Starting phenix.real_space_refine on Sat Jun 29 22:46:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgz_19163/06_2024/8rgz_19163.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgz_19163/06_2024/8rgz_19163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgz_19163/06_2024/8rgz_19163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgz_19163/06_2024/8rgz_19163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgz_19163/06_2024/8rgz_19163.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgz_19163/06_2024/8rgz_19163.pdb" } resolution = 3.27 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 12387 2.51 5 N 3384 2.21 5 O 3681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 19545 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "E" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "C" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4705 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Time building chain proxies: 10.82, per 1000 atoms: 0.55 Number of scatterers: 19545 At special positions: 0 Unit cell: (184.127, 168.676, 159.662, 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 93 16.00 O 3681 8.00 N 3384 7.00 C 12387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.06 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.13 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.02 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 116 " distance=2.06 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.15 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.06 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.16 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.02 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 116 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 116 " distance=2.04 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.02 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 112 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.58 Conformation dependent library (CDL) restraints added in 3.2 seconds 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 52 sheets defined 17.4% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 429 removed outlier: 4.695A pdb=" N GLY A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 4.203A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 690 through 698 removed outlier: 3.789A pdb=" N GLY A 698 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 429 removed outlier: 4.507A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 4.363A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 removed outlier: 3.899A pdb=" N ILE B 550 " --> pdb=" O ASN B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 690 through 698 removed outlier: 3.962A pdb=" N GLY B 698 " --> pdb=" O ILE B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 711 removed outlier: 3.531A pdb=" N LEU B 711 " --> pdb=" O ARG B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 429 removed outlier: 4.220A pdb=" N GLY C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 4.681A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.645A pdb=" N ILE C 550 " --> pdb=" O ASN C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 Processing helix chain 'C' and resid 690 through 698 removed outlier: 4.050A pdb=" N GLY C 698 " --> pdb=" O ILE C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 711 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'G' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.182A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.155A pdb=" N MET A 568 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 125 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.544A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.544A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 191 removed outlier: 6.027A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.327A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG A 342 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP A 323 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 344 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR A 346 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE A 319 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 214 Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.132A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.740A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 125 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 568 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.520A pdb=" N SER D 54 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 55 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N HIS D 71 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP D 57 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AB8, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.979A pdb=" N GLY E 108 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU E 57 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR E 73 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.979A pdb=" N GLY E 108 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER E 121 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.978A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.502A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.502A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 180 through 191 removed outlier: 5.900A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 187 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 168 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG B 189 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS B 166 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR B 164 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.130A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG B 342 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP B 323 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU B 344 " --> pdb=" O GLN B 321 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN B 321 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR B 346 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 319 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC7, first strand: chain 'B' and resid 210 through 214 Processing sheet with id=AC8, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC9, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AD1, first strand: chain 'B' and resid 638 through 643 removed outlier: 5.761A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.842A pdb=" N VAL C 125 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET C 568 " --> pdb=" O VAL C 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.695A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU C 601 " --> pdb=" O GLN C 584 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.498A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.498A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 180 through 191 removed outlier: 6.190A pdb=" N GLN C 172 " --> pdb=" O MET C 183 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE C 185 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 170 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU C 187 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 168 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG C 189 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS C 166 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N TYR C 164 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.199A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY C 324 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD9, first strand: chain 'C' and resid 210 through 214 Processing sheet with id=AE1, first strand: chain 'C' and resid 375 through 380 Processing sheet with id=AE2, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AE3, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.401A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AE5, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AE6, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.630A pdb=" N SER H 54 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL H 55 " --> pdb=" O HIS H 71 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS H 71 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP H 57 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 23 through 26 Processing sheet with id=AE8, first strand: chain 'F' and resid 23 through 26 Processing sheet with id=AE9, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.752A pdb=" N SER F 54 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL F 55 " --> pdb=" O HIS F 71 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS F 71 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP F 57 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 30 through 31 removed outlier: 4.175A pdb=" N TYR F 130 " --> pdb=" O ARG F 118 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 23 through 26 Processing sheet with id=AF3, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.714A pdb=" N GLY L 108 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR L 73 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.714A pdb=" N GLY L 108 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 23 through 26 Processing sheet with id=AF6, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.037A pdb=" N GLY G 108 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU G 57 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR G 73 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.037A pdb=" N GLY G 108 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER G 121 " --> pdb=" O GLN G 114 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2325 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: 8.31 Time building geometry restraints manager: 8.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3173 1.30 - 1.44: 5888 1.44 - 1.57: 10847 1.57 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 20052 Sorted by residual: bond pdb=" CE1 HIS B 681 " pdb=" NE2 HIS B 681 " ideal model delta sigma weight residual 1.321 1.411 -0.090 1.00e-02 1.00e+04 8.18e+01 bond pdb=" C THR C 690 " pdb=" N ARG C 691 " ideal model delta sigma weight residual 1.335 1.438 -0.104 1.25e-02 6.40e+03 6.88e+01 bond pdb=" CE1 HIS A 681 " pdb=" NE2 HIS A 681 " ideal model delta sigma weight residual 1.321 1.401 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" CE1 HIS A 712 " pdb=" NE2 HIS A 712 " ideal model delta sigma weight residual 1.321 1.400 -0.079 1.00e-02 1.00e+04 6.31e+01 bond pdb=" CE1 HIS C 681 " pdb=" NE2 HIS C 681 " ideal model delta sigma weight residual 1.321 1.391 -0.070 1.00e-02 1.00e+04 4.94e+01 ... (remaining 20047 not shown) Histogram of bond angle deviations from ideal: 95.80 - 103.63: 272 103.63 - 111.46: 8142 111.46 - 119.29: 8075 119.29 - 127.13: 10579 127.13 - 134.96: 199 Bond angle restraints: 27267 Sorted by residual: angle pdb=" N ILE B 719 " pdb=" CA ILE B 719 " pdb=" C ILE B 719 " ideal model delta sigma weight residual 110.42 117.40 -6.98 9.60e-01 1.09e+00 5.29e+01 angle pdb=" OD1 ASN B 217 " pdb=" CG ASN B 217 " pdb=" ND2 ASN B 217 " ideal model delta sigma weight residual 122.60 116.61 5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" O THR C 690 " pdb=" C THR C 690 " pdb=" N ARG C 691 " ideal model delta sigma weight residual 122.79 129.09 -6.30 1.14e+00 7.69e-01 3.06e+01 angle pdb=" N VAL B 352 " pdb=" CA VAL B 352 " pdb=" CB VAL B 352 " ideal model delta sigma weight residual 111.41 117.72 -6.31 1.38e+00 5.25e-01 2.09e+01 angle pdb=" OD1 ASN A 217 " pdb=" CG ASN A 217 " pdb=" ND2 ASN A 217 " ideal model delta sigma weight residual 122.60 118.04 4.56 1.00e+00 1.00e+00 2.08e+01 ... (remaining 27262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10928 17.76 - 35.51: 781 35.51 - 53.27: 154 53.27 - 71.02: 52 71.02 - 88.78: 16 Dihedral angle restraints: 11931 sinusoidal: 4779 harmonic: 7152 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 633 " pdb=" CB CYS A 633 " ideal model delta sinusoidal sigma weight residual -86.00 -174.78 88.78 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS G 42 " pdb=" SG CYS G 42 " pdb=" SG CYS G 112 " pdb=" CB CYS G 112 " ideal model delta sinusoidal sigma weight residual 93.00 128.98 -35.98 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA THR E 26 " pdb=" C THR E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta harmonic sigma weight residual 0.00 -20.22 20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2029 0.070 - 0.139: 810 0.139 - 0.209: 115 0.209 - 0.278: 11 0.278 - 0.348: 2 Chirality restraints: 2967 Sorted by residual: chirality pdb=" CA PRO H 125 " pdb=" N PRO H 125 " pdb=" C PRO H 125 " pdb=" CB PRO H 125 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA PRO F 125 " pdb=" N PRO F 125 " pdb=" C PRO F 125 " pdb=" CB PRO F 125 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA PRO B 193 " pdb=" N PRO B 193 " pdb=" C PRO B 193 " pdb=" CB PRO B 193 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2964 not shown) Planarity restraints: 3519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 528 " -0.069 2.00e-02 2.50e+03 4.47e-02 5.00e+01 pdb=" CG TRP C 528 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP C 528 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 528 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP C 528 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP C 528 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP C 528 " 0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 528 " -0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 528 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 528 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 528 " -0.088 2.00e-02 2.50e+03 4.44e-02 4.93e+01 pdb=" CG TRP B 528 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 528 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP B 528 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP B 528 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP B 528 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP B 528 " 0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 528 " -0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 528 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 528 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 73 " 0.021 2.00e-02 2.50e+03 4.23e-02 4.46e+01 pdb=" CG TRP D 73 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 73 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 73 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP D 73 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP D 73 " -0.077 2.00e-02 2.50e+03 pdb=" CE3 TRP D 73 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 73 " 0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 73 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP D 73 " 0.054 2.00e-02 2.50e+03 ... (remaining 3516 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1811 2.74 - 3.28: 19014 3.28 - 3.82: 33297 3.82 - 4.36: 42250 4.36 - 4.90: 71195 Nonbonded interactions: 167567 Sorted by model distance: nonbonded pdb=" OH TYR A 303 " pdb=" OD2 ASP D 77 " model vdw 2.198 2.440 nonbonded pdb=" O TRP C 528 " pdb=" NE2 GLN C 532 " model vdw 2.209 2.520 nonbonded pdb=" O GLN A 321 " pdb=" OH TYR D 79 " model vdw 2.213 2.440 nonbonded pdb=" OG SER B 392 " pdb=" NE2 HIS C 681 " model vdw 2.218 2.520 nonbonded pdb=" OG1 THR B 665 " pdb=" O VAL C 124 " model vdw 2.219 2.440 ... (remaining 167562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.530 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 54.130 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.011 0.114 20052 Z= 0.694 Angle : 1.096 8.259 27267 Z= 0.707 Chirality : 0.070 0.348 2967 Planarity : 0.011 0.140 3519 Dihedral : 13.473 82.745 7284 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.19 % Allowed : 1.83 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.38 (0.17), residues: 2418 helix: -0.90 (0.26), residues: 321 sheet: -0.16 (0.16), residues: 930 loop : 0.05 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.016 TRP B 528 HIS 0.035 0.006 HIS B 712 PHE 0.066 0.010 PHE B 300 TYR 0.061 0.010 TYR C 157 ARG 0.049 0.003 ARG B 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 412 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8909 (mt-10) REVERT: A 384 PHE cc_start: 0.8236 (m-10) cc_final: 0.7928 (m-80) REVERT: A 502 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8791 (mp0) REVERT: A 562 ARG cc_start: 0.7888 (ttt180) cc_final: 0.7597 (mtm110) REVERT: A 638 ARG cc_start: 0.7674 (mtp-110) cc_final: 0.7002 (mtm110) REVERT: A 649 TYR cc_start: 0.7400 (t80) cc_final: 0.6855 (t80) REVERT: D 43 PHE cc_start: 0.8317 (m-10) cc_final: 0.7930 (m-10) REVERT: D 97 ASN cc_start: 0.6797 (t0) cc_final: 0.6265 (t0) REVERT: D 106 MET cc_start: 0.6896 (mmt) cc_final: 0.6538 (mmm) REVERT: D 110 ASP cc_start: 0.7528 (m-30) cc_final: 0.6406 (m-30) REVERT: D 126 TYR cc_start: 0.8672 (p90) cc_final: 0.8375 (p90) REVERT: E 22 VAL cc_start: 0.8410 (t) cc_final: 0.8195 (p) REVERT: B 317 ASP cc_start: 0.9089 (m-30) cc_final: 0.8681 (t0) REVERT: B 529 CYS cc_start: 0.8425 (m) cc_final: 0.8141 (t) REVERT: B 587 MET cc_start: 0.5993 (mmm) cc_final: 0.5557 (mmm) REVERT: C 112 ASN cc_start: 0.7176 (t0) cc_final: 0.6754 (t0) REVERT: C 142 TYR cc_start: 0.8559 (m-80) cc_final: 0.8133 (m-80) REVERT: C 188 ASP cc_start: 0.9190 (t0) cc_final: 0.8768 (t0) REVERT: C 220 THR cc_start: 0.9089 (p) cc_final: 0.8818 (p) REVERT: C 297 MET cc_start: 0.9208 (ttm) cc_final: 0.8849 (ttp) REVERT: C 562 ARG cc_start: 0.8025 (ptt-90) cc_final: 0.7733 (ttp80) REVERT: C 563 MET cc_start: 0.6341 (mmm) cc_final: 0.6074 (mmp) REVERT: C 675 ILE cc_start: 0.8463 (mm) cc_final: 0.8258 (mm) REVERT: H 57 TRP cc_start: 0.8564 (m100) cc_final: 0.8353 (m100) REVERT: H 68 TRP cc_start: 0.8171 (t60) cc_final: 0.7957 (t60) REVERT: H 80 TYR cc_start: 0.8173 (m-80) cc_final: 0.7922 (m-10) REVERT: H 106 MET cc_start: 0.8189 (mmt) cc_final: 0.7913 (mmt) REVERT: F 77 ASP cc_start: 0.8988 (t0) cc_final: 0.8641 (t0) REVERT: F 78 LYS cc_start: 0.8972 (mttt) cc_final: 0.8445 (mttt) REVERT: F 80 TYR cc_start: 0.8657 (m-80) cc_final: 0.8443 (m-10) REVERT: F 120 TYR cc_start: 0.8263 (m-80) cc_final: 0.8038 (m-80) REVERT: G 23 MET cc_start: 0.7428 (mmm) cc_final: 0.7228 (mmm) REVERT: G 46 GLN cc_start: 0.7496 (mt0) cc_final: 0.7230 (mp10) outliers start: 4 outliers final: 2 residues processed: 413 average time/residue: 0.3406 time to fit residues: 206.2531 Evaluate side-chains 326 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain C residue 154 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.0970 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 20052 Z= 0.260 Angle : 0.571 8.325 27267 Z= 0.304 Chirality : 0.043 0.152 2967 Planarity : 0.005 0.058 3519 Dihedral : 4.696 51.159 2738 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.41 % Allowed : 8.74 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.07 (0.17), residues: 2418 helix: -0.04 (0.28), residues: 303 sheet: -0.06 (0.17), residues: 876 loop : 0.13 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 354 HIS 0.013 0.001 HIS C 534 PHE 0.015 0.002 PHE A 159 TYR 0.016 0.002 TYR B 213 ARG 0.010 0.001 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 353 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8808 (mt-10) REVERT: A 502 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8746 (mp0) REVERT: A 520 MET cc_start: 0.8074 (mmp) cc_final: 0.7451 (mmt) REVERT: A 562 ARG cc_start: 0.8099 (ttt180) cc_final: 0.7750 (mtm110) REVERT: A 638 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.7109 (mtm110) REVERT: A 649 TYR cc_start: 0.7386 (t80) cc_final: 0.6497 (t80) REVERT: D 24 LYS cc_start: 0.6851 (ttpp) cc_final: 0.6582 (ttpp) REVERT: D 110 ASP cc_start: 0.7265 (m-30) cc_final: 0.6202 (m-30) REVERT: D 126 TYR cc_start: 0.8632 (p90) cc_final: 0.8304 (p90) REVERT: B 317 ASP cc_start: 0.9053 (m-30) cc_final: 0.8824 (p0) REVERT: B 562 ARG cc_start: 0.6929 (ptt90) cc_final: 0.6678 (ptt90) REVERT: B 587 MET cc_start: 0.6073 (mmm) cc_final: 0.5680 (mmm) REVERT: B 641 PHE cc_start: 0.7789 (m-80) cc_final: 0.7522 (m-80) REVERT: C 112 ASN cc_start: 0.6964 (t0) cc_final: 0.6525 (t0) REVERT: C 188 ASP cc_start: 0.9167 (t0) cc_final: 0.8920 (t70) REVERT: C 220 THR cc_start: 0.9008 (p) cc_final: 0.8791 (p) REVERT: C 286 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7509 (pt0) REVERT: C 562 ARG cc_start: 0.8037 (ptt-90) cc_final: 0.7831 (ttp80) REVERT: C 709 ASN cc_start: 0.9086 (m-40) cc_final: 0.8865 (m110) REVERT: H 130 TYR cc_start: 0.8934 (m-80) cc_final: 0.8644 (m-10) REVERT: F 59 ARG cc_start: 0.8147 (ptt180) cc_final: 0.7703 (ptm-80) REVERT: F 68 TRP cc_start: 0.8358 (t60) cc_final: 0.8131 (t60) REVERT: F 78 LYS cc_start: 0.8989 (mttt) cc_final: 0.8497 (mttt) REVERT: F 80 TYR cc_start: 0.8759 (m-80) cc_final: 0.8538 (m-10) REVERT: F 110 ASP cc_start: 0.8667 (m-30) cc_final: 0.8259 (m-30) REVERT: L 36 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8428 (mp0) REVERT: L 84 ASP cc_start: 0.7553 (t0) cc_final: 0.7176 (m-30) REVERT: G 42 CYS cc_start: 0.5661 (OUTLIER) cc_final: 0.5234 (t) REVERT: G 46 GLN cc_start: 0.7639 (mt0) cc_final: 0.7267 (mp10) outliers start: 30 outliers final: 21 residues processed: 370 average time/residue: 0.3242 time to fit residues: 178.0560 Evaluate side-chains 346 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 324 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 238 optimal weight: 0.0010 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20052 Z= 0.225 Angle : 0.536 8.337 27267 Z= 0.285 Chirality : 0.042 0.157 2967 Planarity : 0.005 0.054 3519 Dihedral : 4.437 21.245 2733 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.97 % Allowed : 11.00 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.06 (0.17), residues: 2418 helix: -0.01 (0.28), residues: 309 sheet: 0.10 (0.18), residues: 840 loop : 0.17 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 354 HIS 0.026 0.001 HIS C 516 PHE 0.015 0.002 PHE A 159 TYR 0.021 0.001 TYR B 689 ARG 0.005 0.000 ARG L 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 329 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8843 (mt-10) REVERT: A 384 PHE cc_start: 0.8151 (m-80) cc_final: 0.7894 (m-80) REVERT: A 520 MET cc_start: 0.8028 (mmp) cc_final: 0.7336 (mmt) REVERT: A 638 ARG cc_start: 0.7597 (mtp-110) cc_final: 0.7128 (mtm110) REVERT: A 649 TYR cc_start: 0.7346 (t80) cc_final: 0.6317 (t80) REVERT: A 718 ASP cc_start: 0.8513 (t70) cc_final: 0.8231 (t70) REVERT: D 24 LYS cc_start: 0.6948 (ttpp) cc_final: 0.6693 (ttpp) REVERT: D 126 TYR cc_start: 0.8573 (p90) cc_final: 0.8301 (p90) REVERT: E 124 GLN cc_start: 0.8228 (mp10) cc_final: 0.7966 (mp10) REVERT: B 177 HIS cc_start: 0.7513 (t-90) cc_final: 0.7260 (t70) REVERT: B 317 ASP cc_start: 0.9049 (m-30) cc_final: 0.8833 (p0) REVERT: B 384 PHE cc_start: 0.8167 (m-80) cc_final: 0.7896 (m-80) REVERT: B 515 ARG cc_start: 0.8754 (mtp-110) cc_final: 0.8126 (mtm-85) REVERT: B 587 MET cc_start: 0.6085 (mmm) cc_final: 0.5600 (mmm) REVERT: B 641 PHE cc_start: 0.7798 (m-80) cc_final: 0.7543 (m-80) REVERT: B 670 PHE cc_start: 0.8987 (m-10) cc_final: 0.8781 (m-10) REVERT: C 112 ASN cc_start: 0.6981 (t0) cc_final: 0.6542 (t0) REVERT: C 188 ASP cc_start: 0.9082 (t0) cc_final: 0.8851 (t70) REVERT: C 220 THR cc_start: 0.9011 (p) cc_final: 0.8767 (p) REVERT: C 286 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7616 (pt0) REVERT: C 562 ARG cc_start: 0.8080 (ptt-90) cc_final: 0.7847 (ttp80) REVERT: C 709 ASN cc_start: 0.9277 (m-40) cc_final: 0.9068 (m110) REVERT: C 714 LEU cc_start: 0.8149 (mt) cc_final: 0.7935 (mt) REVERT: H 128 MET cc_start: 0.9017 (mtm) cc_final: 0.8754 (mtm) REVERT: H 130 TYR cc_start: 0.8723 (m-80) cc_final: 0.8458 (m-10) REVERT: F 32 LYS cc_start: 0.7406 (ptpp) cc_final: 0.6725 (mtpt) REVERT: F 35 GLN cc_start: 0.7590 (mt0) cc_final: 0.7333 (mt0) REVERT: F 78 LYS cc_start: 0.8990 (mttt) cc_final: 0.8506 (mttt) REVERT: L 84 ASP cc_start: 0.7464 (t0) cc_final: 0.7196 (m-30) REVERT: L 103 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8057 (mp0) REVERT: G 42 CYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5589 (t) REVERT: G 46 GLN cc_start: 0.7724 (mt0) cc_final: 0.7328 (mp10) outliers start: 42 outliers final: 28 residues processed: 349 average time/residue: 0.3414 time to fit residues: 177.2775 Evaluate side-chains 342 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 313 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 234 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 210 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS G 77 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20052 Z= 0.289 Angle : 0.547 7.992 27267 Z= 0.291 Chirality : 0.043 0.172 2967 Planarity : 0.004 0.051 3519 Dihedral : 4.474 25.162 2733 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.44 % Allowed : 11.94 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.05 (0.17), residues: 2418 helix: 0.00 (0.27), residues: 306 sheet: -0.05 (0.17), residues: 885 loop : 0.14 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.012 0.001 HIS C 516 PHE 0.016 0.002 PHE C 650 TYR 0.025 0.002 TYR A 164 ARG 0.006 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 324 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.8329 (m-80) cc_final: 0.8069 (m-80) REVERT: A 520 MET cc_start: 0.8035 (mmp) cc_final: 0.7372 (mmt) REVERT: A 638 ARG cc_start: 0.7595 (mtp-110) cc_final: 0.7181 (mtm110) REVERT: A 649 TYR cc_start: 0.7482 (t80) cc_final: 0.6633 (t80) REVERT: A 718 ASP cc_start: 0.8523 (t70) cc_final: 0.8276 (t70) REVERT: D 24 LYS cc_start: 0.7113 (ttpp) cc_final: 0.6799 (ttpp) REVERT: E 93 THR cc_start: 0.8225 (p) cc_final: 0.7904 (t) REVERT: B 177 HIS cc_start: 0.7510 (t-90) cc_final: 0.7254 (t70) REVERT: B 317 ASP cc_start: 0.9044 (m-30) cc_final: 0.8841 (p0) REVERT: B 374 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7171 (tm-30) REVERT: B 375 MET cc_start: 0.8633 (ttt) cc_final: 0.8407 (ttt) REVERT: B 384 PHE cc_start: 0.8320 (m-80) cc_final: 0.8095 (m-80) REVERT: B 587 MET cc_start: 0.6083 (mmm) cc_final: 0.5561 (mmm) REVERT: B 641 PHE cc_start: 0.7801 (m-80) cc_final: 0.7542 (m-80) REVERT: B 670 PHE cc_start: 0.8998 (m-10) cc_final: 0.8783 (m-10) REVERT: C 112 ASN cc_start: 0.6975 (t0) cc_final: 0.6552 (t0) REVERT: C 220 THR cc_start: 0.8997 (p) cc_final: 0.8770 (p) REVERT: C 562 ARG cc_start: 0.8107 (ptt-90) cc_final: 0.7880 (ttp80) REVERT: C 709 ASN cc_start: 0.9332 (m-40) cc_final: 0.9085 (m110) REVERT: H 128 MET cc_start: 0.9104 (mtm) cc_final: 0.8800 (mtm) REVERT: H 130 TYR cc_start: 0.8747 (m-80) cc_final: 0.8488 (m-10) REVERT: F 32 LYS cc_start: 0.7395 (ptpp) cc_final: 0.6534 (mttm) REVERT: F 35 GLN cc_start: 0.7694 (mt0) cc_final: 0.7348 (mt0) REVERT: F 43 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: F 78 LYS cc_start: 0.8986 (mttt) cc_final: 0.8516 (mttt) REVERT: F 129 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: L 84 ASP cc_start: 0.7453 (t0) cc_final: 0.7184 (m-30) REVERT: G 42 CYS cc_start: 0.5687 (OUTLIER) cc_final: 0.5293 (t) REVERT: G 46 GLN cc_start: 0.7771 (mt0) cc_final: 0.7357 (mp10) outliers start: 52 outliers final: 35 residues processed: 352 average time/residue: 0.3306 time to fit residues: 175.1595 Evaluate side-chains 347 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 309 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 59 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20052 Z= 0.190 Angle : 0.510 7.816 27267 Z= 0.271 Chirality : 0.042 0.205 2967 Planarity : 0.004 0.048 3519 Dihedral : 4.333 23.754 2733 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 13.21 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.12 (0.17), residues: 2418 helix: 0.16 (0.28), residues: 312 sheet: 0.11 (0.17), residues: 888 loop : 0.21 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 354 HIS 0.009 0.001 HIS C 516 PHE 0.019 0.001 PHE C 650 TYR 0.022 0.001 TYR A 164 ARG 0.005 0.000 ARG L 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 333 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.8165 (m-10) cc_final: 0.7946 (m-80) REVERT: A 502 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8660 (mp0) REVERT: A 520 MET cc_start: 0.7989 (mmp) cc_final: 0.7264 (mmt) REVERT: A 562 ARG cc_start: 0.8082 (ttt180) cc_final: 0.7787 (ptm160) REVERT: A 638 ARG cc_start: 0.7592 (mtp-110) cc_final: 0.7308 (mpp80) REVERT: A 649 TYR cc_start: 0.7420 (t80) cc_final: 0.6612 (t80) REVERT: D 24 LYS cc_start: 0.7190 (ttpp) cc_final: 0.6870 (ttpp) REVERT: B 375 MET cc_start: 0.8550 (ttt) cc_final: 0.8330 (ttt) REVERT: B 384 PHE cc_start: 0.8230 (m-80) cc_final: 0.7979 (m-80) REVERT: B 587 MET cc_start: 0.6121 (mmm) cc_final: 0.5668 (mmm) REVERT: B 641 PHE cc_start: 0.7764 (m-80) cc_final: 0.7500 (m-80) REVERT: B 670 PHE cc_start: 0.8945 (m-10) cc_final: 0.8730 (m-10) REVERT: C 112 ASN cc_start: 0.7013 (t0) cc_final: 0.6603 (t0) REVERT: C 220 THR cc_start: 0.9013 (p) cc_final: 0.8792 (p) REVERT: C 286 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7673 (pt0) REVERT: C 562 ARG cc_start: 0.8117 (ptt-90) cc_final: 0.7896 (ttp80) REVERT: C 709 ASN cc_start: 0.9330 (m-40) cc_final: 0.9081 (m110) REVERT: H 128 MET cc_start: 0.9078 (mtm) cc_final: 0.8696 (mtm) REVERT: F 32 LYS cc_start: 0.7303 (ptpp) cc_final: 0.6475 (mttm) REVERT: F 35 GLN cc_start: 0.7763 (mt0) cc_final: 0.7405 (mt0) REVERT: F 77 ASP cc_start: 0.8736 (t0) cc_final: 0.8046 (t0) REVERT: F 78 LYS cc_start: 0.8975 (mttt) cc_final: 0.8497 (mttt) REVERT: F 80 TYR cc_start: 0.8590 (m-80) cc_final: 0.8346 (m-10) REVERT: G 42 CYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5644 (t) REVERT: G 46 GLN cc_start: 0.7803 (mt0) cc_final: 0.7403 (mp10) outliers start: 50 outliers final: 37 residues processed: 357 average time/residue: 0.3281 time to fit residues: 176.7332 Evaluate side-chains 350 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 312 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 195 optimal weight: 0.0070 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 ASN G 77 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20052 Z= 0.269 Angle : 0.541 8.829 27267 Z= 0.287 Chirality : 0.043 0.176 2967 Planarity : 0.004 0.049 3519 Dihedral : 4.384 22.215 2733 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.91 % Allowed : 13.45 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.05 (0.17), residues: 2418 helix: 0.11 (0.27), residues: 306 sheet: 0.06 (0.17), residues: 888 loop : 0.16 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 354 HIS 0.014 0.001 HIS B 177 PHE 0.018 0.002 PHE C 650 TYR 0.030 0.002 TYR B 655 ARG 0.006 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 322 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.8071 (m-10) cc_final: 0.7815 (m-80) REVERT: A 413 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 502 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8721 (mp0) REVERT: A 520 MET cc_start: 0.7992 (mmp) cc_final: 0.7254 (mmt) REVERT: A 562 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7752 (ptm160) REVERT: A 580 ASN cc_start: 0.7009 (m110) cc_final: 0.6743 (m-40) REVERT: A 638 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7316 (mpp80) REVERT: A 649 TYR cc_start: 0.7482 (t80) cc_final: 0.6698 (t80) REVERT: A 718 ASP cc_start: 0.8465 (t70) cc_final: 0.8106 (t70) REVERT: D 24 LYS cc_start: 0.7233 (ttpp) cc_final: 0.6903 (ttpp) REVERT: B 374 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7182 (tm-30) REVERT: B 375 MET cc_start: 0.8608 (ttt) cc_final: 0.8352 (ttt) REVERT: B 587 MET cc_start: 0.6104 (mmm) cc_final: 0.5629 (mmm) REVERT: B 641 PHE cc_start: 0.7794 (m-80) cc_final: 0.7527 (m-80) REVERT: B 670 PHE cc_start: 0.8935 (m-10) cc_final: 0.8725 (m-10) REVERT: C 112 ASN cc_start: 0.6979 (t0) cc_final: 0.6576 (t0) REVERT: C 220 THR cc_start: 0.9000 (p) cc_final: 0.8788 (p) REVERT: C 562 ARG cc_start: 0.8108 (ptt-90) cc_final: 0.7871 (ttp80) REVERT: C 709 ASN cc_start: 0.9340 (m-40) cc_final: 0.9085 (m110) REVERT: H 128 MET cc_start: 0.9133 (mtm) cc_final: 0.8748 (mtm) REVERT: H 135 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8558 (p) REVERT: F 43 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: F 68 TRP cc_start: 0.8206 (t60) cc_final: 0.7960 (t60) REVERT: F 78 LYS cc_start: 0.8972 (mttt) cc_final: 0.8516 (mttt) REVERT: L 101 ARG cc_start: 0.7640 (ttt90) cc_final: 0.7236 (tpt170) REVERT: L 103 GLU cc_start: 0.8211 (mp0) cc_final: 0.7824 (mp0) REVERT: G 46 GLN cc_start: 0.7754 (mt0) cc_final: 0.7331 (mp10) outliers start: 62 outliers final: 44 residues processed: 359 average time/residue: 0.3221 time to fit residues: 173.2054 Evaluate side-chains 361 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 314 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 171 optimal weight: 0.0050 chunk 197 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN E 25 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20052 Z= 0.200 Angle : 0.520 8.415 27267 Z= 0.275 Chirality : 0.042 0.224 2967 Planarity : 0.004 0.047 3519 Dihedral : 4.293 21.073 2733 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.63 % Allowed : 13.63 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.06 (0.17), residues: 2418 helix: 0.20 (0.27), residues: 306 sheet: 0.00 (0.17), residues: 900 loop : 0.21 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 356 HIS 0.010 0.001 HIS B 177 PHE 0.020 0.001 PHE C 650 TYR 0.020 0.001 TYR B 689 ARG 0.007 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 323 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8721 (mtt180) cc_final: 0.8286 (mmm-85) REVERT: A 384 PHE cc_start: 0.8054 (m-10) cc_final: 0.7794 (m-80) REVERT: A 502 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8681 (mp0) REVERT: A 520 MET cc_start: 0.7974 (mmp) cc_final: 0.7230 (mmt) REVERT: A 562 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7750 (ptm160) REVERT: A 638 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7288 (mpp80) REVERT: A 649 TYR cc_start: 0.7334 (t80) cc_final: 0.6344 (t80) REVERT: A 718 ASP cc_start: 0.8398 (t70) cc_final: 0.8038 (t70) REVERT: D 24 LYS cc_start: 0.7229 (ttpp) cc_final: 0.6881 (ttpp) REVERT: D 80 TYR cc_start: 0.8798 (m-80) cc_final: 0.7908 (m-80) REVERT: B 375 MET cc_start: 0.8549 (ttt) cc_final: 0.8326 (ttt) REVERT: B 587 MET cc_start: 0.6104 (mmm) cc_final: 0.5579 (mmm) REVERT: B 641 PHE cc_start: 0.7770 (m-80) cc_final: 0.7515 (m-80) REVERT: B 670 PHE cc_start: 0.8913 (m-10) cc_final: 0.8702 (m-10) REVERT: C 112 ASN cc_start: 0.7189 (t0) cc_final: 0.6784 (t0) REVERT: C 286 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7510 (pt0) REVERT: C 562 ARG cc_start: 0.8120 (ptt-90) cc_final: 0.7885 (ttp80) REVERT: C 709 ASN cc_start: 0.9344 (m-40) cc_final: 0.9081 (m110) REVERT: H 128 MET cc_start: 0.9109 (mtm) cc_final: 0.8718 (mtm) REVERT: H 135 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8524 (p) REVERT: F 43 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: F 64 LYS cc_start: 0.7800 (mptt) cc_final: 0.6978 (tmtt) REVERT: F 77 ASP cc_start: 0.8705 (t0) cc_final: 0.8013 (t0) REVERT: F 78 LYS cc_start: 0.8960 (mttt) cc_final: 0.8477 (mttt) REVERT: F 80 TYR cc_start: 0.8597 (m-80) cc_final: 0.8357 (m-10) REVERT: L 98 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6741 (mtmt) REVERT: L 101 ARG cc_start: 0.7636 (ttt90) cc_final: 0.7357 (tpt170) REVERT: G 46 GLN cc_start: 0.7750 (mt0) cc_final: 0.7205 (mp10) outliers start: 56 outliers final: 44 residues processed: 353 average time/residue: 0.3234 time to fit residues: 171.5932 Evaluate side-chains 362 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 315 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 148 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 0.2980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20052 Z= 0.344 Angle : 0.580 10.206 27267 Z= 0.305 Chirality : 0.044 0.233 2967 Planarity : 0.004 0.048 3519 Dihedral : 4.556 31.129 2733 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.77 % Allowed : 14.57 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.09 (0.17), residues: 2418 helix: 0.05 (0.27), residues: 303 sheet: -0.07 (0.17), residues: 888 loop : 0.09 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 354 HIS 0.010 0.001 HIS B 177 PHE 0.017 0.002 PHE C 650 TYR 0.025 0.002 TYR B 689 ARG 0.008 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 316 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8728 (mtt180) cc_final: 0.8290 (mmm-85) REVERT: A 502 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8675 (mp0) REVERT: A 520 MET cc_start: 0.8001 (mmp) cc_final: 0.7328 (mmt) REVERT: A 562 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7769 (ptm160) REVERT: A 638 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.7330 (mpp80) REVERT: A 649 TYR cc_start: 0.7403 (t80) cc_final: 0.6543 (t80) REVERT: A 718 ASP cc_start: 0.8522 (t70) cc_final: 0.8151 (t70) REVERT: D 24 LYS cc_start: 0.7242 (ttpp) cc_final: 0.6890 (ttpp) REVERT: B 374 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7179 (tm-30) REVERT: B 375 MET cc_start: 0.8592 (ttt) cc_final: 0.8325 (ttt) REVERT: B 587 MET cc_start: 0.6217 (mmm) cc_final: 0.5705 (mmm) REVERT: B 670 PHE cc_start: 0.8954 (m-10) cc_final: 0.8748 (m-10) REVERT: C 112 ASN cc_start: 0.6994 (t0) cc_final: 0.6580 (t0) REVERT: C 562 ARG cc_start: 0.8160 (ptt-90) cc_final: 0.7904 (ttp80) REVERT: C 709 ASN cc_start: 0.9367 (m-40) cc_final: 0.9140 (m110) REVERT: H 128 MET cc_start: 0.9181 (mtm) cc_final: 0.8960 (mtm) REVERT: H 135 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8431 (p) REVERT: F 43 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: F 64 LYS cc_start: 0.7954 (mptt) cc_final: 0.7136 (tmtt) REVERT: F 78 LYS cc_start: 0.8949 (mttt) cc_final: 0.8474 (mttt) REVERT: F 80 TYR cc_start: 0.8755 (m-80) cc_final: 0.8543 (m-10) REVERT: L 98 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6738 (mtmt) REVERT: L 101 ARG cc_start: 0.7662 (ttt90) cc_final: 0.7395 (tpt170) REVERT: G 46 GLN cc_start: 0.7769 (mt0) cc_final: 0.7344 (mp10) outliers start: 59 outliers final: 50 residues processed: 349 average time/residue: 0.3262 time to fit residues: 169.8338 Evaluate side-chains 359 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 chunk 218 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20052 Z= 0.295 Angle : 0.569 10.896 27267 Z= 0.299 Chirality : 0.043 0.194 2967 Planarity : 0.004 0.047 3519 Dihedral : 4.546 25.932 2733 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.91 % Allowed : 14.34 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.14 (0.17), residues: 2418 helix: 0.04 (0.28), residues: 303 sheet: -0.12 (0.17), residues: 888 loop : 0.06 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 68 HIS 0.009 0.001 HIS B 177 PHE 0.021 0.002 PHE B 641 TYR 0.026 0.002 TYR C 689 ARG 0.008 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 315 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8301 (mmm-85) REVERT: A 262 PHE cc_start: 0.7873 (m-80) cc_final: 0.7631 (m-80) REVERT: A 520 MET cc_start: 0.7994 (mmp) cc_final: 0.7327 (mmt) REVERT: A 562 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7762 (ptm160) REVERT: A 638 ARG cc_start: 0.7635 (mtp-110) cc_final: 0.7327 (mpp80) REVERT: A 649 TYR cc_start: 0.7400 (t80) cc_final: 0.6439 (t80) REVERT: A 718 ASP cc_start: 0.8519 (t70) cc_final: 0.8141 (t70) REVERT: D 24 LYS cc_start: 0.7240 (ttpp) cc_final: 0.6879 (ttpp) REVERT: D 80 TYR cc_start: 0.8781 (m-80) cc_final: 0.7827 (m-80) REVERT: D 97 ASN cc_start: 0.6459 (t0) cc_final: 0.6213 (t0) REVERT: B 374 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7168 (tm-30) REVERT: B 375 MET cc_start: 0.8578 (ttt) cc_final: 0.8315 (ttt) REVERT: B 587 MET cc_start: 0.6203 (mmm) cc_final: 0.5696 (mmm) REVERT: B 641 PHE cc_start: 0.7675 (m-80) cc_final: 0.7384 (m-80) REVERT: B 670 PHE cc_start: 0.8937 (m-10) cc_final: 0.8733 (m-10) REVERT: C 112 ASN cc_start: 0.7083 (t0) cc_final: 0.6666 (t0) REVERT: C 286 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: C 562 ARG cc_start: 0.8200 (ptt-90) cc_final: 0.7942 (ttp80) REVERT: C 709 ASN cc_start: 0.9377 (m-40) cc_final: 0.9109 (m110) REVERT: H 128 MET cc_start: 0.9162 (mtm) cc_final: 0.8876 (mtm) REVERT: H 135 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8391 (p) REVERT: F 43 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: F 64 LYS cc_start: 0.7972 (mptt) cc_final: 0.7148 (tmtt) REVERT: F 78 LYS cc_start: 0.8936 (mttt) cc_final: 0.8457 (mttt) REVERT: F 80 TYR cc_start: 0.8762 (m-80) cc_final: 0.8542 (m-10) REVERT: G 46 GLN cc_start: 0.7742 (mt0) cc_final: 0.7357 (mp10) outliers start: 62 outliers final: 51 residues processed: 349 average time/residue: 0.3336 time to fit residues: 174.5068 Evaluate side-chains 362 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 308 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 222 optimal weight: 0.0870 chunk 192 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20052 Z= 0.226 Angle : 0.549 10.003 27267 Z= 0.289 Chirality : 0.042 0.217 2967 Planarity : 0.004 0.047 3519 Dihedral : 4.487 26.260 2733 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.44 % Allowed : 14.90 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.08 (0.17), residues: 2418 helix: 0.13 (0.28), residues: 303 sheet: -0.06 (0.17), residues: 888 loop : 0.07 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.008 0.001 HIS B 534 PHE 0.021 0.001 PHE C 650 TYR 0.025 0.001 TYR B 689 ARG 0.008 0.000 ARG E 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 313 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8706 (mtt180) cc_final: 0.8289 (mmm-85) REVERT: A 262 PHE cc_start: 0.7860 (m-80) cc_final: 0.7633 (m-80) REVERT: A 384 PHE cc_start: 0.8017 (m-10) cc_final: 0.7788 (m-80) REVERT: A 502 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8799 (mp0) REVERT: A 520 MET cc_start: 0.7974 (mmp) cc_final: 0.7270 (mmt) REVERT: A 562 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7802 (ptm160) REVERT: A 638 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7338 (mpp80) REVERT: A 649 TYR cc_start: 0.7355 (t80) cc_final: 0.6420 (t80) REVERT: A 718 ASP cc_start: 0.8506 (t70) cc_final: 0.8126 (t70) REVERT: D 80 TYR cc_start: 0.8790 (m-80) cc_final: 0.7768 (m-80) REVERT: D 97 ASN cc_start: 0.6464 (t0) cc_final: 0.6197 (t0) REVERT: B 178 ARG cc_start: 0.8882 (tpt90) cc_final: 0.8492 (tpp-160) REVERT: B 375 MET cc_start: 0.8571 (ttt) cc_final: 0.8353 (ttt) REVERT: B 587 MET cc_start: 0.6216 (mmm) cc_final: 0.5671 (mmm) REVERT: B 641 PHE cc_start: 0.7414 (m-80) cc_final: 0.7087 (m-80) REVERT: B 670 PHE cc_start: 0.8927 (m-10) cc_final: 0.8717 (m-10) REVERT: C 112 ASN cc_start: 0.7107 (t0) cc_final: 0.6679 (t0) REVERT: C 286 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: C 562 ARG cc_start: 0.8282 (ptt-90) cc_final: 0.8016 (ttp80) REVERT: C 709 ASN cc_start: 0.9372 (m-40) cc_final: 0.9101 (m110) REVERT: H 135 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8387 (p) REVERT: F 43 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: F 64 LYS cc_start: 0.7982 (mptt) cc_final: 0.7192 (tmtt) REVERT: F 78 LYS cc_start: 0.8921 (mttt) cc_final: 0.8433 (mttt) REVERT: F 80 TYR cc_start: 0.8771 (m-80) cc_final: 0.8557 (m-10) REVERT: G 46 GLN cc_start: 0.7795 (mt0) cc_final: 0.7421 (mp10) outliers start: 52 outliers final: 46 residues processed: 341 average time/residue: 0.3254 time to fit residues: 165.1296 Evaluate side-chains 354 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 305 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN E 25 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115793 restraints weight = 28268.062| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.26 r_work: 0.3203 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20052 Z= 0.250 Angle : 0.561 9.710 27267 Z= 0.294 Chirality : 0.043 0.275 2967 Planarity : 0.004 0.055 3519 Dihedral : 4.469 25.387 2733 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 15.33 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.24 (0.17), residues: 2418 helix: -0.26 (0.27), residues: 321 sheet: -0.08 (0.17), residues: 888 loop : -0.03 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 539 HIS 0.007 0.001 HIS B 534 PHE 0.020 0.002 PHE C 650 TYR 0.023 0.001 TYR B 689 ARG 0.009 0.000 ARG E 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4740.23 seconds wall clock time: 85 minutes 1.03 seconds (5101.03 seconds total)