Starting phenix.real_space_refine on Wed Mar 20 12:21:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jme_36417/03_2024/8jme_36417_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jme_36417/03_2024/8jme_36417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jme_36417/03_2024/8jme_36417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jme_36417/03_2024/8jme_36417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jme_36417/03_2024/8jme_36417_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jme_36417/03_2024/8jme_36417_neut.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 8824 2.51 5 N 2212 2.21 5 O 2220 1.98 5 H 13812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 374": "OD1" <-> "OD2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 374": "OD1" <-> "OD2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27164 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "B" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "C" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "D" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Time building chain proxies: 11.95, per 1000 atoms: 0.44 Number of scatterers: 27164 At special positions: 0 Unit cell: (116.25, 116.25, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 2220 8.00 N 2212 7.00 C 8824 6.00 H 13812 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 Time building additional restraints: 22.89 Conformation dependent library (CDL) restraints added in 2.8 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.773A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 125 through 164 removed outlier: 3.998A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.561A pdb=" N PHE A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.171A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 339 removed outlier: 3.571A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 387 removed outlier: 3.953A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 448 removed outlier: 4.243A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Proline residue: A 445 - end of helix Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.773A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 125 through 164 removed outlier: 3.998A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.561A pdb=" N PHE B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.171A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 339 removed outlier: 3.571A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 387 removed outlier: 3.953A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 448 removed outlier: 4.243A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Proline residue: B 445 - end of helix Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.773A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 125 through 164 removed outlier: 3.997A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.561A pdb=" N PHE C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.171A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 339 removed outlier: 3.571A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 387 removed outlier: 3.954A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 448 removed outlier: 4.242A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Proline residue: C 445 - end of helix Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.772A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 125 through 164 removed outlier: 3.997A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.561A pdb=" N PHE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.172A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 339 removed outlier: 3.571A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 3.953A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 448 removed outlier: 4.242A pdb=" N GLN D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Proline residue: D 445 - end of helix 984 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.98 Time building geometry restraints manager: 23.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13772 1.03 - 1.23: 40 1.23 - 1.42: 5775 1.42 - 1.62: 7761 1.62 - 1.81: 152 Bond restraints: 27500 Sorted by residual: bond pdb=" C VAL B 438 " pdb=" N LEU B 439 " ideal model delta sigma weight residual 1.333 1.424 -0.091 1.50e-02 4.44e+03 3.69e+01 bond pdb=" C VAL C 438 " pdb=" N LEU C 439 " ideal model delta sigma weight residual 1.333 1.411 -0.079 1.50e-02 4.44e+03 2.77e+01 bond pdb=" C LEU C 437 " pdb=" N VAL C 438 " ideal model delta sigma weight residual 1.335 1.396 -0.061 1.20e-02 6.94e+03 2.62e+01 bond pdb=" C LEU A 437 " pdb=" N VAL A 438 " ideal model delta sigma weight residual 1.334 1.390 -0.055 1.26e-02 6.30e+03 1.93e+01 bond pdb=" C LEU B 437 " pdb=" N VAL B 438 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.20e-02 6.94e+03 1.59e+01 ... (remaining 27495 not shown) Histogram of bond angle deviations from ideal: 100.69 - 107.35: 1008 107.35 - 114.00: 31774 114.00 - 120.66: 10647 120.66 - 127.32: 6134 127.32 - 133.97: 133 Bond angle restraints: 49696 Sorted by residual: angle pdb=" O VAL C 438 " pdb=" C VAL C 438 " pdb=" N LEU C 439 " ideal model delta sigma weight residual 121.80 116.46 5.34 1.13e+00 7.83e-01 2.23e+01 angle pdb=" CA VAL C 438 " pdb=" C VAL C 438 " pdb=" N LEU C 439 " ideal model delta sigma weight residual 117.69 122.59 -4.90 1.27e+00 6.20e-01 1.49e+01 angle pdb=" O VAL B 438 " pdb=" C VAL B 438 " pdb=" N LEU B 439 " ideal model delta sigma weight residual 121.80 117.57 4.23 1.13e+00 7.83e-01 1.40e+01 angle pdb=" CA VAL B 438 " pdb=" C VAL B 438 " pdb=" N LEU B 439 " ideal model delta sigma weight residual 117.69 121.49 -3.80 1.27e+00 6.20e-01 8.94e+00 angle pdb=" O LEU C 437 " pdb=" C LEU C 437 " pdb=" N VAL C 438 " ideal model delta sigma weight residual 122.07 124.81 -2.74 1.03e+00 9.43e-01 7.07e+00 ... (remaining 49691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 11433 17.34 - 34.68: 1055 34.68 - 52.02: 332 52.02 - 69.36: 76 69.36 - 86.69: 20 Dihedral angle restraints: 12916 sinusoidal: 6912 harmonic: 6004 Sorted by residual: dihedral pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " pdb=" OE1 GLU C 83 " ideal model delta sinusoidal sigma weight residual 0.00 -83.94 83.94 1 3.00e+01 1.11e-03 9.54e+00 dihedral pdb=" CB GLU D 83 " pdb=" CG GLU D 83 " pdb=" CD GLU D 83 " pdb=" OE1 GLU D 83 " ideal model delta sinusoidal sigma weight residual 0.00 -83.92 83.92 1 3.00e+01 1.11e-03 9.54e+00 dihedral pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " pdb=" CD GLU A 83 " pdb=" OE1 GLU A 83 " ideal model delta sinusoidal sigma weight residual 0.00 -83.89 83.89 1 3.00e+01 1.11e-03 9.53e+00 ... (remaining 12913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1480 0.026 - 0.052: 355 0.052 - 0.078: 189 0.078 - 0.104: 95 0.104 - 0.130: 21 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CA ILE C 173 " pdb=" N ILE C 173 " pdb=" C ILE C 173 " pdb=" CB ILE C 173 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE D 173 " pdb=" N ILE D 173 " pdb=" C ILE D 173 " pdb=" CB ILE D 173 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE B 173 " pdb=" N ILE B 173 " pdb=" C ILE B 173 " pdb=" CB ILE B 173 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 2137 not shown) Planarity restraints: 3836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 346 " 0.154 9.50e-02 1.11e+02 5.15e-02 3.29e+00 pdb=" NE ARG B 346 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 346 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 346 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 346 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 346 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 346 " 0.153 9.50e-02 1.11e+02 5.14e-02 3.28e+00 pdb=" NE ARG D 346 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 346 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 346 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 346 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG D 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 346 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 346 " 0.154 9.50e-02 1.11e+02 5.16e-02 3.27e+00 pdb=" NE ARG C 346 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 346 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 346 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 346 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG C 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 346 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 346 " 0.000 2.00e-02 2.50e+03 ... (remaining 3833 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1357 2.19 - 2.79: 55465 2.79 - 3.39: 81476 3.39 - 4.00: 103775 4.00 - 4.60: 161669 Nonbonded interactions: 403742 Sorted by model distance: nonbonded pdb=" OD2 ASP A 316 " pdb=" HG SER A 413 " model vdw 1.584 1.850 nonbonded pdb=" OD2 ASP D 316 " pdb=" HG SER D 413 " model vdw 1.584 1.850 nonbonded pdb=" OD2 ASP B 316 " pdb=" HG SER B 413 " model vdw 1.585 1.850 nonbonded pdb=" OD2 ASP C 316 " pdb=" HG SER C 413 " model vdw 1.585 1.850 nonbonded pdb="HE22 GLN C 441 " pdb=" OE1 GLN D 441 " model vdw 1.624 1.850 ... (remaining 403737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.390 Extract box with map and model: 4.690 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 86.750 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.003 0.091 13688 Z= 0.168 Angle : 0.504 5.341 18572 Z= 0.272 Chirality : 0.034 0.130 2140 Planarity : 0.005 0.068 2276 Dihedral : 16.254 86.694 4996 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.27 % Allowed : 14.95 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.95 (0.21), residues: 1620 helix: 2.65 (0.14), residues: 1184 sheet: None (None), residues: 0 loop : -0.04 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 355 HIS 0.001 0.000 HIS C 118 PHE 0.007 0.001 PHE A 417 TYR 0.009 0.001 TYR C 208 ARG 0.011 0.001 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 220 average time/residue: 3.5778 time to fit residues: 845.7284 Evaluate side-chains 211 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13688 Z= 0.275 Angle : 0.539 5.286 18572 Z= 0.287 Chirality : 0.038 0.123 2140 Planarity : 0.005 0.043 2276 Dihedral : 4.080 29.407 1832 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.77 % Allowed : 12.50 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.95 (0.20), residues: 1620 helix: 2.67 (0.14), residues: 1188 sheet: None (None), residues: 0 loop : -0.10 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 355 HIS 0.003 0.001 HIS B 197 PHE 0.014 0.002 PHE A 419 TYR 0.015 0.002 TYR B 353 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8392 (mttp) REVERT: B 415 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8389 (mttp) REVERT: C 415 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8376 (mttp) REVERT: D 415 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8374 (mttp) outliers start: 26 outliers final: 13 residues processed: 221 average time/residue: 3.3963 time to fit residues: 806.9116 Evaluate side-chains 223 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13688 Z= 0.322 Angle : 0.552 5.219 18572 Z= 0.295 Chirality : 0.039 0.122 2140 Planarity : 0.006 0.090 2276 Dihedral : 4.315 30.152 1832 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.49 % Allowed : 11.96 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.68 (0.20), residues: 1620 helix: 2.44 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 355 HIS 0.003 0.001 HIS D 197 PHE 0.016 0.002 PHE A 419 TYR 0.017 0.002 TYR D 353 ARG 0.012 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 2.116 Fit side-chains REVERT: A 295 GLU cc_start: 0.7617 (tt0) cc_final: 0.7343 (tt0) REVERT: A 415 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: B 295 GLU cc_start: 0.7616 (tt0) cc_final: 0.7344 (tt0) REVERT: B 415 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8447 (mttp) REVERT: C 295 GLU cc_start: 0.7615 (tt0) cc_final: 0.7345 (tt0) REVERT: C 415 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8307 (mttp) REVERT: D 295 GLU cc_start: 0.7617 (tt0) cc_final: 0.7344 (tt0) REVERT: D 415 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8350 (mttp) outliers start: 22 outliers final: 13 residues processed: 222 average time/residue: 3.6158 time to fit residues: 862.7391 Evaluate side-chains 217 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 337 GLN C 337 GLN D 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13688 Z= 0.184 Angle : 0.495 5.312 18572 Z= 0.261 Chirality : 0.036 0.128 2140 Planarity : 0.005 0.076 2276 Dihedral : 3.885 27.712 1826 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.36 % Allowed : 13.25 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.93 (0.20), residues: 1620 helix: 2.66 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.18 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 355 HIS 0.002 0.001 HIS B 197 PHE 0.012 0.001 PHE C 66 TYR 0.013 0.001 TYR D 353 ARG 0.009 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7600 (tt0) cc_final: 0.7321 (tt0) REVERT: A 415 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8445 (mttp) REVERT: B 295 GLU cc_start: 0.7603 (tt0) cc_final: 0.7324 (tt0) REVERT: B 415 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8370 (mttp) REVERT: C 295 GLU cc_start: 0.7589 (tt0) cc_final: 0.7318 (tt0) REVERT: C 415 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8406 (mttp) REVERT: D 295 GLU cc_start: 0.7603 (tt0) cc_final: 0.7323 (tt0) REVERT: D 415 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8406 (mttp) outliers start: 20 outliers final: 11 residues processed: 216 average time/residue: 3.5693 time to fit residues: 828.2066 Evaluate side-chains 220 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13688 Z= 0.209 Angle : 0.498 5.251 18572 Z= 0.264 Chirality : 0.036 0.126 2140 Planarity : 0.005 0.083 2276 Dihedral : 3.838 14.748 1824 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.15 % Allowed : 13.52 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.98 (0.20), residues: 1620 helix: 2.69 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.16 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 355 HIS 0.002 0.001 HIS C 197 PHE 0.013 0.001 PHE A 66 TYR 0.015 0.002 TYR A 353 ARG 0.009 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.5997 (tmtt) REVERT: A 258 PHE cc_start: 0.8598 (t80) cc_final: 0.8184 (t80) REVERT: A 295 GLU cc_start: 0.7587 (tt0) cc_final: 0.7314 (tt0) REVERT: A 415 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8327 (mttp) REVERT: B 295 GLU cc_start: 0.7587 (tt0) cc_final: 0.7315 (tt0) REVERT: B 415 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8379 (mttp) REVERT: C 258 PHE cc_start: 0.8600 (t80) cc_final: 0.8182 (t80) REVERT: C 295 GLU cc_start: 0.7589 (tt0) cc_final: 0.7317 (tt0) REVERT: C 415 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8380 (mttp) REVERT: D 258 PHE cc_start: 0.8598 (t80) cc_final: 0.8184 (t80) REVERT: D 295 GLU cc_start: 0.7591 (tt0) cc_final: 0.7318 (tt0) REVERT: D 415 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8383 (mttp) outliers start: 17 outliers final: 11 residues processed: 221 average time/residue: 3.4287 time to fit residues: 814.4335 Evaluate side-chains 222 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.0170 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13688 Z= 0.155 Angle : 0.475 5.539 18572 Z= 0.250 Chirality : 0.035 0.129 2140 Planarity : 0.005 0.086 2276 Dihedral : 3.737 13.812 1824 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.22 % Allowed : 13.32 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 3.17 (0.20), residues: 1620 helix: 2.85 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.12 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 355 HIS 0.002 0.001 HIS B 118 PHE 0.011 0.001 PHE D 66 TYR 0.012 0.001 TYR D 353 ARG 0.011 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 PHE cc_start: 0.8572 (t80) cc_final: 0.8155 (t80) REVERT: A 295 GLU cc_start: 0.7568 (tt0) cc_final: 0.7296 (tt0) REVERT: A 415 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8341 (mttp) REVERT: B 94 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6004 (tmtt) REVERT: B 258 PHE cc_start: 0.8567 (t80) cc_final: 0.8141 (t80) REVERT: B 295 GLU cc_start: 0.7567 (tt0) cc_final: 0.7295 (tt0) REVERT: C 94 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6022 (tmtt) REVERT: C 258 PHE cc_start: 0.8569 (t80) cc_final: 0.8143 (t80) REVERT: C 295 GLU cc_start: 0.7568 (tt0) cc_final: 0.7297 (tt0) REVERT: D 94 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6012 (tmtt) REVERT: D 258 PHE cc_start: 0.8569 (t80) cc_final: 0.8158 (t80) REVERT: D 295 GLU cc_start: 0.7571 (tt0) cc_final: 0.7299 (tt0) outliers start: 18 outliers final: 11 residues processed: 217 average time/residue: 3.4294 time to fit residues: 799.0410 Evaluate side-chains 217 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13688 Z= 0.149 Angle : 0.469 5.273 18572 Z= 0.246 Chirality : 0.035 0.131 2140 Planarity : 0.005 0.090 2276 Dihedral : 3.689 13.629 1824 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.15 % Allowed : 13.79 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 3.28 (0.20), residues: 1620 helix: 2.92 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.06 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 355 HIS 0.002 0.001 HIS C 118 PHE 0.011 0.001 PHE D 66 TYR 0.011 0.001 TYR A 353 ARG 0.010 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6025 (tmtt) REVERT: A 258 PHE cc_start: 0.8566 (t80) cc_final: 0.8122 (t80) REVERT: A 295 GLU cc_start: 0.7566 (tt0) cc_final: 0.7275 (tt0) REVERT: A 415 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8404 (mttp) REVERT: B 94 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6023 (tmtt) REVERT: B 258 PHE cc_start: 0.8556 (t80) cc_final: 0.8152 (t80) REVERT: B 295 GLU cc_start: 0.7567 (tt0) cc_final: 0.7277 (tt0) REVERT: C 94 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6021 (tmtt) REVERT: C 258 PHE cc_start: 0.8571 (t80) cc_final: 0.8171 (t80) REVERT: C 295 GLU cc_start: 0.7567 (tt0) cc_final: 0.7277 (tt0) REVERT: D 94 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6018 (tmtt) REVERT: D 258 PHE cc_start: 0.8562 (t80) cc_final: 0.8123 (t80) REVERT: D 295 GLU cc_start: 0.7568 (tt0) cc_final: 0.7276 (tt0) outliers start: 17 outliers final: 9 residues processed: 213 average time/residue: 3.5009 time to fit residues: 802.8573 Evaluate side-chains 222 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8031 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13688 Z= 0.338 Angle : 0.558 5.248 18572 Z= 0.299 Chirality : 0.039 0.119 2140 Planarity : 0.006 0.089 2276 Dihedral : 4.029 16.410 1824 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.63 % Allowed : 13.04 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.78 (0.20), residues: 1620 helix: 2.53 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.17 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 152 HIS 0.004 0.001 HIS A 197 PHE 0.018 0.002 PHE D 419 TYR 0.017 0.002 TYR A 353 ARG 0.012 0.001 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 2.141 Fit side-chains REVERT: A 94 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6034 (tmtt) REVERT: A 258 PHE cc_start: 0.8574 (t80) cc_final: 0.8186 (t80) REVERT: A 295 GLU cc_start: 0.7603 (tt0) cc_final: 0.7343 (tt0) REVERT: A 415 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8264 (mttp) REVERT: B 94 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6048 (tmtt) REVERT: B 258 PHE cc_start: 0.8560 (t80) cc_final: 0.8161 (t80) REVERT: B 295 GLU cc_start: 0.7602 (tt0) cc_final: 0.7342 (tt0) REVERT: B 415 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8551 (mttp) REVERT: C 94 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6049 (tmtt) REVERT: C 258 PHE cc_start: 0.8558 (t80) cc_final: 0.8201 (t80) REVERT: C 295 GLU cc_start: 0.7603 (tt0) cc_final: 0.7345 (tt0) REVERT: C 415 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8559 (mttp) REVERT: D 94 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6046 (tmtt) REVERT: D 258 PHE cc_start: 0.8572 (t80) cc_final: 0.8185 (t80) REVERT: D 295 GLU cc_start: 0.7605 (tt0) cc_final: 0.7345 (tt0) REVERT: D 415 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8568 (mttp) outliers start: 24 outliers final: 16 residues processed: 231 average time/residue: 3.4035 time to fit residues: 845.2347 Evaluate side-chains 236 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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: 0.8008 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13688 Z= 0.208 Angle : 0.507 5.411 18572 Z= 0.267 Chirality : 0.036 0.125 2140 Planarity : 0.006 0.093 2276 Dihedral : 3.946 16.135 1824 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.36 % Allowed : 14.33 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.93 (0.20), residues: 1620 helix: 2.66 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.16 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 355 HIS 0.002 0.001 HIS C 197 PHE 0.011 0.001 PHE A 66 TYR 0.014 0.002 TYR D 353 ARG 0.014 0.001 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6043 (tmtt) REVERT: A 258 PHE cc_start: 0.8541 (t80) cc_final: 0.8159 (t80) REVERT: A 295 GLU cc_start: 0.7595 (tt0) cc_final: 0.7330 (tt0) REVERT: A 415 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8411 (mttp) REVERT: B 94 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6041 (tmtt) REVERT: B 258 PHE cc_start: 0.8541 (t80) cc_final: 0.8158 (t80) REVERT: B 295 GLU cc_start: 0.7596 (tt0) cc_final: 0.7322 (tt0) REVERT: C 94 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6036 (tmtt) REVERT: C 196 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: C 258 PHE cc_start: 0.8553 (t80) cc_final: 0.8163 (t80) REVERT: C 295 GLU cc_start: 0.7594 (tt0) cc_final: 0.7325 (tt0) REVERT: D 94 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6034 (tmtt) REVERT: D 258 PHE cc_start: 0.8539 (t80) cc_final: 0.8159 (t80) REVERT: D 295 GLU cc_start: 0.7597 (tt0) cc_final: 0.7333 (tt0) outliers start: 20 outliers final: 11 residues processed: 223 average time/residue: 3.3853 time to fit residues: 811.6915 Evaluate side-chains 227 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 0.0270 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13688 Z= 0.218 Angle : 0.511 5.508 18572 Z= 0.270 Chirality : 0.036 0.124 2140 Planarity : 0.006 0.096 2276 Dihedral : 3.930 15.999 1824 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.56 % Allowed : 14.13 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.98 (0.20), residues: 1620 helix: 2.70 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.16 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 355 HIS 0.002 0.001 HIS C 197 PHE 0.013 0.002 PHE D 66 TYR 0.015 0.002 TYR A 353 ARG 0.013 0.001 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6056 (tmtt) REVERT: A 258 PHE cc_start: 0.8542 (t80) cc_final: 0.8162 (t80) REVERT: A 295 GLU cc_start: 0.7599 (tt0) cc_final: 0.7332 (tt0) REVERT: A 415 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: B 94 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6050 (tmtt) REVERT: B 258 PHE cc_start: 0.8539 (t80) cc_final: 0.8164 (t80) REVERT: B 295 GLU cc_start: 0.7597 (tt0) cc_final: 0.7322 (tt0) REVERT: C 94 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6052 (tmtt) REVERT: C 258 PHE cc_start: 0.8537 (t80) cc_final: 0.8150 (t80) REVERT: C 295 GLU cc_start: 0.7597 (tt0) cc_final: 0.7323 (tt0) REVERT: D 94 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6034 (tmtt) REVERT: D 258 PHE cc_start: 0.8542 (t80) cc_final: 0.8168 (t80) REVERT: D 295 GLU cc_start: 0.7599 (tt0) cc_final: 0.7323 (tt0) outliers start: 23 outliers final: 15 residues processed: 224 average time/residue: 3.4558 time to fit residues: 835.2727 Evaluate side-chains 230 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 16 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.138309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104893 restraints weight = 36100.594| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.38 r_work: 0.2899 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13688 Z= 0.191 Angle : 0.496 5.405 18572 Z= 0.261 Chirality : 0.036 0.126 2140 Planarity : 0.006 0.096 2276 Dihedral : 3.895 15.616 1824 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.49 % Allowed : 14.13 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 3.08 (0.20), residues: 1620 helix: 2.78 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.16 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 355 HIS 0.002 0.001 HIS C 118 PHE 0.011 0.001 PHE A 66 TYR 0.014 0.002 TYR D 353 ARG 0.015 0.001 ARG D 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12074.54 seconds wall clock time: 210 minutes 23.38 seconds (12623.38 seconds total)