Starting phenix.real_space_refine on Mon Mar 18 15:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yif_33857/03_2024/7yif_33857.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yif_33857/03_2024/7yif_33857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yif_33857/03_2024/7yif_33857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yif_33857/03_2024/7yif_33857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yif_33857/03_2024/7yif_33857.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yif_33857/03_2024/7yif_33857.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 6 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 57": "OD1" <-> "OD2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ASP 611": "OD1" <-> "OD2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B ASP 611": "OD1" <-> "OD2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C ASP 611": "OD1" <-> "OD2" Residue "C PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "D ASP 443": "OD1" <-> "OD2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D ASP 611": "OD1" <-> "OD2" Residue "D PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21322 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' K': 6} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.92, per 1000 atoms: 0.51 Number of scatterers: 21322 At special positions: 0 Unit cell: (160.461, 160.461, 130.746, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 6 19.00 S 128 16.00 O 3848 8.00 N 3544 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.52 Conformation dependent library (CDL) restraints added in 3.6 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 24 sheets defined 52.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.006A pdb=" N MET A 68 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 74 through 87 removed outlier: 4.101A pdb=" N GLU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 4.161A pdb=" N LYS A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.811A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 245 through 265 removed outlier: 3.946A pdb=" N ASP A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 293 through 300 removed outlier: 4.038A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 345 through 374 removed outlier: 3.612A pdb=" N LEU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 416 through 431 removed outlier: 4.112A pdb=" N VAL A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 476 removed outlier: 3.795A pdb=" N MET A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 removed outlier: 3.936A pdb=" N ARG A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.648A pdb=" N ILE A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.853A pdb=" N ALA A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.573A pdb=" N PHE A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 546' Processing helix chain 'A' and resid 548 through 552 removed outlier: 3.505A pdb=" N ARG A 552 " --> pdb=" O PRO A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.556A pdb=" N ARG A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 643 through 651 Processing helix chain 'A' and resid 655 through 664 removed outlier: 4.043A pdb=" N SER A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 692 Processing helix chain 'B' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 65 through 69 removed outlier: 4.006A pdb=" N MET B 68 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 69' Processing helix chain 'B' and resid 74 through 87 removed outlier: 4.101A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 4.161A pdb=" N LYS B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.811A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.946A pdb=" N ASP B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 293 through 300 removed outlier: 4.038A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 345 through 374 removed outlier: 3.612A pdb=" N LEU B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 416 through 431 removed outlier: 4.113A pdb=" N VAL B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 476 removed outlier: 3.795A pdb=" N MET B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 495 removed outlier: 3.922A pdb=" N ARG B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.648A pdb=" N ILE B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.853A pdb=" N ALA B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.573A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 546' Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.505A pdb=" N ARG B 552 " --> pdb=" O PRO B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.556A pdb=" N ARG B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 655 through 664 removed outlier: 4.043A pdb=" N SER B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 692 Processing helix chain 'C' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 65 through 69 removed outlier: 4.006A pdb=" N MET C 68 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 69' Processing helix chain 'C' and resid 74 through 87 removed outlier: 4.101A pdb=" N GLU C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 156 removed outlier: 4.161A pdb=" N LYS C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.811A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 245 through 265 removed outlier: 3.946A pdb=" N ASP C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 293 through 300 removed outlier: 4.038A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 345 through 374 removed outlier: 3.611A pdb=" N LEU C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 416 through 431 removed outlier: 4.113A pdb=" N VAL C 420 " --> pdb=" O ASP C 416 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 476 removed outlier: 3.795A pdb=" N MET C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 495 removed outlier: 3.922A pdb=" N ARG C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 516 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.648A pdb=" N ILE C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 541 removed outlier: 3.853A pdb=" N ALA C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.573A pdb=" N PHE C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 546' Processing helix chain 'C' and resid 548 through 552 removed outlier: 3.505A pdb=" N ARG C 552 " --> pdb=" O PRO C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.556A pdb=" N ARG C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 643 through 651 Processing helix chain 'C' and resid 655 through 664 removed outlier: 4.043A pdb=" N SER C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 692 Processing helix chain 'D' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 65 through 69 removed outlier: 4.006A pdb=" N MET D 68 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 69' Processing helix chain 'D' and resid 74 through 87 removed outlier: 4.101A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 82 " --> pdb=" O ILE D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 156 removed outlier: 4.161A pdb=" N LYS D 148 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 178 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.811A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 245 through 265 removed outlier: 3.946A pdb=" N ASP D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 293 through 300 removed outlier: 4.038A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS D 300 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'D' and resid 345 through 374 removed outlier: 3.611A pdb=" N LEU D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 395 Processing helix chain 'D' and resid 416 through 431 removed outlier: 4.113A pdb=" N VAL D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 476 removed outlier: 3.795A pdb=" N MET D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET D 454 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 495 removed outlier: 3.908A pdb=" N ARG D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 516 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.648A pdb=" N ILE D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 541 removed outlier: 3.853A pdb=" N ALA D 534 " --> pdb=" O LYS D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.573A pdb=" N PHE D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 546' Processing helix chain 'D' and resid 548 through 552 removed outlier: 3.505A pdb=" N ARG D 552 " --> pdb=" O PRO D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 563 removed outlier: 3.556A pdb=" N ARG D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA D 561 " --> pdb=" O GLY D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 566 No H-bonds generated for 'chain 'D' and resid 564 through 566' Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 655 through 664 removed outlier: 4.043A pdb=" N SER D 659 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.227A pdb=" N THR A 127 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.413A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 578 removed outlier: 6.766A pdb=" N VAL A 630 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 605 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 583 through 584 removed outlier: 3.659A pdb=" N VAL A 584 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA A 624 " --> pdb=" O VAL A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.227A pdb=" N THR B 127 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 97 Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 377 Processing sheet with id=AB1, first strand: chain 'B' and resid 567 through 569 removed outlier: 6.413A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 576 through 578 removed outlier: 6.766A pdb=" N VAL B 630 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 583 through 584 removed outlier: 3.659A pdb=" N VAL B 584 " --> pdb=" O ALA B 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA B 624 " --> pdb=" O VAL B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 31 through 32 removed outlier: 4.227A pdb=" N THR C 127 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 94 through 97 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AB7, first strand: chain 'C' and resid 567 through 569 removed outlier: 6.413A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 576 through 578 removed outlier: 6.766A pdb=" N VAL C 630 " --> pdb=" O ILE C 577 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 605 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 583 through 584 removed outlier: 3.659A pdb=" N VAL C 584 " --> pdb=" O ALA C 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA C 624 " --> pdb=" O VAL C 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.227A pdb=" N THR D 127 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 94 through 97 Processing sheet with id=AC3, first strand: chain 'D' and resid 376 through 377 Processing sheet with id=AC4, first strand: chain 'D' and resid 567 through 569 removed outlier: 6.413A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 576 through 578 removed outlier: 6.766A pdb=" N VAL D 630 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 605 " --> pdb=" O VAL D 597 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 583 through 584 removed outlier: 3.659A pdb=" N VAL D 584 " --> pdb=" O ALA D 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA D 624 " --> pdb=" O VAL D 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 920 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 8.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6700 1.34 - 1.46: 4763 1.46 - 1.58: 10149 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" CA ILE B 191 " pdb=" CB ILE B 191 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.46e+00 bond pdb=" CA ILE D 191 " pdb=" CB ILE D 191 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.46e+00 bond pdb=" CA ILE C 191 " pdb=" CB ILE C 191 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.46e+00 bond pdb=" CA ILE A 191 " pdb=" CB ILE A 191 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.46e+00 bond pdb=" CG ARG D 21 " pdb=" CD ARG D 21 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.46e-01 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 484 106.57 - 113.42: 12052 113.42 - 120.28: 7855 120.28 - 127.13: 8977 127.13 - 133.98: 216 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N ASP A 57 " pdb=" CA ASP A 57 " pdb=" C ASP A 57 " ideal model delta sigma weight residual 114.04 108.11 5.93 1.24e+00 6.50e-01 2.29e+01 angle pdb=" N ASP D 57 " pdb=" CA ASP D 57 " pdb=" C ASP D 57 " ideal model delta sigma weight residual 114.04 108.11 5.93 1.24e+00 6.50e-01 2.29e+01 angle pdb=" N ASP B 57 " pdb=" CA ASP B 57 " pdb=" C ASP B 57 " ideal model delta sigma weight residual 114.04 108.11 5.93 1.24e+00 6.50e-01 2.29e+01 angle pdb=" N ASP C 57 " pdb=" CA ASP C 57 " pdb=" C ASP C 57 " ideal model delta sigma weight residual 114.04 108.11 5.93 1.24e+00 6.50e-01 2.29e+01 angle pdb=" C THR C 441 " pdb=" N THR C 442 " pdb=" CA THR C 442 " ideal model delta sigma weight residual 121.54 114.78 6.76 1.91e+00 2.74e-01 1.25e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 11429 16.44 - 32.87: 1182 32.87 - 49.31: 265 49.31 - 65.74: 40 65.74 - 82.18: 16 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA THR C 291 " pdb=" C THR C 291 " pdb=" N TRP C 292 " pdb=" CA TRP C 292 " ideal model delta harmonic sigma weight residual 180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA THR A 291 " pdb=" C THR A 291 " pdb=" N TRP A 292 " pdb=" CA TRP A 292 " ideal model delta harmonic sigma weight residual 180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA THR D 291 " pdb=" C THR D 291 " pdb=" N TRP D 292 " pdb=" CA TRP D 292 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1943 0.028 - 0.055: 965 0.055 - 0.083: 338 0.083 - 0.110: 118 0.110 - 0.138: 40 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA THR A 441 " pdb=" N THR A 441 " pdb=" C THR A 441 " pdb=" CB THR A 441 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA THR C 441 " pdb=" N THR C 441 " pdb=" C THR C 441 " pdb=" CB THR C 441 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA THR D 441 " pdb=" N THR D 441 " pdb=" C THR D 441 " pdb=" CB THR D 441 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 103 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 104 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 103 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 104 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 103 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO D 104 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.023 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 6694 2.84 - 3.41: 22290 3.41 - 3.99: 36904 3.99 - 4.56: 52089 4.56 - 5.14: 79465 Nonbonded interactions: 197442 Sorted by model distance: nonbonded pdb=" OE2 GLU A 596 " pdb=" OH TYR D 195 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR A 195 " pdb=" OE2 GLU B 596 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR C 195 " pdb=" OE2 GLU D 596 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR B 195 " pdb=" OE2 GLU C 596 " model vdw 2.259 2.440 nonbonded pdb=" O LEU D 418 " pdb=" OG SER D 422 " model vdw 2.280 2.440 ... (remaining 197437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 692) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 14.210 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 54.030 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.002 0.026 21804 Z= 0.141 Angle : 0.576 8.436 29584 Z= 0.328 Chirality : 0.039 0.138 3404 Planarity : 0.004 0.042 3668 Dihedral : 14.019 82.179 7884 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.49 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2616 helix: 0.28 (0.15), residues: 1256 sheet: -3.62 (0.37), residues: 188 loop : -2.55 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 217 HIS 0.006 0.001 HIS A 209 PHE 0.016 0.001 PHE D 226 TYR 0.011 0.001 TYR A 460 ARG 0.009 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.0244 (ppp) cc_final: -0.0988 (ppp) REVERT: A 290 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7071 (tptt) REVERT: B 169 MET cc_start: 0.0246 (ppp) cc_final: -0.0993 (ppp) REVERT: B 290 LYS cc_start: 0.7430 (ttmm) cc_final: 0.7068 (tptt) REVERT: C 169 MET cc_start: 0.0245 (ppp) cc_final: -0.0997 (ppp) REVERT: C 290 LYS cc_start: 0.7407 (ttmm) cc_final: 0.7067 (tptt) REVERT: D 169 MET cc_start: 0.0246 (ppp) cc_final: -0.0994 (ppp) REVERT: D 290 LYS cc_start: 0.7410 (ttmm) cc_final: 0.7069 (tptt) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2673 time to fit residues: 137.2775 Evaluate side-chains 253 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 0.0980 chunk 80 optimal weight: 0.0470 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21804 Z= 0.155 Angle : 0.524 7.966 29584 Z= 0.279 Chirality : 0.040 0.142 3404 Planarity : 0.004 0.037 3668 Dihedral : 4.483 29.342 2864 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.19 % Favored : 92.66 % Rotamer: Outliers : 0.84 % Allowed : 5.50 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.16), residues: 2616 helix: 0.54 (0.15), residues: 1280 sheet: -3.67 (0.38), residues: 164 loop : -2.69 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 388 HIS 0.004 0.001 HIS C 176 PHE 0.015 0.001 PHE C 93 TYR 0.013 0.001 TYR C 288 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 266 time to evaluate : 2.134 Fit side-chains REVERT: A 169 MET cc_start: 0.0428 (ppp) cc_final: -0.0786 (ppp) REVERT: B 169 MET cc_start: 0.0418 (ppp) cc_final: -0.0791 (ppp) REVERT: C 169 MET cc_start: 0.0422 (ppp) cc_final: -0.0789 (ppp) REVERT: D 169 MET cc_start: 0.0424 (ppp) cc_final: -0.0787 (ppp) REVERT: D 473 GLN cc_start: 0.8117 (tp40) cc_final: 0.7870 (tt0) outliers start: 20 outliers final: 13 residues processed: 276 average time/residue: 0.2757 time to fit residues: 125.7543 Evaluate side-chains 263 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 250 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 213 optimal weight: 0.0470 chunk 238 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 265 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21804 Z= 0.199 Angle : 0.532 7.994 29584 Z= 0.282 Chirality : 0.041 0.145 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.526 29.338 2864 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.34 % Favored : 92.51 % Rotamer: Outliers : 1.26 % Allowed : 9.16 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2616 helix: 0.63 (0.15), residues: 1280 sheet: -3.68 (0.37), residues: 164 loop : -2.70 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 217 HIS 0.003 0.001 HIS D 176 PHE 0.015 0.001 PHE D 93 TYR 0.011 0.001 TYR D 460 ARG 0.001 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 2.292 Fit side-chains REVERT: A 169 MET cc_start: 0.0547 (ppp) cc_final: -0.0748 (ppp) REVERT: A 601 ASP cc_start: 0.6527 (t0) cc_final: 0.6324 (t0) REVERT: B 169 MET cc_start: 0.0543 (ppp) cc_final: -0.0755 (ppp) REVERT: B 601 ASP cc_start: 0.6534 (t0) cc_final: 0.6321 (t0) REVERT: C 169 MET cc_start: 0.0545 (ppp) cc_final: -0.0749 (ppp) REVERT: D 169 MET cc_start: 0.0546 (ppp) cc_final: -0.0749 (ppp) REVERT: D 473 GLN cc_start: 0.8108 (tp40) cc_final: 0.7881 (tt0) REVERT: D 601 ASP cc_start: 0.6545 (t0) cc_final: 0.6343 (t0) outliers start: 30 outliers final: 18 residues processed: 272 average time/residue: 0.2689 time to fit residues: 121.2389 Evaluate side-chains 271 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 535 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 114 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 228 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21804 Z= 0.150 Angle : 0.494 7.057 29584 Z= 0.262 Chirality : 0.040 0.139 3404 Planarity : 0.003 0.037 3668 Dihedral : 4.381 28.629 2864 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.76 % Favored : 92.09 % Rotamer: Outliers : 1.39 % Allowed : 11.51 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2616 helix: 0.87 (0.15), residues: 1288 sheet: -2.69 (0.31), residues: 260 loop : -2.72 (0.15), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 388 HIS 0.003 0.001 HIS A 176 PHE 0.015 0.001 PHE C 93 TYR 0.007 0.001 TYR D 390 ARG 0.001 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 2.295 Fit side-chains REVERT: A 169 MET cc_start: 0.0571 (ppp) cc_final: -0.0652 (ppp) REVERT: A 601 ASP cc_start: 0.6587 (t0) cc_final: 0.6363 (t0) REVERT: B 169 MET cc_start: 0.0562 (ppp) cc_final: -0.0662 (ppp) REVERT: B 601 ASP cc_start: 0.6586 (t0) cc_final: 0.6361 (t0) REVERT: C 169 MET cc_start: 0.0562 (ppp) cc_final: -0.0657 (ppp) REVERT: D 169 MET cc_start: 0.0573 (ppp) cc_final: -0.0650 (ppp) REVERT: D 473 GLN cc_start: 0.8066 (tp40) cc_final: 0.7794 (tt0) REVERT: D 601 ASP cc_start: 0.6607 (t0) cc_final: 0.6382 (t0) outliers start: 33 outliers final: 20 residues processed: 276 average time/residue: 0.2734 time to fit residues: 124.5227 Evaluate side-chains 267 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 217 optimal weight: 0.0670 chunk 176 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21804 Z= 0.147 Angle : 0.491 7.871 29584 Z= 0.260 Chirality : 0.040 0.138 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.328 28.340 2864 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 1.97 % Allowed : 12.27 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2616 helix: 0.99 (0.15), residues: 1292 sheet: -3.63 (0.37), residues: 164 loop : -2.55 (0.15), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 388 HIS 0.002 0.001 HIS A 176 PHE 0.016 0.001 PHE D 93 TYR 0.007 0.001 TYR A 460 ARG 0.001 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 249 time to evaluate : 2.538 Fit side-chains REVERT: A 169 MET cc_start: 0.0605 (ppp) cc_final: 0.0016 (ppp) REVERT: A 339 ASP cc_start: 0.7337 (t0) cc_final: 0.7012 (t0) REVERT: A 601 ASP cc_start: 0.6611 (t0) cc_final: 0.6330 (t0) REVERT: B 169 MET cc_start: 0.0592 (ppp) cc_final: 0.0011 (ppp) REVERT: B 339 ASP cc_start: 0.7336 (t0) cc_final: 0.7012 (t0) REVERT: B 601 ASP cc_start: 0.6611 (t0) cc_final: 0.6335 (t0) REVERT: C 169 MET cc_start: 0.0596 (ppp) cc_final: 0.0013 (ppp) REVERT: C 339 ASP cc_start: 0.7332 (t0) cc_final: 0.7021 (t0) REVERT: D 169 MET cc_start: 0.0604 (ppp) cc_final: 0.0016 (ppp) REVERT: D 339 ASP cc_start: 0.7335 (t0) cc_final: 0.7017 (t0) REVERT: D 473 GLN cc_start: 0.8060 (tp40) cc_final: 0.7786 (tt0) REVERT: D 601 ASP cc_start: 0.6631 (t0) cc_final: 0.6351 (t0) outliers start: 47 outliers final: 35 residues processed: 275 average time/residue: 0.2723 time to fit residues: 124.5590 Evaluate side-chains 280 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 245 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 535 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.0470 chunk 229 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 255 optimal weight: 0.0470 chunk 212 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.0978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21804 Z= 0.224 Angle : 0.530 7.618 29584 Z= 0.283 Chirality : 0.041 0.153 3404 Planarity : 0.003 0.035 3668 Dihedral : 4.452 27.725 2864 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.30 % Favored : 92.55 % Rotamer: Outliers : 2.02 % Allowed : 12.52 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.16), residues: 2616 helix: 0.92 (0.15), residues: 1288 sheet: -3.63 (0.37), residues: 164 loop : -2.59 (0.15), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 219 HIS 0.003 0.001 HIS A 176 PHE 0.014 0.001 PHE A 93 TYR 0.011 0.001 TYR B 288 ARG 0.002 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 2.594 Fit side-chains REVERT: A 339 ASP cc_start: 0.7388 (t0) cc_final: 0.7047 (t0) REVERT: A 601 ASP cc_start: 0.6662 (t0) cc_final: 0.6350 (t0) REVERT: B 339 ASP cc_start: 0.7386 (t0) cc_final: 0.7046 (t0) REVERT: B 601 ASP cc_start: 0.6660 (t0) cc_final: 0.6352 (t0) REVERT: C 339 ASP cc_start: 0.7383 (t0) cc_final: 0.7042 (t0) REVERT: D 339 ASP cc_start: 0.7387 (t0) cc_final: 0.7052 (t0) REVERT: D 473 GLN cc_start: 0.8072 (tp40) cc_final: 0.7855 (tt0) REVERT: D 601 ASP cc_start: 0.6680 (t0) cc_final: 0.6368 (t0) outliers start: 48 outliers final: 20 residues processed: 271 average time/residue: 0.2715 time to fit residues: 121.8672 Evaluate side-chains 264 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 117 optimal weight: 0.0670 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21804 Z= 0.170 Angle : 0.506 7.885 29584 Z= 0.269 Chirality : 0.040 0.166 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.438 28.333 2864 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.65 % Favored : 92.20 % Rotamer: Outliers : 1.85 % Allowed : 13.24 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2616 helix: 1.05 (0.15), residues: 1280 sheet: -3.67 (0.37), residues: 164 loop : -2.62 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 388 HIS 0.004 0.001 HIS B 176 PHE 0.016 0.001 PHE A 93 TYR 0.010 0.001 TYR D 288 ARG 0.001 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 2.255 Fit side-chains REVERT: A 339 ASP cc_start: 0.7375 (t0) cc_final: 0.7026 (t0) REVERT: A 601 ASP cc_start: 0.6666 (t0) cc_final: 0.6309 (t0) REVERT: B 339 ASP cc_start: 0.7374 (t0) cc_final: 0.7029 (t0) REVERT: B 601 ASP cc_start: 0.6665 (t0) cc_final: 0.6310 (t0) REVERT: C 339 ASP cc_start: 0.7369 (t0) cc_final: 0.7027 (t0) REVERT: D 339 ASP cc_start: 0.7377 (t0) cc_final: 0.7032 (t0) REVERT: D 601 ASP cc_start: 0.6688 (t0) cc_final: 0.6327 (t0) outliers start: 44 outliers final: 36 residues processed: 267 average time/residue: 0.2704 time to fit residues: 120.2351 Evaluate side-chains 270 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 234 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 231 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 110 GLN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21804 Z= 0.163 Angle : 0.504 9.584 29584 Z= 0.266 Chirality : 0.040 0.141 3404 Planarity : 0.003 0.035 3668 Dihedral : 4.350 28.162 2864 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.91 % Favored : 91.93 % Rotamer: Outliers : 1.81 % Allowed : 14.29 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.16), residues: 2616 helix: 1.09 (0.15), residues: 1312 sheet: -3.69 (0.37), residues: 164 loop : -2.62 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 388 HIS 0.004 0.001 HIS A 176 PHE 0.016 0.001 PHE D 93 TYR 0.008 0.001 TYR D 653 ARG 0.001 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 242 time to evaluate : 2.304 Fit side-chains REVERT: A 339 ASP cc_start: 0.7404 (t0) cc_final: 0.7064 (t0) REVERT: A 601 ASP cc_start: 0.6715 (t0) cc_final: 0.6332 (t0) REVERT: B 339 ASP cc_start: 0.7399 (t0) cc_final: 0.7061 (t0) REVERT: B 601 ASP cc_start: 0.6708 (t0) cc_final: 0.6331 (t0) REVERT: C 339 ASP cc_start: 0.7393 (t0) cc_final: 0.7055 (t0) REVERT: D 339 ASP cc_start: 0.7401 (t0) cc_final: 0.7065 (t0) REVERT: D 601 ASP cc_start: 0.6733 (t0) cc_final: 0.6350 (t0) outliers start: 43 outliers final: 36 residues processed: 268 average time/residue: 0.2652 time to fit residues: 117.9225 Evaluate side-chains 269 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 237 optimal weight: 0.3980 chunk 142 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 186 optimal weight: 0.0030 chunk 72 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 224 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 0.0060 overall best weight: 0.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21804 Z= 0.117 Angle : 0.482 8.681 29584 Z= 0.253 Chirality : 0.038 0.133 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.248 28.396 2864 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.34 % Favored : 92.51 % Rotamer: Outliers : 1.18 % Allowed : 14.92 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2616 helix: 1.20 (0.15), residues: 1324 sheet: -3.58 (0.38), residues: 164 loop : -2.51 (0.15), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 388 HIS 0.004 0.001 HIS A 176 PHE 0.018 0.001 PHE D 93 TYR 0.017 0.001 TYR B 288 ARG 0.001 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 2.346 Fit side-chains REVERT: A 339 ASP cc_start: 0.7389 (t0) cc_final: 0.7047 (t0) REVERT: A 454 MET cc_start: 0.7301 (mmt) cc_final: 0.7062 (mmt) REVERT: A 601 ASP cc_start: 0.6691 (t0) cc_final: 0.6311 (t0) REVERT: B 339 ASP cc_start: 0.7388 (t0) cc_final: 0.7043 (t0) REVERT: B 454 MET cc_start: 0.7236 (mmt) cc_final: 0.7005 (mmt) REVERT: B 601 ASP cc_start: 0.6683 (t0) cc_final: 0.6308 (t0) REVERT: C 339 ASP cc_start: 0.7378 (t0) cc_final: 0.7039 (t0) REVERT: C 454 MET cc_start: 0.7074 (mmt) cc_final: 0.6857 (mmt) REVERT: D 339 ASP cc_start: 0.7387 (t0) cc_final: 0.7050 (t0) REVERT: D 454 MET cc_start: 0.7210 (mmt) cc_final: 0.6979 (mmt) REVERT: D 601 ASP cc_start: 0.6711 (t0) cc_final: 0.6329 (t0) outliers start: 28 outliers final: 28 residues processed: 256 average time/residue: 0.2760 time to fit residues: 115.8827 Evaluate side-chains 259 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.3980 chunk 153 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 263 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21804 Z= 0.159 Angle : 0.490 9.002 29584 Z= 0.259 Chirality : 0.040 0.166 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.265 28.380 2864 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.61 % Favored : 92.24 % Rotamer: Outliers : 1.09 % Allowed : 15.21 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2616 helix: 1.18 (0.15), residues: 1324 sheet: -3.62 (0.37), residues: 164 loop : -2.41 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 388 HIS 0.004 0.001 HIS D 176 PHE 0.017 0.001 PHE D 93 TYR 0.007 0.001 TYR D 653 ARG 0.001 0.000 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 2.392 Fit side-chains REVERT: A 169 MET cc_start: 0.0585 (ppp) cc_final: -0.0408 (ppp) REVERT: A 339 ASP cc_start: 0.7435 (t0) cc_final: 0.7086 (t0) REVERT: A 601 ASP cc_start: 0.6746 (t0) cc_final: 0.6354 (t0) REVERT: B 169 MET cc_start: 0.0585 (ppp) cc_final: -0.0408 (ppp) REVERT: B 339 ASP cc_start: 0.7437 (t0) cc_final: 0.7084 (t0) REVERT: B 601 ASP cc_start: 0.6740 (t0) cc_final: 0.6355 (t0) REVERT: C 169 MET cc_start: 0.0576 (ppp) cc_final: -0.0421 (ppp) REVERT: C 339 ASP cc_start: 0.7423 (t0) cc_final: 0.7074 (t0) REVERT: D 169 MET cc_start: 0.0590 (ppp) cc_final: -0.0403 (ppp) REVERT: D 339 ASP cc_start: 0.7436 (t0) cc_final: 0.7086 (t0) REVERT: D 601 ASP cc_start: 0.6767 (t0) cc_final: 0.6371 (t0) outliers start: 26 outliers final: 17 residues processed: 243 average time/residue: 0.2794 time to fit residues: 111.9109 Evaluate side-chains 237 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 220 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 193 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 184 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.185892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.172234 restraints weight = 23650.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150833 restraints weight = 43450.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.145061 restraints weight = 36982.734| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21804 Z= 0.151 Angle : 0.496 8.570 29584 Z= 0.260 Chirality : 0.039 0.139 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.257 28.678 2864 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.30 % Favored : 92.55 % Rotamer: Outliers : 1.30 % Allowed : 15.42 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2616 helix: 1.26 (0.15), residues: 1320 sheet: -3.70 (0.37), residues: 164 loop : -2.44 (0.15), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 388 HIS 0.004 0.001 HIS D 176 PHE 0.018 0.001 PHE D 93 TYR 0.008 0.001 TYR A 653 ARG 0.001 0.000 ARG A 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.62 seconds wall clock time: 67 minutes 3.55 seconds (4023.55 seconds total)