Starting phenix.real_space_refine on Sun Mar 17 09:47:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epa_31235/03_2024/7epa_31235.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epa_31235/03_2024/7epa_31235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epa_31235/03_2024/7epa_31235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epa_31235/03_2024/7epa_31235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epa_31235/03_2024/7epa_31235.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epa_31235/03_2024/7epa_31235.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.194 sd= 0.754 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6779 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6676 2.51 5 N 1956 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10635 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 5310 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 38, 'TRANS': 743} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 814 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 684 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 10, 'TYR:plan': 13, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 22, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 481 Chain: "B" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 5325 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PTRANS': 38, 'TRANS': 743} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 799 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 669 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 12, 'TYR:plan': 13, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 22, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 464 Time building chain proxies: 6.48, per 1000 atoms: 0.61 Number of scatterers: 10635 At special positions: 0 Unit cell: (118.9, 77.9, 188.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1941 8.00 N 1956 7.00 C 6676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 632 " - pdb=" SG CYS B 721 " distance=2.03 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: 4.39 Conformation dependent library (CDL) restraints added in 2.3 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 48.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 57 through 74 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.919A pdb=" N LEU A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.594A pdb=" N GLN A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.536A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.990A pdb=" N PHE A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.587A pdb=" N ALA A 305 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.538A pdb=" N ALA A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 311 " --> pdb=" O GLU A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.567A pdb=" N SER A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 4.523A pdb=" N GLU A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.940A pdb=" N ALA A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 400 Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.753A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 592 removed outlier: 4.139A pdb=" N GLY A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.549A pdb=" N ALA A 600 " --> pdb=" O PRO A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 623 Processing helix chain 'A' and resid 628 through 656 Processing helix chain 'A' and resid 677 through 700 removed outlier: 3.717A pdb=" N ALA A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 748 removed outlier: 3.778A pdb=" N GLY A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 783 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 788 through 820 Proline residue: A 812 - end of helix Processing helix chain 'B' and resid 57 through 74 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.865A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.552A pdb=" N GLN B 191 " --> pdb=" O PRO B 187 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.550A pdb=" N ARG B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 4.094A pdb=" N PHE B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.592A pdb=" N ALA B 305 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.555A pdb=" N ALA B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 311 " --> pdb=" O GLU B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.614A pdb=" N SER B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 removed outlier: 4.470A pdb=" N GLU B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 400 Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.515A pdb=" N MET B 410 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 407 through 411' Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.630A pdb=" N PHE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 592 removed outlier: 4.143A pdb=" N GLY B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.551A pdb=" N ALA B 600 " --> pdb=" O PRO B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 623 Processing helix chain 'B' and resid 628 through 656 Processing helix chain 'B' and resid 677 through 700 removed outlier: 3.758A pdb=" N ALA B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 747 removed outlier: 3.701A pdb=" N GLY B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 784 Proline residue: B 778 - end of helix Processing helix chain 'B' and resid 788 through 820 Proline residue: B 812 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.537A pdb=" N LEU A 32 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N HIS A 87 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N ILE A 140 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY A 35 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL A 139 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 241 removed outlier: 7.785A pdb=" N VAL A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER A 238 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR A 209 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS A 240 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA A 211 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA A 266 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 317 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 472 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 457 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYS A 470 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 459 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR A 468 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 473 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 479 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 428 through 429 removed outlier: 4.444A pdb=" N PHE A 428 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.601A pdb=" N LEU B 32 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS B 87 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU B 34 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 89 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 36 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 33 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY B 138 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ILE B 163 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL B 139 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.539A pdb=" N GLU B 239 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA B 266 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 317 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY B 472 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR B 457 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS B 470 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 459 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR B 468 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B 473 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 479 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 428 through 429 removed outlier: 4.506A pdb=" N PHE B 428 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 441 " --> pdb=" O PHE B 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 512 571 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3684 1.35 - 1.46: 2466 1.46 - 1.58: 4617 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10847 Sorted by residual: bond pdb=" C ARG A 411 " pdb=" N PRO A 412 " ideal model delta sigma weight residual 1.333 1.348 -0.015 1.01e-02 9.80e+03 2.13e+00 bond pdb=" C GLU A 502 " pdb=" N PRO A 503 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" C GLU B 502 " pdb=" N PRO B 503 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.31e+00 bond pdb=" C GLY A 116 " pdb=" O GLY A 116 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 7.32e-01 bond pdb=" CA ASP B 421 " pdb=" CB ASP B 421 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 6.03e-01 ... (remaining 10842 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 331 107.09 - 113.82: 5973 113.82 - 120.54: 4374 120.54 - 127.27: 4047 127.27 - 134.00: 114 Bond angle restraints: 14839 Sorted by residual: angle pdb=" C GLY B 130 " pdb=" N ASP B 131 " pdb=" CA ASP B 131 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.62e+00 angle pdb=" N GLN B 42 " pdb=" CA GLN B 42 " pdb=" C GLN B 42 " ideal model delta sigma weight residual 108.34 111.19 -2.85 1.31e+00 5.83e-01 4.72e+00 angle pdb=" N GLU B 502 " pdb=" CA GLU B 502 " pdb=" C GLU B 502 " ideal model delta sigma weight residual 109.81 114.19 -4.38 2.21e+00 2.05e-01 3.94e+00 angle pdb=" N GLU A 502 " pdb=" CA GLU A 502 " pdb=" C GLU A 502 " ideal model delta sigma weight residual 109.81 114.14 -4.33 2.21e+00 2.05e-01 3.84e+00 angle pdb=" C ALA A 230 " pdb=" N ARG A 231 " pdb=" CA ARG A 231 " ideal model delta sigma weight residual 122.76 119.74 3.02 1.63e+00 3.76e-01 3.42e+00 ... (remaining 14834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 5987 16.08 - 32.16: 367 32.16 - 48.24: 91 48.24 - 64.33: 13 64.33 - 80.41: 2 Dihedral angle restraints: 6460 sinusoidal: 1958 harmonic: 4502 Sorted by residual: dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual 93.00 14.04 78.96 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS A 632 " pdb=" SG CYS A 632 " pdb=" SG CYS A 721 " pdb=" CB CYS A 721 " ideal model delta sinusoidal sigma weight residual -86.00 -21.68 -64.32 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS B 234 " pdb=" SG CYS B 234 " pdb=" SG CYS B 518 " pdb=" CB CYS B 518 " ideal model delta sinusoidal sigma weight residual 93.00 29.55 63.45 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 964 0.024 - 0.049: 476 0.049 - 0.073: 172 0.073 - 0.098: 76 0.098 - 0.122: 42 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CA ILE B 317 " pdb=" N ILE B 317 " pdb=" C ILE B 317 " pdb=" CB ILE B 317 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE B 140 " pdb=" N ILE B 140 " pdb=" C ILE B 140 " pdb=" CB ILE B 140 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ILE B 315 " pdb=" N ILE B 315 " pdb=" C ILE B 315 " pdb=" CB ILE B 315 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 1727 not shown) Planarity restraints: 1976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 523 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO B 524 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 523 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 524 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 502 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 503 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " 0.018 5.00e-02 4.00e+02 ... (remaining 1973 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2872 2.80 - 3.32: 9937 3.32 - 3.85: 17382 3.85 - 4.37: 17184 4.37 - 4.90: 30790 Nonbonded interactions: 78165 Sorted by model distance: nonbonded pdb=" OG SER B 356 " pdb=" OE1 GLN B 359 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 294 " pdb=" OD1 ASP A 295 " model vdw 2.315 2.440 nonbonded pdb=" OG SER B 294 " pdb=" OD1 ASP B 295 " model vdw 2.338 2.440 nonbonded pdb=" NH1 ARG B 720 " pdb=" O ASP B 786 " model vdw 2.341 2.520 nonbonded pdb=" N GLY A 35 " pdb=" O GLY A 138 " model vdw 2.349 2.520 ... (remaining 78160 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 24 through 62 or (resid 63 through 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 88 or (resid 89 and (na \ me N or name CA or name C or name O or name CB )) or resid 90 through 109 or (re \ sid 110 through 112 and (name N or name CA or name C or name O or name CB )) or \ resid 113 through 254 or (resid 255 through 256 and (name N or name CA or name C \ or name O or name CB )) or resid 257 through 300 or (resid 301 and (name N or n \ ame CA or name C or name O or name CB )) or resid 302 through 317 or (resid 318 \ and (name N or name CA or name C or name O or name CB )) or resid 319 through 34 \ 5 or (resid 346 through 347 and (name N or name CA or name C or name O or name C \ B )) or resid 348 through 532 or (resid 533 and (name N or name CA or name C or \ name O or name CB )) or resid 534 through 538 or (resid 539 and (name N or name \ CA or name C or name O or name CB )) or resid 540 through 604 or (resid 605 and \ (name N or name CA or name C or name O or name CB )) or resid 606 through 644 or \ (resid 645 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 6 through 685 or (resid 686 through 688 and (name N or name CA or name C or name \ O or name CB )) or resid 689 through 820)) selection = (chain 'B' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 93 or (resid 94 and ( \ name N or name CA or name C or name O or name CB )) or resid 95 through 196 or ( \ resid 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 199 or (resid 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 272 or (resid 273 and (name N or name CA or name C or na \ me O or name CB )) or resid 274 through 285 or (resid 286 through 287 and (name \ N or name CA or name C or name O or name CB )) or resid 288 through 432 or (resi \ d 433 and (name N or name CA or name C or name O or name CB )) or resid 434 thro \ ugh 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) o \ r resid 471 through 505 or (resid 506 through 507 and (name N or name CA or name \ C or name O or name CB )) or resid 508 through 525 or (resid 526 and (name N or \ name CA or name C or name O or name CB )) or resid 527 through 607 or (resid 60 \ 8 through 610 and (name N or name CA or name C or name O or name CB )) or resid \ 611 through 719 or (resid 720 and (name N or name CA or name C or name O or name \ CB )) or resid 721 through 820)) } 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 11.170 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.040 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 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 0.036 10847 Z= 0.128 Angle : 0.482 6.408 14839 Z= 0.273 Chirality : 0.038 0.122 1730 Planarity : 0.003 0.041 1976 Dihedral : 11.031 80.407 3495 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -1.51 (0.19), residues: 1556 helix: 0.45 (0.18), residues: 718 sheet: -0.80 (0.40), residues: 166 loop : -2.76 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 487 HIS 0.002 0.000 HIS B 41 PHE 0.008 0.000 PHE B 189 TYR 0.005 0.001 TYR B 386 ARG 0.001 0.000 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8369 (mm-30) REVERT: A 70 ASP cc_start: 0.7933 (t0) cc_final: 0.7656 (t0) REVERT: A 137 THR cc_start: 0.9223 (m) cc_final: 0.9016 (p) REVERT: A 159 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7298 (mm-40) REVERT: A 180 TYR cc_start: 0.7840 (m-10) cc_final: 0.6820 (m-10) REVERT: B 70 ASP cc_start: 0.8290 (t0) cc_final: 0.8082 (t0) REVERT: B 162 GLN cc_start: 0.7825 (tt0) cc_final: 0.7623 (tm-30) REVERT: B 269 PHE cc_start: 0.8476 (m-80) cc_final: 0.7720 (m-80) REVERT: B 399 LEU cc_start: 0.8935 (tp) cc_final: 0.8659 (tp) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2451 time to fit residues: 82.1387 Evaluate side-chains 189 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0170 chunk 118 optimal weight: 0.0970 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10847 Z= 0.197 Angle : 0.545 8.847 14839 Z= 0.272 Chirality : 0.039 0.131 1730 Planarity : 0.004 0.047 1976 Dihedral : 3.371 22.658 1677 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.33 % Allowed : 17.13 % Favored : 80.54 % 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: 0.01 (0.22), residues: 1556 helix: 1.87 (0.19), residues: 724 sheet: -0.26 (0.45), residues: 144 loop : -2.11 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 349 HIS 0.002 0.001 HIS A 87 PHE 0.014 0.001 PHE A 158 TYR 0.015 0.001 TYR A 180 ARG 0.008 0.001 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 1.182 Fit side-chains REVERT: A 63 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8403 (mm-30) REVERT: A 70 ASP cc_start: 0.7960 (t0) cc_final: 0.7617 (t0) REVERT: A 159 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7927 (mm110) REVERT: A 162 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8498 (tm-30) REVERT: A 165 TYR cc_start: 0.8419 (p90) cc_final: 0.8068 (p90) REVERT: A 173 SER cc_start: 0.8804 (m) cc_final: 0.8434 (p) REVERT: A 334 LEU cc_start: 0.9129 (mt) cc_final: 0.8885 (mt) REVERT: B 70 ASP cc_start: 0.8114 (t0) cc_final: 0.7825 (t0) REVERT: B 165 TYR cc_start: 0.8187 (p90) cc_final: 0.7772 (p90) REVERT: B 399 LEU cc_start: 0.8975 (tp) cc_final: 0.8669 (tp) outliers start: 20 outliers final: 10 residues processed: 213 average time/residue: 0.2333 time to fit residues: 68.9093 Evaluate side-chains 192 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 526 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10847 Z= 0.433 Angle : 0.729 6.396 14839 Z= 0.387 Chirality : 0.044 0.232 1730 Planarity : 0.006 0.049 1976 Dihedral : 4.996 24.011 1677 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.90 % Allowed : 22.49 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1556 helix: 1.56 (0.19), residues: 706 sheet: -0.96 (0.41), residues: 144 loop : -2.06 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 291 HIS 0.006 0.002 HIS A 77 PHE 0.028 0.002 PHE A 158 TYR 0.029 0.002 TYR B 386 ARG 0.008 0.001 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 1.316 Fit side-chains REVERT: A 63 GLU cc_start: 0.9040 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 66 LEU cc_start: 0.8726 (mm) cc_final: 0.8526 (mm) REVERT: A 70 ASP cc_start: 0.8312 (t0) cc_final: 0.7970 (t0) REVERT: A 162 GLN cc_start: 0.8788 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 173 SER cc_start: 0.9053 (m) cc_final: 0.8669 (p) REVERT: A 195 MET cc_start: 0.8390 (mmm) cc_final: 0.8133 (mmm) REVERT: A 339 ASN cc_start: 0.9100 (t0) cc_final: 0.8897 (t0) REVERT: A 396 HIS cc_start: 0.8553 (t70) cc_final: 0.8327 (t-90) REVERT: A 421 ASP cc_start: 0.7785 (m-30) cc_final: 0.7560 (m-30) REVERT: A 483 SER cc_start: 0.8924 (m) cc_final: 0.8645 (p) REVERT: B 70 ASP cc_start: 0.8400 (t0) cc_final: 0.8181 (t0) REVERT: B 206 TYR cc_start: 0.7239 (t80) cc_final: 0.7033 (t80) REVERT: B 339 ASN cc_start: 0.8990 (t0) cc_final: 0.8779 (t0) REVERT: B 351 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8675 (tp-100) outliers start: 42 outliers final: 24 residues processed: 197 average time/residue: 0.2464 time to fit residues: 67.3208 Evaluate side-chains 176 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10847 Z= 0.194 Angle : 0.576 7.809 14839 Z= 0.285 Chirality : 0.040 0.146 1730 Planarity : 0.004 0.048 1976 Dihedral : 4.077 24.849 1677 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.38 % Allowed : 26.57 % Favored : 70.05 % 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: 0.22 (0.22), residues: 1556 helix: 2.20 (0.19), residues: 712 sheet: -0.77 (0.41), residues: 154 loop : -1.98 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 291 HIS 0.003 0.001 HIS A 390 PHE 0.015 0.001 PHE B 432 TYR 0.019 0.001 TYR A 180 ARG 0.010 0.001 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.325 Fit side-chains REVERT: A 70 ASP cc_start: 0.8161 (t0) cc_final: 0.7737 (t0) REVERT: A 162 GLN cc_start: 0.8787 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 173 SER cc_start: 0.8920 (m) cc_final: 0.8560 (p) REVERT: A 339 ASN cc_start: 0.9040 (t0) cc_final: 0.8811 (t0) REVERT: A 396 HIS cc_start: 0.8468 (t70) cc_final: 0.8219 (t-90) REVERT: A 421 ASP cc_start: 0.7639 (m-30) cc_final: 0.7399 (m-30) REVERT: A 483 SER cc_start: 0.8619 (m) cc_final: 0.8403 (p) REVERT: A 499 ARG cc_start: 0.7341 (mmm160) cc_final: 0.7111 (mmm160) REVERT: A 766 MET cc_start: 0.5471 (ppp) cc_final: 0.5139 (ppp) REVERT: B 70 ASP cc_start: 0.8197 (t0) cc_final: 0.7928 (t0) REVERT: B 94 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8217 (mmtm) REVERT: B 197 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 351 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8574 (tp-100) REVERT: B 406 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8179 (pt) REVERT: B 639 LEU cc_start: 0.8238 (tt) cc_final: 0.8027 (pp) outliers start: 29 outliers final: 16 residues processed: 191 average time/residue: 0.2321 time to fit residues: 62.2338 Evaluate side-chains 178 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0770 chunk 85 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 38 optimal weight: 0.0060 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10847 Z= 0.156 Angle : 0.547 7.848 14839 Z= 0.267 Chirality : 0.040 0.134 1730 Planarity : 0.004 0.033 1976 Dihedral : 3.654 25.985 1677 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.61 % Allowed : 28.79 % Favored : 67.60 % 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: 0.54 (0.22), residues: 1556 helix: 2.49 (0.20), residues: 712 sheet: -0.41 (0.44), residues: 146 loop : -1.89 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 291 HIS 0.004 0.001 HIS A 393 PHE 0.016 0.001 PHE B 269 TYR 0.016 0.001 TYR B 386 ARG 0.007 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8892 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 70 ASP cc_start: 0.8051 (t0) cc_final: 0.7649 (t0) REVERT: A 99 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 162 GLN cc_start: 0.8709 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 173 SER cc_start: 0.8804 (m) cc_final: 0.8422 (p) REVERT: A 195 MET cc_start: 0.8302 (mmm) cc_final: 0.8050 (mmm) REVERT: A 245 MET cc_start: 0.7399 (ptp) cc_final: 0.7014 (ptp) REVERT: A 396 HIS cc_start: 0.8410 (t70) cc_final: 0.7988 (t70) REVERT: A 421 ASP cc_start: 0.7598 (m-30) cc_final: 0.7329 (m-30) REVERT: B 70 ASP cc_start: 0.8091 (t0) cc_final: 0.7805 (t0) REVERT: B 94 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8100 (mmtm) REVERT: B 154 LEU cc_start: 0.9109 (tp) cc_final: 0.8857 (tt) REVERT: B 351 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8385 (tp-100) REVERT: B 499 ARG cc_start: 0.7269 (mmm160) cc_final: 0.6998 (mmm160) outliers start: 31 outliers final: 14 residues processed: 200 average time/residue: 0.2187 time to fit residues: 61.5790 Evaluate side-chains 186 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 37 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10847 Z= 0.217 Angle : 0.586 7.751 14839 Z= 0.287 Chirality : 0.040 0.143 1730 Planarity : 0.004 0.042 1976 Dihedral : 3.812 25.741 1677 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.96 % Allowed : 28.67 % Favored : 67.37 % 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: 0.59 (0.22), residues: 1556 helix: 2.55 (0.20), residues: 712 sheet: -1.01 (0.48), residues: 126 loop : -1.71 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 291 HIS 0.002 0.001 HIS B 390 PHE 0.014 0.001 PHE B 158 TYR 0.014 0.001 TYR B 386 ARG 0.009 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8059 (mm-30) REVERT: A 70 ASP cc_start: 0.8116 (t0) cc_final: 0.7695 (t0) REVERT: A 162 GLN cc_start: 0.8778 (tm-30) cc_final: 0.7414 (tm-30) REVERT: A 173 SER cc_start: 0.8856 (m) cc_final: 0.8503 (p) REVERT: A 245 MET cc_start: 0.7846 (ptp) cc_final: 0.7630 (ptp) REVERT: A 396 HIS cc_start: 0.8490 (t70) cc_final: 0.8057 (t70) REVERT: A 421 ASP cc_start: 0.7557 (m-30) cc_final: 0.7275 (m-30) REVERT: A 616 CYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8978 (p) REVERT: A 766 MET cc_start: 0.5378 (ppp) cc_final: 0.5075 (ppp) REVERT: B 70 ASP cc_start: 0.8185 (t0) cc_final: 0.7901 (t0) REVERT: B 154 LEU cc_start: 0.9103 (tp) cc_final: 0.8884 (tt) REVERT: B 351 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8448 (tp-100) REVERT: B 499 ARG cc_start: 0.7327 (mmm160) cc_final: 0.7107 (mmm160) outliers start: 34 outliers final: 22 residues processed: 186 average time/residue: 0.2180 time to fit residues: 57.4297 Evaluate side-chains 182 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10847 Z= 0.252 Angle : 0.627 9.761 14839 Z= 0.309 Chirality : 0.041 0.156 1730 Planarity : 0.004 0.049 1976 Dihedral : 4.105 22.351 1677 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.90 % Allowed : 29.02 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1556 helix: 2.52 (0.20), residues: 706 sheet: -1.14 (0.47), residues: 126 loop : -1.69 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 291 HIS 0.003 0.001 HIS A 390 PHE 0.019 0.002 PHE B 158 TYR 0.014 0.001 TYR B 386 ARG 0.013 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.146 Fit side-chains REVERT: A 63 GLU cc_start: 0.8922 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 70 ASP cc_start: 0.8166 (t0) cc_final: 0.7735 (t0) REVERT: A 140 ILE cc_start: 0.8886 (mp) cc_final: 0.8419 (pt) REVERT: A 173 SER cc_start: 0.8906 (m) cc_final: 0.8666 (p) REVERT: A 318 GLU cc_start: 0.8144 (tp30) cc_final: 0.7612 (tm-30) REVERT: A 396 HIS cc_start: 0.8483 (t70) cc_final: 0.8226 (t-90) REVERT: A 421 ASP cc_start: 0.7597 (m-30) cc_final: 0.7318 (m-30) REVERT: A 616 CYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8939 (p) REVERT: B 70 ASP cc_start: 0.8205 (t0) cc_final: 0.7914 (t0) REVERT: B 154 LEU cc_start: 0.9088 (tp) cc_final: 0.8832 (tt) REVERT: B 351 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8516 (tp-100) REVERT: B 406 LEU cc_start: 0.8325 (tt) cc_final: 0.8050 (tt) outliers start: 42 outliers final: 30 residues processed: 187 average time/residue: 0.2426 time to fit residues: 64.3323 Evaluate side-chains 182 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 646 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10847 Z= 0.335 Angle : 0.690 9.881 14839 Z= 0.348 Chirality : 0.043 0.182 1730 Planarity : 0.005 0.061 1976 Dihedral : 4.589 22.027 1677 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.01 % Allowed : 29.25 % Favored : 65.73 % 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: 0.18 (0.22), residues: 1556 helix: 2.18 (0.19), residues: 708 sheet: -1.15 (0.40), residues: 154 loop : -1.88 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 291 HIS 0.006 0.001 HIS A 390 PHE 0.023 0.002 PHE B 158 TYR 0.014 0.002 TYR B 386 ARG 0.011 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 157 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8042 (mm-30) REVERT: A 70 ASP cc_start: 0.8233 (t0) cc_final: 0.7811 (t0) REVERT: A 173 SER cc_start: 0.9092 (m) cc_final: 0.8801 (p) REVERT: A 396 HIS cc_start: 0.8535 (t70) cc_final: 0.8295 (t-90) REVERT: A 421 ASP cc_start: 0.7696 (m-30) cc_final: 0.7430 (m-30) REVERT: A 499 ARG cc_start: 0.7446 (mmm160) cc_final: 0.7153 (mmm160) REVERT: A 766 MET cc_start: 0.5819 (ppp) cc_final: 0.5558 (ppp) REVERT: B 70 ASP cc_start: 0.8328 (t0) cc_final: 0.8046 (t0) REVERT: B 93 SER cc_start: 0.9132 (t) cc_final: 0.8727 (p) REVERT: B 154 LEU cc_start: 0.9092 (tp) cc_final: 0.8782 (tt) REVERT: B 351 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8669 (tp-100) REVERT: B 406 LEU cc_start: 0.8446 (tt) cc_final: 0.8094 (tt) REVERT: B 766 MET cc_start: 0.4440 (ppp) cc_final: 0.4164 (ppp) outliers start: 43 outliers final: 36 residues processed: 183 average time/residue: 0.2249 time to fit residues: 57.4563 Evaluate side-chains 191 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 646 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10847 Z= 0.241 Angle : 0.654 9.064 14839 Z= 0.319 Chirality : 0.042 0.187 1730 Planarity : 0.004 0.055 1976 Dihedral : 4.315 22.021 1677 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.55 % Allowed : 29.14 % Favored : 66.32 % 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: 0.32 (0.22), residues: 1556 helix: 2.26 (0.19), residues: 708 sheet: -1.02 (0.41), residues: 150 loop : -1.78 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 291 HIS 0.006 0.001 HIS A 390 PHE 0.018 0.001 PHE B 158 TYR 0.025 0.001 TYR A 180 ARG 0.014 0.001 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 70 ASP cc_start: 0.8149 (t0) cc_final: 0.7727 (t0) REVERT: A 140 ILE cc_start: 0.8859 (mp) cc_final: 0.8410 (pt) REVERT: A 173 SER cc_start: 0.9068 (m) cc_final: 0.8827 (p) REVERT: A 175 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8826 (mmmt) REVERT: A 396 HIS cc_start: 0.8478 (t70) cc_final: 0.8254 (t-90) REVERT: A 421 ASP cc_start: 0.7648 (m-30) cc_final: 0.7370 (m-30) REVERT: A 499 ARG cc_start: 0.7389 (mmm160) cc_final: 0.7102 (mmm160) REVERT: A 766 MET cc_start: 0.5713 (ppp) cc_final: 0.5439 (ppp) REVERT: B 70 ASP cc_start: 0.8247 (t0) cc_final: 0.7961 (t0) REVERT: B 93 SER cc_start: 0.9060 (t) cc_final: 0.8671 (p) REVERT: B 154 LEU cc_start: 0.9069 (tp) cc_final: 0.8755 (tt) REVERT: B 351 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8595 (tp-100) REVERT: B 406 LEU cc_start: 0.8394 (tt) cc_final: 0.8025 (tt) REVERT: B 499 ARG cc_start: 0.7196 (mmm160) cc_final: 0.6842 (mmm160) outliers start: 39 outliers final: 32 residues processed: 176 average time/residue: 0.2320 time to fit residues: 57.3015 Evaluate side-chains 181 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 544 TYR Chi-restraints excluded: chain B residue 646 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10847 Z= 0.286 Angle : 0.676 9.372 14839 Z= 0.334 Chirality : 0.042 0.201 1730 Planarity : 0.005 0.070 1976 Dihedral : 4.431 21.740 1677 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.90 % Allowed : 29.37 % Favored : 65.73 % 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: 0.21 (0.22), residues: 1556 helix: 2.16 (0.19), residues: 708 sheet: -1.06 (0.41), residues: 150 loop : -1.84 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 291 HIS 0.006 0.001 HIS A 390 PHE 0.019 0.002 PHE B 158 TYR 0.022 0.001 TYR A 180 ARG 0.013 0.001 ARG A 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8182 (t0) cc_final: 0.7758 (t0) REVERT: A 140 ILE cc_start: 0.8892 (mp) cc_final: 0.8479 (pt) REVERT: A 173 SER cc_start: 0.9090 (m) cc_final: 0.8872 (p) REVERT: A 175 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8872 (mmmt) REVERT: A 396 HIS cc_start: 0.8498 (t70) cc_final: 0.8269 (t-90) REVERT: A 421 ASP cc_start: 0.7673 (m-30) cc_final: 0.7401 (m-30) REVERT: A 499 ARG cc_start: 0.7367 (mmm160) cc_final: 0.7136 (mmm160) REVERT: A 766 MET cc_start: 0.5735 (ppp) cc_final: 0.5467 (ppp) REVERT: B 70 ASP cc_start: 0.8271 (t0) cc_final: 0.7980 (t0) REVERT: B 93 SER cc_start: 0.9089 (t) cc_final: 0.8685 (p) REVERT: B 154 LEU cc_start: 0.9061 (tp) cc_final: 0.8748 (tt) REVERT: B 162 GLN cc_start: 0.8626 (tt0) cc_final: 0.8409 (tt0) REVERT: B 351 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8639 (tp-100) REVERT: B 406 LEU cc_start: 0.8441 (tt) cc_final: 0.8073 (tt) REVERT: B 433 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7663 (ttt90) REVERT: B 499 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6925 (mmm160) outliers start: 42 outliers final: 38 residues processed: 181 average time/residue: 0.2305 time to fit residues: 58.8138 Evaluate side-chains 190 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 544 TYR Chi-restraints excluded: chain B residue 646 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.115021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094966 restraints weight = 30309.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098054 restraints weight = 15031.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100030 restraints weight = 8657.688| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10847 Z= 0.203 Angle : 0.648 10.591 14839 Z= 0.310 Chirality : 0.041 0.176 1730 Planarity : 0.004 0.052 1976 Dihedral : 4.149 22.886 1677 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.55 % Allowed : 29.60 % Favored : 65.85 % 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: 0.40 (0.22), residues: 1556 helix: 2.33 (0.19), residues: 708 sheet: -1.18 (0.47), residues: 120 loop : -1.68 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 291 HIS 0.005 0.001 HIS A 390 PHE 0.015 0.001 PHE B 158 TYR 0.019 0.001 TYR A 180 ARG 0.013 0.001 ARG A 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.45 seconds wall clock time: 41 minutes 10.18 seconds (2470.18 seconds total)