C6 40F B 901 " both_signs ideal model delta sigma weight residual True 2.64 1.35 1.29 2.00e-01 2.50e+01 4.16e+01 chirality pdb=" C2 40F B 901 " pdb=" C1 40F B 901 " pdb=" C3 40F B 901 " pdb=" C5 40F B 901 " both_signs ideal model delta sigma weight residual True 2.60 2.13 0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 2062 not shown) Planarity restraints: 2402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 41 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 526 " -0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 527 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 40 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO D 41 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " -0.019 5.00e-02 4.00e+02 ... (remaining 2399 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3920 2.81 - 3.33: 12520 3.33 - 3.86: 22023 3.86 - 4.38: 24288 4.38 - 4.90: 41223 Nonbonded interactions: 103974 Sorted by model distance: nonbonded pdb=" O TYR A 206 " pdb=" OG SER A 498 " model vdw 2.292 2.440 nonbonded pdb=" OD1 ASP C 98 " pdb=" OG1 THR C 106 " model vdw 2.297 2.440 nonbonded pdb=" OG SER A 321 " pdb=" O SER A 376 " model vdw 2.301 2.440 nonbonded pdb=" O SER A 628 " pdb=" OG SER A 628 " model vdw 2.306 2.440 nonbonded pdb=" O SER B 628 " pdb=" OG SER B 628 " model vdw 2.313 2.440 ... (remaining 103969 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 22 through 558 or (resid 559 through 562 and (name N or na \ me CA or name C or name O or name CB )) or resid 563 through 716 or (resid 717 a \ nd (name N or name CA or name C or name O or name CB )) or resid 718 or (resid 7 \ 19 and (name N or name CA or name C or name O or name CB )) or resid 720 through \ 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) or r \ esid 749 through 754 or (resid 755 and (name N or name CA or name C or name O or \ name CB )) or resid 756 through 780 or (resid 781 and (name N or name CA or nam \ e C or name O or name CB )) or resid 782 through 817 or resid 901)) selection = (chain 'B' and (resid 22 through 571 or (resid 572 through 575 and (name N or na \ me CA or name C or name O or name CB )) or resid 576 through 623 or (resid 624 t \ hrough 626 and (name N or name CA or name C or name O or name CB )) or resid 627 \ through 642 or (resid 643 through 644 and (name N or name CA or name C or name \ O or name CB )) or resid 645 through 756 or (resid 757 through 759 and (name N o \ r name CA or name C or name O or name CB )) or resid 760 through 770 or (resid 7 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 772 through \ 775 or (resid 776 and (name N or name CA or name C or name O or name CB )) or r \ esid 777 through 779 or (resid 780 through 781 and (name N or name CA or name C \ or name O or name CB )) or resid 782 through 817 or resid 901)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 118)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 5.050 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 35.490 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.004 0.141 13382 Z= 0.267 Angle : 0.619 34.483 18240 Z= 0.297 Chirality : 0.058 1.294 2065 Planarity : 0.003 0.041 2402 Dihedral : 13.843 89.443 4643 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.65 (0.18), residues: 1782 helix: 0.17 (0.18), residues: 722 sheet: -1.23 (0.32), residues: 242 loop : -2.25 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 297 HIS 0.002 0.000 HIS D 104 PHE 0.018 0.001 PHE A 456 TYR 0.011 0.001 TYR A 787 ARG 0.004 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 1.549 Fit side-chains REVERT: A 149 ILE cc_start: 0.8899 (pt) cc_final: 0.8664 (pt) REVERT: A 150 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8164 (mm110) REVERT: A 251 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 414 ASN cc_start: 0.7330 (p0) cc_final: 0.7073 (p0) REVERT: A 725 ASP cc_start: 0.4939 (m-30) cc_final: 0.4425 (m-30) REVERT: B 149 ILE cc_start: 0.8956 (pt) cc_final: 0.8672 (pt) REVERT: B 189 PHE cc_start: 0.7856 (m-80) cc_final: 0.7638 (m-80) REVERT: B 229 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7454 (mtt180) REVERT: B 251 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7685 (mt-10) REVERT: C 45 ARG cc_start: 0.7546 (ptp90) cc_final: 0.7103 (ptt180) REVERT: C 46 GLU cc_start: 0.7513 (mp0) cc_final: 0.7058 (mp0) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.2301 time to fit residues: 92.6707 Evaluate side-chains 233 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 0.0980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 101 GLN A 338 ASN B 101 GLN B 338 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13382 Z= 0.350 Angle : 0.630 11.673 18240 Z= 0.327 Chirality : 0.044 0.266 2065 Planarity : 0.004 0.041 2402 Dihedral : 3.967 17.201 1999 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.79 % Allowed : 15.95 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.00 (0.20), residues: 1782 helix: 0.96 (0.20), residues: 712 sheet: -1.27 (0.32), residues: 260 loop : -1.98 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 297 HIS 0.005 0.001 HIS D 104 PHE 0.052 0.002 PHE A 456 TYR 0.013 0.002 TYR D 99 ARG 0.005 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: A 149 ILE cc_start: 0.8918 (pt) cc_final: 0.8591 (pt) REVERT: A 150 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8414 (mm-40) REVERT: A 193 LYS cc_start: 0.8327 (mtmt) cc_final: 0.7897 (mtmm) REVERT: A 197 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 350 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 414 ASN cc_start: 0.8338 (p0) cc_final: 0.7985 (p0) REVERT: A 476 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7384 (mm-30) REVERT: B 25 VAL cc_start: 0.9024 (t) cc_final: 0.8682 (p) REVERT: B 189 PHE cc_start: 0.7986 (m-80) cc_final: 0.7748 (m-80) REVERT: B 317 ILE cc_start: 0.9208 (mt) cc_final: 0.8922 (mt) REVERT: B 476 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7277 (mm-30) REVERT: B 756 PHE cc_start: 0.7956 (p90) cc_final: 0.7414 (p90) REVERT: C 100 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8763 (tptt) REVERT: D 76 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7312 (p0) REVERT: D 110 GLN cc_start: 0.7784 (mp10) cc_final: 0.7393 (mp10) outliers start: 35 outliers final: 29 residues processed: 284 average time/residue: 0.2508 time to fit residues: 102.9574 Evaluate side-chains 261 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 128 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 150 GLN B 790 GLN C 76 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13382 Z= 0.169 Angle : 0.519 9.958 18240 Z= 0.260 Chirality : 0.041 0.158 2065 Planarity : 0.004 0.038 2402 Dihedral : 3.550 15.474 1999 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.63 % Allowed : 18.90 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.71 (0.20), residues: 1782 helix: 1.30 (0.21), residues: 720 sheet: -1.35 (0.32), residues: 260 loop : -1.86 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS A 97 PHE 0.033 0.001 PHE A 456 TYR 0.017 0.001 TYR B 466 ARG 0.005 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 252 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 149 ILE cc_start: 0.8898 (pt) cc_final: 0.8599 (pt) REVERT: A 193 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7976 (mtmm) REVERT: A 197 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7546 (mt-10) REVERT: A 245 MET cc_start: 0.7528 (tpp) cc_final: 0.6625 (tpt) REVERT: A 350 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 379 MET cc_start: 0.8330 (ptm) cc_final: 0.7950 (ptt) REVERT: A 414 ASN cc_start: 0.8136 (p0) cc_final: 0.7853 (p0) REVERT: A 476 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7182 (tm-30) REVERT: B 25 VAL cc_start: 0.9038 (t) cc_final: 0.8694 (p) REVERT: B 189 PHE cc_start: 0.7860 (m-80) cc_final: 0.7660 (m-80) REVERT: B 350 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 396 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6848 (t-90) REVERT: B 410 MET cc_start: 0.7491 (mmp) cc_final: 0.7150 (mmt) REVERT: C 100 LYS cc_start: 0.8967 (tmtt) cc_final: 0.8730 (tptt) REVERT: D 110 GLN cc_start: 0.7779 (mp10) cc_final: 0.7353 (mp10) outliers start: 33 outliers final: 27 residues processed: 272 average time/residue: 0.2706 time to fit residues: 108.2712 Evaluate side-chains 258 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 230 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 506 GLN B 506 GLN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13382 Z= 0.327 Angle : 0.610 9.141 18240 Z= 0.316 Chirality : 0.043 0.193 2065 Planarity : 0.004 0.046 2402 Dihedral : 4.061 15.874 1999 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.31 % Allowed : 19.62 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.80 (0.20), residues: 1782 helix: 1.30 (0.21), residues: 720 sheet: -1.43 (0.32), residues: 248 loop : -1.99 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 297 HIS 0.005 0.001 HIS B 396 PHE 0.029 0.002 PHE A 456 TYR 0.024 0.002 TYR B 466 ARG 0.005 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 258 time to evaluate : 1.521 Fit side-chains REVERT: A 29 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: A 149 ILE cc_start: 0.8856 (pt) cc_final: 0.8583 (pt) REVERT: A 193 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8045 (mtmm) REVERT: A 197 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 245 MET cc_start: 0.7795 (tpp) cc_final: 0.7014 (tpt) REVERT: A 350 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 379 MET cc_start: 0.8384 (ptm) cc_final: 0.8117 (ptt) REVERT: A 414 ASN cc_start: 0.8456 (p0) cc_final: 0.8095 (p0) REVERT: B 274 ASP cc_start: 0.8044 (t0) cc_final: 0.7749 (t0) REVERT: B 350 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7753 (mt-10) REVERT: B 392 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8703 (mt) REVERT: B 396 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.7122 (t-90) REVERT: B 406 LEU cc_start: 0.7847 (tp) cc_final: 0.7639 (tp) REVERT: B 756 PHE cc_start: 0.7985 (p90) cc_final: 0.7426 (p90) REVERT: C 100 LYS cc_start: 0.9025 (tmtt) cc_final: 0.8785 (tptt) REVERT: D 76 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7493 (p0) REVERT: D 110 GLN cc_start: 0.7780 (mp10) cc_final: 0.7475 (mp10) outliers start: 54 outliers final: 41 residues processed: 293 average time/residue: 0.2477 time to fit residues: 105.2326 Evaluate side-chains 285 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 240 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 0.2980 chunk 57 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 191 GLN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13382 Z= 0.176 Angle : 0.547 10.379 18240 Z= 0.274 Chirality : 0.041 0.164 2065 Planarity : 0.004 0.037 2402 Dihedral : 3.753 16.526 1999 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.99 % Allowed : 22.17 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.63 (0.20), residues: 1782 helix: 1.54 (0.21), residues: 708 sheet: -1.42 (0.32), residues: 246 loop : -1.91 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 291 HIS 0.003 0.001 HIS A 97 PHE 0.023 0.001 PHE A 456 TYR 0.016 0.001 TYR B 466 ARG 0.006 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 257 time to evaluate : 1.532 Fit side-chains REVERT: A 29 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: A 149 ILE cc_start: 0.8858 (pt) cc_final: 0.8542 (pt) REVERT: A 193 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8020 (mtmm) REVERT: A 197 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 245 MET cc_start: 0.7620 (tpp) cc_final: 0.6773 (tpt) REVERT: A 273 GLU cc_start: 0.7606 (pm20) cc_final: 0.7393 (pm20) REVERT: A 277 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 350 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 379 MET cc_start: 0.8262 (ptm) cc_final: 0.7988 (ptt) REVERT: A 414 ASN cc_start: 0.8280 (p0) cc_final: 0.7919 (p0) REVERT: A 639 LEU cc_start: 0.8192 (mt) cc_final: 0.7875 (pt) REVERT: B 189 PHE cc_start: 0.7858 (m-80) cc_final: 0.7642 (m-80) REVERT: B 274 ASP cc_start: 0.7935 (t0) cc_final: 0.7634 (t0) REVERT: B 350 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 392 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8701 (mt) REVERT: B 756 PHE cc_start: 0.8017 (p90) cc_final: 0.7462 (p90) REVERT: C 100 LYS cc_start: 0.8957 (tmtt) cc_final: 0.8711 (tptt) REVERT: D 101 TYR cc_start: 0.7767 (t80) cc_final: 0.7545 (t80) REVERT: D 110 GLN cc_start: 0.7780 (mp10) cc_final: 0.7451 (mp10) outliers start: 50 outliers final: 38 residues processed: 290 average time/residue: 0.2532 time to fit residues: 105.9741 Evaluate side-chains 283 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 243 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.0060 chunk 170 optimal weight: 0.0170 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13382 Z= 0.166 Angle : 0.553 11.758 18240 Z= 0.272 Chirality : 0.040 0.166 2065 Planarity : 0.004 0.037 2402 Dihedral : 3.612 16.549 1999 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.75 % Allowed : 23.37 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.53 (0.20), residues: 1782 helix: 1.64 (0.21), residues: 708 sheet: -1.44 (0.32), residues: 246 loop : -1.84 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 108 HIS 0.004 0.001 HIS B 97 PHE 0.019 0.001 PHE A 456 TYR 0.016 0.001 TYR B 466 ARG 0.009 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 149 ILE cc_start: 0.8857 (pt) cc_final: 0.8542 (pt) REVERT: A 193 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7987 (mtmm) REVERT: A 197 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7547 (mt-10) REVERT: A 245 MET cc_start: 0.7311 (tpp) cc_final: 0.6586 (tpt) REVERT: A 277 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 318 GLU cc_start: 0.6343 (pm20) cc_final: 0.5890 (pm20) REVERT: A 350 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 379 MET cc_start: 0.8216 (ptm) cc_final: 0.7970 (ptt) REVERT: A 414 ASN cc_start: 0.8307 (p0) cc_final: 0.7994 (p0) REVERT: A 619 MET cc_start: 0.5819 (mmm) cc_final: 0.5598 (mmm) REVERT: B 189 PHE cc_start: 0.7803 (m-80) cc_final: 0.7588 (m-80) REVERT: B 274 ASP cc_start: 0.7932 (t0) cc_final: 0.7644 (t0) REVERT: B 350 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 392 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8576 (mt) REVERT: B 410 MET cc_start: 0.7755 (mmp) cc_final: 0.7357 (mmt) REVERT: B 756 PHE cc_start: 0.8011 (p90) cc_final: 0.7467 (p90) REVERT: C 76 ASN cc_start: 0.7601 (p0) cc_final: 0.7272 (p0) REVERT: C 100 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8706 (tptt) REVERT: D 59 TYR cc_start: 0.9098 (m-80) cc_final: 0.8885 (m-80) REVERT: D 76 ASN cc_start: 0.7789 (p0) cc_final: 0.7573 (p0) REVERT: D 110 GLN cc_start: 0.7785 (mp10) cc_final: 0.7449 (mp10) outliers start: 47 outliers final: 37 residues processed: 284 average time/residue: 0.2434 time to fit residues: 101.1012 Evaluate side-chains 282 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 244 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 124 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 169 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13382 Z= 0.201 Angle : 0.566 11.413 18240 Z= 0.282 Chirality : 0.041 0.164 2065 Planarity : 0.004 0.037 2402 Dihedral : 3.688 16.554 1999 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.83 % Allowed : 23.37 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.52 (0.20), residues: 1782 helix: 1.65 (0.20), residues: 708 sheet: -1.41 (0.32), residues: 246 loop : -1.84 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 349 HIS 0.004 0.001 HIS B 97 PHE 0.015 0.001 PHE A 456 TYR 0.018 0.001 TYR B 466 ARG 0.007 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 260 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7606 (pp20) REVERT: A 140 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8648 (pt) REVERT: A 149 ILE cc_start: 0.8875 (pt) cc_final: 0.8562 (pt) REVERT: A 180 TYR cc_start: 0.8027 (m-10) cc_final: 0.7747 (m-10) REVERT: A 193 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8008 (mtmm) REVERT: A 197 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 245 MET cc_start: 0.7326 (tpp) cc_final: 0.7096 (tpt) REVERT: A 277 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 350 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 379 MET cc_start: 0.8238 (ptm) cc_final: 0.7998 (ptt) REVERT: A 414 ASN cc_start: 0.8319 (p0) cc_final: 0.8014 (p0) REVERT: A 631 VAL cc_start: 0.1856 (OUTLIER) cc_final: 0.1641 (t) REVERT: B 189 PHE cc_start: 0.7848 (m-80) cc_final: 0.7638 (m-80) REVERT: B 274 ASP cc_start: 0.7933 (t0) cc_final: 0.7624 (t0) REVERT: B 350 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7695 (mt-10) REVERT: B 410 MET cc_start: 0.7805 (mmp) cc_final: 0.7478 (mmt) REVERT: B 756 PHE cc_start: 0.7956 (p90) cc_final: 0.7408 (p90) REVERT: C 100 LYS cc_start: 0.8938 (tmtt) cc_final: 0.8695 (tptt) REVERT: D 3 GLN cc_start: 0.7702 (pm20) cc_final: 0.7498 (pm20) REVERT: D 76 ASN cc_start: 0.7727 (p0) cc_final: 0.7500 (p0) REVERT: D 110 GLN cc_start: 0.7784 (mp10) cc_final: 0.7440 (mp10) outliers start: 48 outliers final: 41 residues processed: 289 average time/residue: 0.2493 time to fit residues: 103.9683 Evaluate side-chains 295 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 251 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 115 optimal weight: 0.0170 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13382 Z= 0.182 Angle : 0.575 12.485 18240 Z= 0.283 Chirality : 0.041 0.167 2065 Planarity : 0.004 0.037 2402 Dihedral : 3.658 16.770 1999 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.83 % Allowed : 23.60 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.52 (0.20), residues: 1782 helix: 1.64 (0.20), residues: 708 sheet: -1.37 (0.32), residues: 256 loop : -1.86 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 349 HIS 0.004 0.001 HIS B 97 PHE 0.051 0.001 PHE A 456 TYR 0.016 0.001 TYR B 466 ARG 0.006 0.000 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 1.629 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: A 149 ILE cc_start: 0.8952 (pt) cc_final: 0.8601 (pt) REVERT: A 193 LYS cc_start: 0.8364 (mtmt) cc_final: 0.8008 (mtmm) REVERT: A 197 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7536 (mt-10) REVERT: A 245 MET cc_start: 0.7314 (tpp) cc_final: 0.7073 (tpt) REVERT: A 277 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 350 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 379 MET cc_start: 0.8196 (ptm) cc_final: 0.7958 (ptt) REVERT: A 414 ASN cc_start: 0.8331 (p0) cc_final: 0.8116 (p0) REVERT: A 631 VAL cc_start: 0.1886 (OUTLIER) cc_final: 0.1648 (t) REVERT: B 189 PHE cc_start: 0.7823 (m-80) cc_final: 0.7594 (m-80) REVERT: B 245 MET cc_start: 0.7763 (tpt) cc_final: 0.7311 (tpt) REVERT: B 273 GLU cc_start: 0.7488 (pm20) cc_final: 0.7273 (pm20) REVERT: B 274 ASP cc_start: 0.7952 (t0) cc_final: 0.7651 (t0) REVERT: B 350 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7690 (mt-10) REVERT: B 410 MET cc_start: 0.7844 (mmp) cc_final: 0.7567 (mmt) REVERT: B 756 PHE cc_start: 0.7917 (p90) cc_final: 0.7392 (p90) REVERT: C 100 LYS cc_start: 0.8901 (tmtt) cc_final: 0.8666 (tptt) REVERT: D 76 ASN cc_start: 0.7770 (p0) cc_final: 0.7509 (p0) REVERT: D 110 GLN cc_start: 0.7795 (mp10) cc_final: 0.7303 (mp10) outliers start: 48 outliers final: 43 residues processed: 277 average time/residue: 0.2605 time to fit residues: 105.9435 Evaluate side-chains 286 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 13382 Z= 0.379 Angle : 0.663 11.803 18240 Z= 0.342 Chirality : 0.044 0.160 2065 Planarity : 0.005 0.051 2402 Dihedral : 4.293 17.013 1999 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.91 % Allowed : 23.84 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.86 (0.20), residues: 1782 helix: 1.30 (0.20), residues: 720 sheet: -1.55 (0.31), residues: 246 loop : -2.04 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 349 HIS 0.004 0.001 HIS C 104 PHE 0.015 0.002 PHE B 380 TYR 0.022 0.002 TYR B 466 ARG 0.010 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 253 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7829 (pp20) REVERT: A 140 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8815 (pt) REVERT: A 149 ILE cc_start: 0.8897 (pt) cc_final: 0.8569 (pt) REVERT: A 193 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8096 (mtmm) REVERT: A 197 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 245 MET cc_start: 0.7725 (tpp) cc_final: 0.6952 (tpt) REVERT: A 273 GLU cc_start: 0.7949 (pm20) cc_final: 0.7583 (pm20) REVERT: A 277 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 350 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 379 MET cc_start: 0.8402 (ptm) cc_final: 0.8163 (ptt) REVERT: A 414 ASN cc_start: 0.8465 (p0) cc_final: 0.8263 (p0) REVERT: B 245 MET cc_start: 0.7865 (tpt) cc_final: 0.7512 (tpt) REVERT: B 274 ASP cc_start: 0.8120 (t0) cc_final: 0.7854 (t0) REVERT: B 350 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7668 (mt-10) REVERT: B 410 MET cc_start: 0.8002 (mmp) cc_final: 0.7798 (mmt) REVERT: B 728 MET cc_start: 0.8208 (ptp) cc_final: 0.8007 (ttt) REVERT: B 756 PHE cc_start: 0.7950 (p90) cc_final: 0.7416 (p90) REVERT: C 100 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8735 (tptt) REVERT: C 113 GLN cc_start: 0.8240 (tp40) cc_final: 0.8032 (tp40) REVERT: D 76 ASN cc_start: 0.7837 (p0) cc_final: 0.7580 (p0) REVERT: D 101 TYR cc_start: 0.7882 (t80) cc_final: 0.7543 (t80) REVERT: D 110 GLN cc_start: 0.7848 (mp10) cc_final: 0.7535 (mp10) outliers start: 49 outliers final: 46 residues processed: 286 average time/residue: 0.2542 time to fit residues: 105.4891 Evaluate side-chains 293 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 245 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.0870 chunk 175 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13382 Z= 0.195 Angle : 0.609 11.892 18240 Z= 0.302 Chirality : 0.042 0.219 2065 Planarity : 0.004 0.038 2402 Dihedral : 3.960 18.146 1999 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.75 % Allowed : 24.72 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.68 (0.20), residues: 1782 helix: 1.57 (0.20), residues: 706 sheet: -1.58 (0.31), residues: 246 loop : -1.96 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP B 349 HIS 0.004 0.001 HIS B 97 PHE 0.014 0.001 PHE D 28 TYR 0.016 0.001 TYR B 466 ARG 0.010 0.000 ARG B 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 258 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: A 140 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8681 (pt) REVERT: A 149 ILE cc_start: 0.8938 (pt) cc_final: 0.8582 (pt) REVERT: A 193 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8033 (mtmm) REVERT: A 197 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 245 MET cc_start: 0.7442 (tpp) cc_final: 0.6615 (tpt) REVERT: A 273 GLU cc_start: 0.7866 (pm20) cc_final: 0.7385 (pm20) REVERT: A 277 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 350 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 379 MET cc_start: 0.8219 (ptm) cc_final: 0.7974 (ptt) REVERT: A 631 VAL cc_start: 0.1859 (OUTLIER) cc_final: 0.1554 (t) REVERT: B 245 MET cc_start: 0.7700 (tpt) cc_final: 0.7323 (tpt) REVERT: B 274 ASP cc_start: 0.8008 (t0) cc_final: 0.7775 (t0) REVERT: B 350 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 643 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.6166 (t80) REVERT: B 756 PHE cc_start: 0.7907 (p90) cc_final: 0.7380 (p90) REVERT: C 86 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8008 (mtmm) REVERT: C 100 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8650 (tptt) REVERT: D 76 ASN cc_start: 0.7696 (p0) cc_final: 0.7415 (p0) REVERT: D 101 TYR cc_start: 0.7797 (t80) cc_final: 0.7510 (t80) REVERT: D 110 GLN cc_start: 0.7766 (mp10) cc_final: 0.7440 (mp10) outliers start: 47 outliers final: 37 residues processed: 290 average time/residue: 0.2693 time to fit residues: 115.6152 Evaluate side-chains 286 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 245 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 683 CYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.128255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107990 restraints weight = 27982.572| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.89 r_work: 0.3506 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13382 Z= 0.337 Angle : 0.666 11.716 18240 Z= 0.339 Chirality : 0.045 0.257 2065 Planarity : 0.005 0.051 2402 Dihedral : 4.307 22.177 1999 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.59 % Allowed : 24.80 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.89 (0.20), residues: 1782 helix: 1.31 (0.20), residues: 720 sheet: -1.65 (0.31), residues: 246 loop : -2.06 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 349 HIS 0.004 0.001 HIS C 104 PHE 0.020 0.002 PHE B 353 TYR 0.021 0.002 TYR B 466 ARG 0.014 0.001 ARG B 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.43 seconds wall clock time: 57 minutes 45.53 seconds (3465.53 seconds total)