Starting phenix.real_space_refine on Fri Feb 16 10:04:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/02_2024/7jsk_22457_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/02_2024/7jsk_22457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/02_2024/7jsk_22457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/02_2024/7jsk_22457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/02_2024/7jsk_22457_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsk_22457/02_2024/7jsk_22457_neut_trim_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 16 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: 6 Type Number sf(0) Gaussians S 64 5.16 5 Na 4 4.78 5 C 4920 2.51 5 N 1152 2.21 5 O 1232 1.98 5 H 7664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7489 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "B" Number of atoms: 7489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7489 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' NA': 2, 'CIT': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' NA': 2, 'CIT': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.10, per 1000 atoms: 0.47 Number of scatterers: 15036 At special positions: 0 Unit cell: (76.504, 103.752, 84.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 Na 4 11.00 O 1232 8.00 N 1152 7.00 C 4920 6.00 H 7664 1.00 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 562 " " NAG B 601 " - " ASN B 562 " Time building additional restraints: 12.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 0 sheets defined 72.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Proline residue: A 21 - end of helix removed outlier: 4.395A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.760A pdb=" N MET A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 76 through 82 removed outlier: 4.375A pdb=" N GLN A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 142 through 157 Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.924A pdb=" N CYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 250 through 275 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.740A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.520A pdb=" N PHE A 331 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 332 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A 333 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 4.070A pdb=" N PHE A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 408 through 427 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 442 removed outlier: 3.774A pdb=" N ALA A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 445 through 461 removed outlier: 4.145A pdb=" N GLU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Proline residue: A 474 - end of helix Processing helix chain 'A' and resid 487 through 498 removed outlier: 4.789A pdb=" N LEU A 492 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.934A pdb=" N TYR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 removed outlier: 4.302A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'B' and resid 16 through 28 Proline residue: B 21 - end of helix removed outlier: 4.395A pdb=" N LEU B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Proline residue: B 26 - end of helix Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.762A pdb=" N MET B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 76 through 82 removed outlier: 4.376A pdb=" N GLN B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 Processing helix chain 'B' and resid 106 through 117 Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 142 through 157 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.924A pdb=" N CYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 250 through 275 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.740A pdb=" N GLU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 334 removed outlier: 3.520A pdb=" N PHE B 331 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 332 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B 333 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 4.070A pdb=" N PHE B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 439 through 442 removed outlier: 3.775A pdb=" N ALA B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 445 through 461 removed outlier: 4.144A pdb=" N GLU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Proline residue: B 474 - end of helix Processing helix chain 'B' and resid 487 through 498 removed outlier: 4.788A pdb=" N LEU B 492 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.934A pdb=" N TYR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 removed outlier: 4.301A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 400 hydrogen bonds defined for protein. 1080 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: 4.88 Time building geometry restraints manager: 12.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7644 1.03 - 1.22: 24 1.22 - 1.42: 3006 1.42 - 1.61: 4440 1.61 - 1.81: 108 Bond restraints: 15222 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " ideal model delta sigma weight residual 1.532 1.593 -0.061 2.00e-02 2.50e+03 9.20e+00 bond pdb=" C1 NAG A 601 " pdb=" C2 NAG A 601 " ideal model delta sigma weight residual 1.532 1.593 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.391 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C7 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.346 1.390 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" CA ALA A 119 " pdb=" CB ALA A 119 " ideal model delta sigma weight residual 1.525 1.495 0.030 1.47e-02 4.63e+03 4.04e+00 ... (remaining 15217 not shown) Histogram of bond angle deviations from ideal: 71.28 - 84.75: 142 84.75 - 98.22: 13 98.22 - 111.69: 17684 111.69 - 125.16: 9426 125.16 - 138.62: 447 Bond angle restraints: 27712 Sorted by residual: angle pdb=" N VAL B 263 " pdb=" CA VAL B 263 " pdb=" HA VAL B 263 " ideal model delta sigma weight residual 110.00 71.28 38.72 3.00e+00 1.11e-01 1.67e+02 angle pdb=" N VAL A 263 " pdb=" CA VAL A 263 " pdb=" HA VAL A 263 " ideal model delta sigma weight residual 110.00 71.43 38.57 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C PHE A 14 " pdb=" CA PHE A 14 " pdb=" HA PHE A 14 " ideal model delta sigma weight residual 109.00 72.35 36.65 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C PHE B 14 " pdb=" CA PHE B 14 " pdb=" HA PHE B 14 " ideal model delta sigma weight residual 109.00 72.50 36.50 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N SER A 13 " pdb=" CA SER A 13 " pdb=" HA SER A 13 " ideal model delta sigma weight residual 110.00 73.55 36.45 3.00e+00 1.11e-01 1.48e+02 ... (remaining 27707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 6091 15.47 - 30.94: 759 30.94 - 46.42: 186 46.42 - 61.89: 136 61.89 - 77.36: 4 Dihedral angle restraints: 7176 sinusoidal: 3872 harmonic: 3304 Sorted by residual: dihedral pdb=" CA THR A 225 " pdb=" C THR A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA THR B 225 " pdb=" C THR B 225 " pdb=" N GLY B 226 " pdb=" CA GLY B 226 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA TYR A 353 " pdb=" C TYR A 353 " pdb=" N VAL A 354 " pdb=" CA VAL A 354 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 7173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 1216 0.341 - 0.683: 8 0.683 - 1.024: 6 1.024 - 1.365: 2 1.365 - 1.707: 16 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CG LEU A 440 " pdb=" CB LEU A 440 " pdb=" CD1 LEU A 440 " pdb=" CD2 LEU A 440 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" CG LEU B 440 " pdb=" CB LEU B 440 " pdb=" CD1 LEU B 440 " pdb=" CD2 LEU B 440 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.24e+01 chirality pdb=" CG LEU A 111 " pdb=" CB LEU A 111 " pdb=" CD1 LEU A 111 " pdb=" CD2 LEU A 111 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 ... (remaining 1245 not shown) Planarity restraints: 2102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 310 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 311 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 311 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 310 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 311 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 406 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO B 407 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " 0.029 5.00e-02 4.00e+02 ... (remaining 2099 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 286 2.07 - 2.70: 25312 2.70 - 3.34: 45290 3.34 - 3.97: 55264 3.97 - 4.60: 89976 Nonbonded interactions: 216128 Sorted by model distance: nonbonded pdb=" OD1 ASN A 141 " pdb="NA NA A 603 " model vdw 1.439 2.350 nonbonded pdb=" OD1 ASN B 141 " pdb="NA NA B 603 " model vdw 1.442 2.350 nonbonded pdb=" O MET B 31 " pdb=" H ALA B 33 " model vdw 1.611 1.850 nonbonded pdb=" O LYS A 120 " pdb=" H LEU A 124 " model vdw 1.615 1.850 nonbonded pdb=" O MET A 31 " pdb=" H ALA A 33 " model vdw 1.618 1.850 ... (remaining 216123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.300 Extract box with map and model: 4.270 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 50.220 Find NCS groups from input model: 0.530 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.063 7558 Z= 0.724 Angle : 1.157 16.678 10308 Z= 0.576 Chirality : 0.205 1.707 1248 Planarity : 0.006 0.055 1236 Dihedral : 14.761 77.359 2700 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % Rotamer: Outliers : 4.74 % Allowed : 10.10 % Favored : 85.16 % 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: -0.67 (0.29), residues: 916 helix: 0.45 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.89 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 49 HIS 0.006 0.002 HIS A 106 PHE 0.023 0.002 PHE A 35 TYR 0.009 0.002 TYR B 306 ARG 0.004 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7726 (mtt) cc_final: 0.7485 (mtp) REVERT: A 157 GLN cc_start: 0.5902 (OUTLIER) cc_final: 0.5681 (tp40) REVERT: A 236 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: A 271 TRP cc_start: 0.7994 (t-100) cc_final: 0.7604 (t-100) REVERT: A 277 MET cc_start: 0.5352 (mmm) cc_final: 0.5120 (tpt) REVERT: A 300 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6709 (ttmt) REVERT: B 208 MET cc_start: 0.6329 (mtm) cc_final: 0.6045 (mpp) outliers start: 38 outliers final: 13 residues processed: 208 average time/residue: 0.4430 time to fit residues: 122.4680 Evaluate side-chains 141 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 562 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7558 Z= 0.210 Angle : 0.942 15.879 10308 Z= 0.445 Chirality : 0.212 1.762 1248 Planarity : 0.006 0.051 1236 Dihedral : 8.212 69.297 1057 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.31 % Favored : 92.47 % Rotamer: Outliers : 4.49 % Allowed : 12.97 % Favored : 82.54 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.25 (0.30), residues: 916 helix: 0.86 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -3.00 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 49 HIS 0.003 0.001 HIS B 106 PHE 0.010 0.001 PHE A 35 TYR 0.020 0.002 TYR B 353 ARG 0.003 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.6851 (p90) cc_final: 0.6647 (p90) REVERT: A 153 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6738 (mt-10) REVERT: A 157 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.5881 (tp40) REVERT: A 236 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: A 248 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 264 MET cc_start: 0.7820 (mtp) cc_final: 0.7577 (mtp) REVERT: A 300 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6784 (ttmt) REVERT: A 525 MET cc_start: 0.5746 (ttm) cc_final: 0.5468 (ttm) REVERT: B 354 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7862 (t) outliers start: 36 outliers final: 21 residues processed: 176 average time/residue: 0.3511 time to fit residues: 88.8250 Evaluate side-chains 156 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 562 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7741 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7558 Z= 0.259 Angle : 0.943 15.753 10308 Z= 0.444 Chirality : 0.209 1.759 1248 Planarity : 0.006 0.049 1236 Dihedral : 7.484 63.323 1055 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.52 % Favored : 91.27 % Rotamer: Outliers : 2.99 % Allowed : 16.33 % Favored : 80.67 % Cbeta Deviations : 0.22 % 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: -0.17 (0.30), residues: 916 helix: 0.97 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -2.86 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 49 HIS 0.005 0.002 HIS B 106 PHE 0.013 0.001 PHE B 35 TYR 0.011 0.001 TYR B 353 ARG 0.003 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.6034 (tp40) REVERT: A 525 MET cc_start: 0.6052 (ttm) cc_final: 0.5762 (ttm) REVERT: B 354 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.8011 (t) outliers start: 24 outliers final: 17 residues processed: 150 average time/residue: 0.3486 time to fit residues: 75.0892 Evaluate side-chains 144 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7790 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7558 Z= 0.268 Angle : 0.937 15.716 10308 Z= 0.443 Chirality : 0.211 1.796 1248 Planarity : 0.005 0.044 1236 Dihedral : 7.177 58.148 1045 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.41 % Favored : 91.38 % Rotamer: Outliers : 3.62 % Allowed : 16.96 % Favored : 79.43 % Cbeta Deviations : 0.22 % 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: -0.26 (0.30), residues: 916 helix: 0.92 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -3.10 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 49 HIS 0.005 0.002 HIS A 106 PHE 0.012 0.001 PHE B 35 TYR 0.009 0.002 TYR B 353 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6068 (tp40) REVERT: A 525 MET cc_start: 0.6196 (ttm) cc_final: 0.5871 (ttm) outliers start: 29 outliers final: 21 residues processed: 157 average time/residue: 0.3693 time to fit residues: 81.6456 Evaluate side-chains 136 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7558 Z= 0.246 Angle : 0.932 15.653 10308 Z= 0.438 Chirality : 0.211 1.778 1248 Planarity : 0.005 0.046 1236 Dihedral : 6.997 57.241 1044 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.95 % Favored : 90.83 % Rotamer: Outliers : 3.12 % Allowed : 18.83 % Favored : 78.05 % Cbeta Deviations : 0.22 % 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: -0.13 (0.30), residues: 916 helix: 1.03 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -3.10 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 49 HIS 0.004 0.001 HIS B 106 PHE 0.017 0.001 PHE A 274 TYR 0.008 0.001 TYR B 353 ARG 0.005 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6100 (tp40) REVERT: A 525 MET cc_start: 0.6200 (ttm) cc_final: 0.5865 (ttm) outliers start: 25 outliers final: 21 residues processed: 148 average time/residue: 0.3883 time to fit residues: 80.7689 Evaluate side-chains 141 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7558 Z= 0.282 Angle : 0.943 15.728 10308 Z= 0.446 Chirality : 0.211 1.802 1248 Planarity : 0.005 0.051 1236 Dihedral : 7.018 58.057 1044 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.06 % Favored : 90.72 % Rotamer: Outliers : 3.49 % Allowed : 18.95 % Favored : 77.56 % Cbeta Deviations : 0.22 % 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: -0.14 (0.30), residues: 916 helix: 0.99 (0.21), residues: 662 sheet: None (None), residues: 0 loop : -3.10 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 49 HIS 0.006 0.002 HIS A 106 PHE 0.018 0.001 PHE A 274 TYR 0.009 0.001 TYR A 276 ARG 0.006 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6201 (tp40) REVERT: A 525 MET cc_start: 0.6238 (ttm) cc_final: 0.5905 (ttm) outliers start: 28 outliers final: 24 residues processed: 150 average time/residue: 0.3821 time to fit residues: 82.4726 Evaluate side-chains 141 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7558 Z= 0.225 Angle : 0.923 15.702 10308 Z= 0.432 Chirality : 0.210 1.784 1248 Planarity : 0.005 0.056 1236 Dihedral : 6.843 59.289 1044 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.16 % Rotamer: Outliers : 3.49 % Allowed : 18.95 % Favored : 77.56 % Cbeta Deviations : 0.22 % 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: 0.13 (0.30), residues: 916 helix: 1.24 (0.22), residues: 656 sheet: None (None), residues: 0 loop : -3.05 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 49 HIS 0.003 0.001 HIS B 106 PHE 0.020 0.001 PHE A 274 TYR 0.010 0.001 TYR B 353 ARG 0.006 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6261 (tp40) REVERT: A 525 MET cc_start: 0.6173 (ttm) cc_final: 0.5843 (ttm) REVERT: B 102 ARG cc_start: 0.8339 (ttt-90) cc_final: 0.7954 (ttt180) outliers start: 28 outliers final: 23 residues processed: 150 average time/residue: 0.3816 time to fit residues: 81.0792 Evaluate side-chains 145 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7805 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7558 Z= 0.228 Angle : 0.924 15.693 10308 Z= 0.433 Chirality : 0.210 1.781 1248 Planarity : 0.005 0.049 1236 Dihedral : 6.787 59.970 1044 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.16 % Rotamer: Outliers : 3.12 % Allowed : 19.45 % Favored : 77.43 % Cbeta Deviations : 0.22 % 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 (0.30), residues: 916 helix: 1.28 (0.22), residues: 658 sheet: None (None), residues: 0 loop : -2.99 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.004 0.001 HIS B 106 PHE 0.015 0.001 PHE A 274 TYR 0.010 0.001 TYR B 353 ARG 0.006 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6241 (tp40) REVERT: A 525 MET cc_start: 0.6169 (ttm) cc_final: 0.5841 (ttm) outliers start: 25 outliers final: 23 residues processed: 144 average time/residue: 0.3377 time to fit residues: 70.0884 Evaluate side-chains 145 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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: 0.7774 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7558 Z= 0.198 Angle : 0.910 15.680 10308 Z= 0.424 Chirality : 0.210 1.783 1248 Planarity : 0.005 0.065 1236 Dihedral : 6.547 58.282 1044 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.62 % Favored : 91.27 % Rotamer: Outliers : 3.12 % Allowed : 19.58 % Favored : 77.31 % Cbeta Deviations : 0.22 % 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: 0.42 (0.31), residues: 916 helix: 1.40 (0.22), residues: 670 sheet: None (None), residues: 0 loop : -3.04 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 49 HIS 0.002 0.001 HIS B 106 PHE 0.015 0.001 PHE A 274 TYR 0.011 0.001 TYR B 353 ARG 0.008 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6277 (tp-100) REVERT: A 236 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: A 525 MET cc_start: 0.6119 (ttm) cc_final: 0.5802 (ttm) REVERT: B 102 ARG cc_start: 0.8344 (ttt-90) cc_final: 0.7941 (ttt180) outliers start: 25 outliers final: 22 residues processed: 153 average time/residue: 0.3630 time to fit residues: 81.4683 Evaluate side-chains 148 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 562 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7558 Z= 0.276 Angle : 0.943 15.793 10308 Z= 0.444 Chirality : 0.210 1.790 1248 Planarity : 0.005 0.058 1236 Dihedral : 6.716 58.796 1044 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.73 % Favored : 91.05 % Rotamer: Outliers : 2.87 % Allowed : 20.45 % Favored : 76.68 % Cbeta Deviations : 0.22 % 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: 0.23 (0.31), residues: 916 helix: 1.28 (0.22), residues: 662 sheet: None (None), residues: 0 loop : -3.02 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.006 0.002 HIS B 106 PHE 0.014 0.001 PHE A 274 TYR 0.009 0.001 TYR B 353 ARG 0.007 0.001 ARG B 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6368 (tp40) REVERT: A 525 MET cc_start: 0.6282 (ttm) cc_final: 0.5967 (ttm) outliers start: 23 outliers final: 21 residues processed: 141 average time/residue: 0.3491 time to fit residues: 70.7600 Evaluate side-chains 143 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.0470 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112725 restraints weight = 33629.857| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.03 r_work: 0.3452 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7558 Z= 0.202 Angle : 0.914 15.694 10308 Z= 0.426 Chirality : 0.210 1.790 1248 Planarity : 0.005 0.066 1236 Dihedral : 6.475 58.652 1044 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.08 % Favored : 91.81 % Rotamer: Outliers : 2.37 % Allowed : 20.95 % Favored : 76.68 % Cbeta Deviations : 0.22 % 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: 0.46 (0.31), residues: 916 helix: 1.43 (0.22), residues: 672 sheet: None (None), residues: 0 loop : -3.05 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 49 HIS 0.002 0.001 HIS B 106 PHE 0.024 0.001 PHE A 274 TYR 0.011 0.001 TYR B 353 ARG 0.008 0.000 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3735.97 seconds wall clock time: 66 minutes 55.12 seconds (4015.12 seconds total)