Starting phenix.real_space_refine on Wed Feb 21 16:59:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5b_10693/02_2024/6y5b_10693.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5b_10693/02_2024/6y5b_10693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5b_10693/02_2024/6y5b_10693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5b_10693/02_2024/6y5b_10693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5b_10693/02_2024/6y5b_10693.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5b_10693/02_2024/6y5b_10693.pdb" } resolution = 3.1 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= 0.002 sd= 0.017 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 45 5.16 5 C 10311 2.51 5 N 2541 2.21 5 O 2738 1.98 5 H 15794 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 327": "OD1" <-> "OD2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 177": "OD1" <-> "OD2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31429 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6299 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 19, 'TRANS': 358} Chain breaks: 2 Chain: "B" Number of atoms: 6243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6243 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 2 Chain: "C" Number of atoms: 6293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6293 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 19, 'TRANS': 358} Chain breaks: 2 Chain: "D" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6281 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 2 Chain: "E" Number of atoms: 6313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6313 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 19, 'TRANS': 359} Chain breaks: 2 Time building chain proxies: 13.96, per 1000 atoms: 0.44 Number of scatterers: 31429 At special positions: 0 Unit cell: (100.672, 95.68, 155.584, 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 45 16.00 O 2738 8.00 N 2541 7.00 C 10311 6.00 H 15794 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.61 Conformation dependent library (CDL) restraints added in 3.0 seconds 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3674 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 19 sheets defined 46.4% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.830A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.569A pdb=" N LEU A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 273 Processing helix chain 'A' and resid 281 through 310 removed outlier: 3.627A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 405 through 422 removed outlier: 4.497A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 4.283A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 461 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 244 removed outlier: 4.422A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.669A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.676A pdb=" N HIS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.979A pdb=" N ARG B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 Processing helix chain 'B' and resid 414 through 460 removed outlier: 5.263A pdb=" N VAL B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.719A pdb=" N ASP C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 244 removed outlier: 3.593A pdb=" N SER C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 249 through 273 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.631A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'C' and resid 419 through 462 removed outlier: 3.865A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.577A pdb=" N ALA D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 243 removed outlier: 4.101A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 3.882A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 273 Processing helix chain 'D' and resid 282 through 309 removed outlier: 4.714A pdb=" N HIS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 404 through 419 Processing helix chain 'D' and resid 419 through 462 removed outlier: 3.938A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 20 removed outlier: 3.944A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.872A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 177 Processing helix chain 'E' and resid 220 through 243 removed outlier: 3.694A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 248 through 273 removed outlier: 3.926A pdb=" N VAL E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.611A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 405 through 418 Processing helix chain 'E' and resid 422 through 462 removed outlier: 3.672A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 52 removed outlier: 6.862A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 4.514A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 149 removed outlier: 4.090A pdb=" N GLN A 147 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.145A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 68 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.145A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 68 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.536A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 89 removed outlier: 7.270A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 99 removed outlier: 4.886A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 148 removed outlier: 5.851A pdb=" N TYR C 213 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL C 192 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE C 215 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 52 removed outlier: 7.710A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 85 through 89 removed outlier: 4.202A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 98 through 99 Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.705A pdb=" N GLN D 147 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE D 201 " --> pdb=" O ASN D 205 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 197 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D 195 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 52 removed outlier: 7.448A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 85 through 89 removed outlier: 4.323A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 99 removed outlier: 4.499A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99 removed outlier: 4.499A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2397 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: 13.17 Time building geometry restraints manager: 26.34 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: 15784 1.03 - 1.23: 83 1.23 - 1.42: 6764 1.42 - 1.62: 9161 1.62 - 1.82: 70 Bond restraints: 31862 Sorted by residual: bond pdb=" C LYS B 24 " pdb=" N LYS B 25 " ideal model delta sigma weight residual 1.335 1.430 -0.095 1.31e-02 5.83e+03 5.25e+01 bond pdb=" C ARG B 420 " pdb=" O ARG B 420 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.17e-02 7.31e+03 3.54e+01 bond pdb=" C ILE E 268 " pdb=" O ILE E 268 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.93e+01 bond pdb=" N THR E 280 " pdb=" CA THR E 280 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.88e+01 bond pdb=" C GLU B 421 " pdb=" O GLU B 421 " ideal model delta sigma weight residual 1.236 1.281 -0.044 1.15e-02 7.56e+03 1.47e+01 ... (remaining 31857 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.91: 1325 106.91 - 113.75: 36918 113.75 - 120.60: 10876 120.60 - 127.44: 8328 127.44 - 134.28: 259 Bond angle restraints: 57706 Sorted by residual: angle pdb=" C LEU A 436 " pdb=" N LEU A 437 " pdb=" CA LEU A 437 " ideal model delta sigma weight residual 120.44 127.74 -7.30 1.36e+00 5.41e-01 2.88e+01 angle pdb=" N ILE E 268 " pdb=" CA ILE E 268 " pdb=" CB ILE E 268 " ideal model delta sigma weight residual 110.54 117.83 -7.29 1.36e+00 5.41e-01 2.88e+01 angle pdb=" CA ILE E 268 " pdb=" C ILE E 268 " pdb=" O ILE E 268 " ideal model delta sigma weight residual 120.95 115.41 5.54 1.04e+00 9.25e-01 2.84e+01 angle pdb=" C LEU E 282 " pdb=" N ILE E 283 " pdb=" CA ILE E 283 " ideal model delta sigma weight residual 120.70 127.35 -6.65 1.25e+00 6.40e-01 2.83e+01 angle pdb=" CA ARG B 420 " pdb=" C ARG B 420 " pdb=" O ARG B 420 " ideal model delta sigma weight residual 120.55 114.94 5.61 1.06e+00 8.90e-01 2.80e+01 ... (remaining 57701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13724 17.95 - 35.90: 892 35.90 - 53.85: 249 53.85 - 71.80: 64 71.80 - 89.74: 19 Dihedral angle restraints: 14948 sinusoidal: 7973 harmonic: 6975 Sorted by residual: dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N PRO A 274 " pdb=" CA PRO A 274 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLN E 130 " pdb=" C GLN E 130 " pdb=" N LEU E 131 " pdb=" CA LEU E 131 " ideal model delta harmonic sigma weight residual 180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA VAL D 308 " pdb=" C VAL D 308 " pdb=" N HIS D 309 " pdb=" CA HIS D 309 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 14945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2066 0.058 - 0.117: 370 0.117 - 0.175: 95 0.175 - 0.233: 11 0.233 - 0.291: 4 Chirality restraints: 2546 Sorted by residual: chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE E 268 " pdb=" CA ILE E 268 " pdb=" CG1 ILE E 268 " pdb=" CG2 ILE E 268 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE B 201 " pdb=" N ILE B 201 " pdb=" C ILE B 201 " pdb=" CB ILE B 201 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2543 not shown) Planarity restraints: 4463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 242 " -0.010 2.00e-02 2.50e+03 2.49e-02 1.86e+01 pdb=" CG PHE A 242 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 242 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 242 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 242 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 242 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 242 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 242 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE A 242 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 242 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 PHE A 242 " -0.049 2.00e-02 2.50e+03 pdb=" HZ PHE A 242 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 142 " -0.022 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C PHE B 142 " 0.074 2.00e-02 2.50e+03 pdb=" O PHE B 142 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO B 143 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 269 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C VAL E 269 " -0.073 2.00e-02 2.50e+03 pdb=" O VAL E 269 " 0.027 2.00e-02 2.50e+03 pdb=" N SER E 270 " 0.025 2.00e-02 2.50e+03 ... (remaining 4460 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1781 2.21 - 2.81: 67441 2.81 - 3.40: 87888 3.40 - 4.00: 113862 4.00 - 4.60: 176401 Nonbonded interactions: 447373 Sorted by model distance: nonbonded pdb=" HG1 THR B 154 " pdb=" O ALA B 208 " model vdw 1.610 1.850 nonbonded pdb=" OE1 GLN C 56 " pdb=" H LEU C 137 " model vdw 1.611 1.850 nonbonded pdb=" HG3 GLU A 188 " pdb=" H LEU A 189 " model vdw 1.619 2.270 nonbonded pdb=" H THR C 90 " pdb=" O PRO C 113 " model vdw 1.632 1.850 nonbonded pdb="HD23 LEU E 15 " pdb="HD22 LEU E 86 " model vdw 1.637 2.440 ... (remaining 447368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 309 or resid 318 through 328 or resid 404 throug \ h 462)) selection = (chain 'B' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 15 through 309 or resid 318 through 328 or (resid 404 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name \ HE22)) or resid 405 through 462)) selection = (chain 'C' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 15 through 309 or resid 318 through 328 or resid 404 through 462)) selection = (chain 'D' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 15 through 309 or resid 318 through 328 or (resid 404 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name \ HE22)) or resid 405 through 462)) selection = (chain 'E' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 15 through 309 or resid 318 through 328 or resid 404 through 462)) } 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: 1.700 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: 0.430 Extract box with map and model: 8.320 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 100.570 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.006 0.095 16068 Z= 0.379 Angle : 0.867 8.565 21945 Z= 0.556 Chirality : 0.051 0.291 2546 Planarity : 0.006 0.056 2685 Dihedral : 13.310 89.745 5769 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -3.11 (0.18), residues: 1857 helix: -1.20 (0.16), residues: 796 sheet: -3.68 (0.18), residues: 448 loop : -1.49 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 68 HIS 0.006 0.001 HIS B 18 PHE 0.034 0.002 PHE A 103 TYR 0.023 0.002 TYR A 441 ARG 0.005 0.001 ARG E 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.599 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: 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 319 ASP cc_start: 0.9102 (m-30) cc_final: 0.8502 (t0) REVERT: B 235 MET cc_start: 0.9232 (mtt) cc_final: 0.9016 (mtp) REVERT: D 210 MET cc_start: 0.7951 (tpt) cc_final: 0.7619 (tpt) REVERT: E 415 LYS cc_start: 0.9621 (tttt) cc_final: 0.9041 (tptt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.9384 time to fit residues: 188.6660 Evaluate side-chains 89 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 184 GLN C 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16068 Z= 0.219 Angle : 0.591 10.944 21945 Z= 0.317 Chirality : 0.043 0.163 2546 Planarity : 0.004 0.059 2685 Dihedral : 5.041 24.501 2067 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.13 % Allowed : 5.49 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1857 helix: 0.12 (0.17), residues: 795 sheet: -3.01 (0.21), residues: 441 loop : -0.92 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 68 HIS 0.003 0.001 HIS C 309 PHE 0.026 0.001 PHE A 242 TYR 0.016 0.001 TYR A 441 ARG 0.003 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 2.811 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: 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 319 ASP cc_start: 0.9102 (m-30) cc_final: 0.8483 (t0) REVERT: B 235 MET cc_start: 0.9275 (mtt) cc_final: 0.9051 (mtp) REVERT: D 210 MET cc_start: 0.8000 (tpt) cc_final: 0.7558 (tpt) REVERT: D 435 ARG cc_start: 0.9163 (mmp-170) cc_final: 0.8813 (mmp-170) REVERT: E 415 LYS cc_start: 0.9657 (tttt) cc_final: 0.9451 (tppt) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.8990 time to fit residues: 126.3614 Evaluate side-chains 96 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16068 Z= 0.196 Angle : 0.544 6.798 21945 Z= 0.293 Chirality : 0.042 0.163 2546 Planarity : 0.004 0.054 2685 Dihedral : 4.753 22.441 2067 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.85 % Allowed : 6.73 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1857 helix: 0.69 (0.18), residues: 794 sheet: -2.69 (0.21), residues: 465 loop : -0.70 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 426 HIS 0.010 0.001 HIS B 323 PHE 0.024 0.001 PHE A 242 TYR 0.018 0.001 TYR A 441 ARG 0.002 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 2.777 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: 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 319 ASP cc_start: 0.9124 (m-30) cc_final: 0.8500 (t0) REVERT: D 210 MET cc_start: 0.8145 (tpt) cc_final: 0.7827 (tpt) REVERT: D 435 ARG cc_start: 0.9170 (mmp-170) cc_final: 0.8825 (mmp-170) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.9260 time to fit residues: 121.4994 Evaluate side-chains 96 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16068 Z= 0.155 Angle : 0.508 9.049 21945 Z= 0.270 Chirality : 0.042 0.172 2546 Planarity : 0.004 0.106 2685 Dihedral : 4.464 21.307 2067 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.02 % Allowed : 7.75 % Favored : 91.23 % 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: -0.51 (0.20), residues: 1857 helix: 1.23 (0.18), residues: 799 sheet: -2.39 (0.22), residues: 459 loop : -0.52 (0.28), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 68 HIS 0.012 0.001 HIS B 323 PHE 0.023 0.001 PHE A 242 TYR 0.018 0.001 TYR D 116 ARG 0.009 0.000 ARG E 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 2.613 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: 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 319 ASP cc_start: 0.9137 (m-30) cc_final: 0.8523 (t0) REVERT: D 435 ARG cc_start: 0.9206 (mmp-170) cc_final: 0.8895 (mmp-170) outliers start: 18 outliers final: 15 residues processed: 96 average time/residue: 0.8999 time to fit residues: 118.8918 Evaluate side-chains 97 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16068 Z= 0.142 Angle : 0.490 7.916 21945 Z= 0.259 Chirality : 0.041 0.144 2546 Planarity : 0.004 0.077 2685 Dihedral : 4.293 20.607 2067 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.07 % Allowed : 8.26 % Favored : 90.67 % 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: -0.20 (0.20), residues: 1857 helix: 1.50 (0.18), residues: 799 sheet: -2.22 (0.23), residues: 459 loop : -0.40 (0.28), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 426 HIS 0.011 0.001 HIS B 323 PHE 0.021 0.001 PHE A 242 TYR 0.014 0.001 TYR A 441 ARG 0.003 0.000 ARG E 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 2.956 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: 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 319 ASP cc_start: 0.9131 (m-30) cc_final: 0.8518 (t0) REVERT: C 419 MET cc_start: 0.5322 (OUTLIER) cc_final: 0.5056 (tpp) REVERT: D 319 ASP cc_start: 0.9175 (m-30) cc_final: 0.8802 (t0) REVERT: D 435 ARG cc_start: 0.9179 (mmp-170) cc_final: 0.8878 (mmp-170) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.9147 time to fit residues: 121.3092 Evaluate side-chains 96 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16068 Z= 0.177 Angle : 0.497 8.151 21945 Z= 0.264 Chirality : 0.041 0.140 2546 Planarity : 0.004 0.076 2685 Dihedral : 4.240 20.069 2067 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.07 % Allowed : 8.71 % Favored : 90.21 % 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: -0.03 (0.20), residues: 1857 helix: 1.67 (0.18), residues: 794 sheet: -2.13 (0.23), residues: 459 loop : -0.36 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 426 HIS 0.011 0.001 HIS B 323 PHE 0.020 0.001 PHE A 242 TYR 0.015 0.001 TYR A 441 ARG 0.015 0.000 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 2.524 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: 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 319 ASP cc_start: 0.9126 (m-30) cc_final: 0.8504 (t0) REVERT: C 419 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.5084 (tpp) REVERT: D 319 ASP cc_start: 0.9169 (m-30) cc_final: 0.8814 (t0) REVERT: D 435 ARG cc_start: 0.9198 (mmp-170) cc_final: 0.8904 (mmp-170) REVERT: E 415 LYS cc_start: 0.9714 (tttt) cc_final: 0.9507 (tppt) outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 1.0022 time to fit residues: 137.8733 Evaluate side-chains 99 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16068 Z= 0.165 Angle : 0.491 7.982 21945 Z= 0.259 Chirality : 0.041 0.141 2546 Planarity : 0.004 0.067 2685 Dihedral : 4.171 19.237 2067 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.13 % Allowed : 8.77 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1857 helix: 1.79 (0.18), residues: 795 sheet: -2.01 (0.23), residues: 459 loop : -0.28 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 426 HIS 0.012 0.001 HIS B 323 PHE 0.020 0.001 PHE A 242 TYR 0.015 0.001 TYR A 441 ARG 0.013 0.000 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 2.614 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: 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 319 ASP cc_start: 0.9112 (m-30) cc_final: 0.8483 (t0) REVERT: C 419 MET cc_start: 0.5304 (OUTLIER) cc_final: 0.5028 (tpp) REVERT: D 319 ASP cc_start: 0.9151 (m-30) cc_final: 0.8788 (t0) REVERT: D 435 ARG cc_start: 0.9225 (mmp-170) cc_final: 0.8941 (mmp-170) REVERT: E 415 LYS cc_start: 0.9706 (tttt) cc_final: 0.9500 (tppt) outliers start: 20 outliers final: 16 residues processed: 102 average time/residue: 0.8367 time to fit residues: 118.0060 Evaluate side-chains 100 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS C 55 ASN E 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16068 Z= 0.321 Angle : 0.567 7.237 21945 Z= 0.305 Chirality : 0.042 0.139 2546 Planarity : 0.004 0.063 2685 Dihedral : 4.377 20.960 2067 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.24 % Allowed : 9.50 % Favored : 89.25 % 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: -0.10 (0.20), residues: 1857 helix: 1.51 (0.18), residues: 794 sheet: -2.06 (0.23), residues: 454 loop : -0.35 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 426 HIS 0.011 0.001 HIS B 323 PHE 0.018 0.001 PHE A 242 TYR 0.020 0.001 TYR A 441 ARG 0.009 0.001 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 2.815 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: 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 319 ASP cc_start: 0.9085 (m-30) cc_final: 0.8444 (t0) REVERT: D 435 ARG cc_start: 0.9236 (mmp-170) cc_final: 0.8943 (mmp-170) REVERT: E 415 LYS cc_start: 0.9706 (tttt) cc_final: 0.9499 (tppt) outliers start: 22 outliers final: 20 residues processed: 99 average time/residue: 0.8500 time to fit residues: 118.2992 Evaluate side-chains 102 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16068 Z= 0.208 Angle : 0.519 7.687 21945 Z= 0.275 Chirality : 0.041 0.141 2546 Planarity : 0.004 0.063 2685 Dihedral : 4.334 19.008 2067 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.07 % Allowed : 9.62 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1857 helix: 1.59 (0.18), residues: 794 sheet: -1.99 (0.23), residues: 452 loop : -0.35 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 426 HIS 0.011 0.001 HIS B 323 PHE 0.020 0.001 PHE A 242 TYR 0.018 0.001 TYR A 441 ARG 0.008 0.000 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 3.029 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: 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 319 ASP cc_start: 0.9092 (m-30) cc_final: 0.8455 (t0) REVERT: D 435 ARG cc_start: 0.9226 (mmp-170) cc_final: 0.8936 (mmp-170) REVERT: E 415 LYS cc_start: 0.9705 (tttt) cc_final: 0.9501 (tppt) outliers start: 19 outliers final: 18 residues processed: 100 average time/residue: 0.8192 time to fit residues: 115.0931 Evaluate side-chains 101 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16068 Z= 0.149 Angle : 0.499 8.735 21945 Z= 0.260 Chirality : 0.041 0.141 2546 Planarity : 0.004 0.061 2685 Dihedral : 4.180 18.096 2067 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.90 % Allowed : 9.90 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1857 helix: 1.79 (0.18), residues: 796 sheet: -1.87 (0.23), residues: 455 loop : -0.26 (0.28), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 68 HIS 0.012 0.001 HIS B 323 PHE 0.020 0.001 PHE A 242 TYR 0.014 0.001 TYR A 441 ARG 0.007 0.000 ARG E 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 2.858 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: 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 319 ASP cc_start: 0.9095 (m-30) cc_final: 0.8460 (t0) REVERT: D 319 ASP cc_start: 0.9139 (m-30) cc_final: 0.8760 (t0) REVERT: D 435 ARG cc_start: 0.9221 (mmp-170) cc_final: 0.8939 (mmp-170) REVERT: E 319 ASP cc_start: 0.9422 (t0) cc_final: 0.8974 (p0) outliers start: 16 outliers final: 15 residues processed: 98 average time/residue: 0.8651 time to fit residues: 117.2873 Evaluate side-chains 101 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 135 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.040711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.032634 restraints weight = 347143.304| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 4.51 r_work: 0.2935 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16068 Z= 0.136 Angle : 0.487 8.741 21945 Z= 0.251 Chirality : 0.041 0.147 2546 Planarity : 0.004 0.058 2685 Dihedral : 4.001 17.258 2067 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.74 % Allowed : 10.18 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1857 helix: 2.04 (0.18), residues: 796 sheet: -1.75 (0.24), residues: 454 loop : -0.20 (0.28), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 68 HIS 0.013 0.001 HIS B 323 PHE 0.019 0.001 PHE A 242 TYR 0.014 0.001 TYR A 441 ARG 0.007 0.000 ARG E 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5797.41 seconds wall clock time: 104 minutes 28.74 seconds (6268.74 seconds total)