Starting phenix.real_space_refine on Mon Mar 11 05:48:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en0_31197/03_2024/7en0_31197_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en0_31197/03_2024/7en0_31197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en0_31197/03_2024/7en0_31197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en0_31197/03_2024/7en0_31197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en0_31197/03_2024/7en0_31197_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en0_31197/03_2024/7en0_31197_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 P 3 5.49 5 S 48 5.16 5 C 4878 2.51 5 N 1137 2.21 5 O 1173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 225": "NH1" <-> "NH2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 482": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7239 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 2399 Chain: "B" Number of atoms: 2350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 2399 Chain: "C" Number of atoms: 2350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 2399 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PLC': 1, 'SPH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PLC': 1, 'SPH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PLC': 1, 'SPH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 357 " occ=0.50 residue: pdb=" N AARG B 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 357 " occ=0.50 residue: pdb=" N AARG C 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 357 " occ=0.50 Time building chain proxies: 7.61, per 1000 atoms: 1.05 Number of scatterers: 7239 At special positions: 0 Unit cell: (106.845, 105.797, 62.85, 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 48 16.00 P 3 15.00 O 1173 8.00 N 1137 7.00 C 4878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 2.7 seconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 0 sheets defined 72.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 199 through 220 removed outlier: 4.126A pdb=" N GLY A 207 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER A 210 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 213 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 258 removed outlier: 3.580A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.578A pdb=" N ARG A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 278 through 288 removed outlier: 4.227A pdb=" N ALA A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 removed outlier: 4.213A pdb=" N ALA A 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA A 312 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Proline residue: A 313 - end of helix removed outlier: 4.046A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 322 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 327 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.710A pdb=" N HIS A 342 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 343 " --> pdb=" O SER A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 361 through 381 removed outlier: 3.890A pdb=" N HIS A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 417 removed outlier: 3.527A pdb=" N MET A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 403 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 405 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR A 406 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Proline residue: A 407 - end of helix removed outlier: 3.853A pdb=" N ALA A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 414 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 417 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 442 removed outlier: 3.708A pdb=" N VAL A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.658A pdb=" N THR A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 506 removed outlier: 3.561A pdb=" N MET A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 199 through 220 removed outlier: 4.126A pdb=" N GLY B 207 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 210 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 213 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 258 removed outlier: 3.580A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 267 removed outlier: 3.578A pdb=" N ARG B 264 " --> pdb=" O PHE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 278 through 288 removed outlier: 4.227A pdb=" N ALA B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 327 removed outlier: 4.213A pdb=" N ALA B 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA B 312 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Proline residue: B 313 - end of helix removed outlier: 4.046A pdb=" N ALA B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR B 322 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 327 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.709A pdb=" N HIS B 342 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 361 through 381 removed outlier: 3.890A pdb=" N HIS B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 417 removed outlier: 3.526A pdb=" N MET B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 403 " --> pdb=" O TYR B 400 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 405 " --> pdb=" O MET B 402 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR B 406 " --> pdb=" O PHE B 403 " (cutoff:3.500A) Proline residue: B 407 - end of helix removed outlier: 3.853A pdb=" N ALA B 413 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP B 414 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 417 " --> pdb=" O TRP B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 442 removed outlier: 3.708A pdb=" N VAL B 441 " --> pdb=" O MET B 437 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.658A pdb=" N THR B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 506 removed outlier: 3.561A pdb=" N MET B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 199 through 220 removed outlier: 4.126A pdb=" N GLY C 207 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER C 210 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 212 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 213 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 258 removed outlier: 3.579A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 252 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 267 removed outlier: 3.577A pdb=" N ARG C 264 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 278 through 288 removed outlier: 4.226A pdb=" N ALA C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 327 removed outlier: 4.213A pdb=" N ALA C 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA C 312 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Proline residue: C 313 - end of helix removed outlier: 4.046A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR C 322 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C 327 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.710A pdb=" N HIS C 342 " --> pdb=" O PRO C 339 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 343 " --> pdb=" O SER C 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 339 through 343' Processing helix chain 'C' and resid 346 through 358 Processing helix chain 'C' and resid 361 through 381 removed outlier: 3.889A pdb=" N HIS C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 417 removed outlier: 3.527A pdb=" N MET C 402 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 403 " --> pdb=" O TYR C 400 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 405 " --> pdb=" O MET C 402 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR C 406 " --> pdb=" O PHE C 403 " (cutoff:3.500A) Proline residue: C 407 - end of helix removed outlier: 3.853A pdb=" N ALA C 413 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP C 414 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 417 " --> pdb=" O TRP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 442 removed outlier: 3.708A pdb=" N VAL C 441 " --> pdb=" O MET C 437 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 Processing helix chain 'C' and resid 460 through 475 removed outlier: 3.658A pdb=" N THR C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 506 removed outlier: 3.561A pdb=" N MET C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 912 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: 1.86 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1008 1.31 - 1.43: 2194 1.43 - 1.56: 4166 1.56 - 1.68: 6 1.68 - 1.81: 78 Bond restraints: 7452 Sorted by residual: bond pdb=" CB PLC B 601 " pdb=" O3 PLC B 601 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CB PLC C 601 " pdb=" O3 PLC C 601 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C' PLC C 601 " pdb=" O2 PLC C 601 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 7447 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.92: 261 106.92 - 113.70: 4207 113.70 - 120.48: 3197 120.48 - 127.25: 2400 127.25 - 134.03: 108 Bond angle restraints: 10173 Sorted by residual: angle pdb=" O3P PLC B 601 " pdb=" P PLC B 601 " pdb=" O4P PLC B 601 " ideal model delta sigma weight residual 93.62 109.45 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 109.44 -15.82 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O3P PLC C 601 " pdb=" P PLC C 601 " pdb=" O4P PLC C 601 " ideal model delta sigma weight residual 93.62 109.43 -15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" N LEU B 504 " pdb=" CA LEU B 504 " pdb=" C LEU B 504 " ideal model delta sigma weight residual 113.20 106.98 6.22 1.21e+00 6.83e-01 2.64e+01 angle pdb=" N LEU C 504 " pdb=" CA LEU C 504 " pdb=" C LEU C 504 " ideal model delta sigma weight residual 113.20 107.01 6.19 1.21e+00 6.83e-01 2.62e+01 ... (remaining 10168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 4059 28.40 - 56.80: 204 56.80 - 85.21: 9 85.21 - 113.61: 3 113.61 - 142.01: 9 Dihedral angle restraints: 4284 sinusoidal: 1533 harmonic: 2751 Sorted by residual: dihedral pdb=" C5 SPH B 602 " pdb=" C3 SPH B 602 " pdb=" C4 SPH B 602 " pdb=" O3 SPH B 602 " ideal model delta sinusoidal sigma weight residual -68.94 38.58 -107.52 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5 SPH A 602 " pdb=" C3 SPH A 602 " pdb=" C4 SPH A 602 " pdb=" O3 SPH A 602 " ideal model delta sinusoidal sigma weight residual -68.94 38.55 -107.49 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5 SPH C 602 " pdb=" C3 SPH C 602 " pdb=" C4 SPH C 602 " pdb=" O3 SPH C 602 " ideal model delta sinusoidal sigma weight residual -68.94 38.48 -107.42 1 2.00e+01 2.50e-03 3.12e+01 ... (remaining 4281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 839 0.046 - 0.093: 268 0.093 - 0.139: 45 0.139 - 0.185: 15 0.185 - 0.231: 18 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA HIS A 506 " pdb=" N HIS A 506 " pdb=" C HIS A 506 " pdb=" CB HIS A 506 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA HIS C 506 " pdb=" N HIS C 506 " pdb=" C HIS C 506 " pdb=" CB HIS C 506 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA HIS B 506 " pdb=" N HIS B 506 " pdb=" C HIS B 506 " pdb=" CB HIS B 506 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1182 not shown) Planarity restraints: 1215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 423 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ALA B 423 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 423 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 424 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 423 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ALA A 423 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 423 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 424 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 423 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.04e+00 pdb=" C ALA C 423 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA C 423 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL C 424 " 0.013 2.00e-02 2.50e+03 ... (remaining 1212 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2278 2.82 - 3.34: 6913 3.34 - 3.86: 12230 3.86 - 4.38: 14632 4.38 - 4.90: 24440 Nonbonded interactions: 60493 Sorted by model distance: nonbonded pdb=" O THR B 459 " pdb=" OG1 THR B 463 " model vdw 2.299 2.440 nonbonded pdb=" O THR A 459 " pdb=" OG1 THR A 463 " model vdw 2.300 2.440 nonbonded pdb=" O THR C 459 " pdb=" OG1 THR C 463 " model vdw 2.300 2.440 nonbonded pdb=" O SER C 340 " pdb=" OG SER C 340 " model vdw 2.324 2.440 nonbonded pdb=" O SER B 340 " pdb=" OG SER B 340 " model vdw 2.325 2.440 ... (remaining 60488 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 191 through 356 or resid 358 through 512 or resid 601 thro \ ugh 602)) selection = (chain 'B' and (resid 191 through 356 or resid 358 through 512 or resid 601 thro \ ugh 602)) selection = (chain 'C' and (resid 191 through 356 or resid 358 through 512 or resid 601 thro \ ugh 602)) } 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=0.38 max=1.00 mean=0.99 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: 0.340 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: 0.010 Extract box with map and model: 2.070 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.690 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:14.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 0.071 7452 Z= 0.417 Angle : 1.058 15.827 10173 Z= 0.596 Chirality : 0.053 0.231 1185 Planarity : 0.005 0.031 1215 Dihedral : 17.729 142.011 2502 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.21 % Favored : 95.15 % Rotamer: Outliers : 4.80 % Allowed : 15.72 % Favored : 79.48 % 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: -3.26 (0.25), residues: 936 helix: -2.04 (0.17), residues: 681 sheet: None (None), residues: 0 loop : -1.92 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 215 HIS 0.005 0.001 HIS B 374 PHE 0.017 0.001 PHE A 421 TYR 0.007 0.001 TYR C 400 ARG 0.015 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 263 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7285 (mt) REVERT: A 332 ARG cc_start: 0.6296 (ttp-110) cc_final: 0.5481 (ttt90) REVERT: A 482 ARG cc_start: 0.7212 (ttm170) cc_final: 0.6940 (mtm-85) REVERT: A 491 MET cc_start: 0.7328 (ttm) cc_final: 0.7032 (ttm) REVERT: A 505 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6175 (mp) REVERT: B 263 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7087 (mt) REVERT: B 264 ARG cc_start: 0.6791 (mtm-85) cc_final: 0.6534 (mtm180) REVERT: B 327 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7538 (p) REVERT: B 332 ARG cc_start: 0.6176 (ttp-110) cc_final: 0.5386 (ttt90) REVERT: B 491 MET cc_start: 0.7502 (ttm) cc_final: 0.7290 (ttm) REVERT: B 505 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5963 (mp) REVERT: C 264 ARG cc_start: 0.6824 (mtm-85) cc_final: 0.6416 (ttp-110) REVERT: C 267 PHE cc_start: 0.7844 (t80) cc_final: 0.7499 (t80) REVERT: C 272 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6666 (mtt180) REVERT: C 331 ARG cc_start: 0.7073 (mtm-85) cc_final: 0.5703 (mmm160) REVERT: C 332 ARG cc_start: 0.6126 (ttp-110) cc_final: 0.5264 (ttt90) REVERT: C 455 TRP cc_start: 0.6427 (t-100) cc_final: 0.6210 (t-100) REVERT: C 482 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7153 (ttm-80) REVERT: C 505 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6048 (mp) outliers start: 30 outliers final: 7 residues processed: 148 average time/residue: 1.1268 time to fit residues: 176.3459 Evaluate side-chains 118 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 374 HIS C 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7452 Z= 0.166 Angle : 0.582 8.621 10173 Z= 0.285 Chirality : 0.037 0.114 1185 Planarity : 0.005 0.025 1215 Dihedral : 17.513 147.186 1183 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.33 % Allowed : 22.71 % Favored : 74.96 % 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: -1.28 (0.29), residues: 936 helix: -0.63 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.03 (0.47), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 455 HIS 0.005 0.001 HIS C 374 PHE 0.017 0.001 PHE B 260 TYR 0.017 0.001 TYR B 259 ARG 0.004 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.801 Fit side-chains REVERT: A 264 ARG cc_start: 0.6466 (mtm-85) cc_final: 0.5991 (ttp-110) REVERT: A 331 ARG cc_start: 0.7187 (mpp80) cc_final: 0.5780 (mmm160) REVERT: A 332 ARG cc_start: 0.6202 (ttp-110) cc_final: 0.5428 (ttt90) REVERT: A 471 LYS cc_start: 0.6894 (mptt) cc_final: 0.5965 (mppt) REVERT: A 482 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6973 (mtm-85) REVERT: A 491 MET cc_start: 0.7282 (ttm) cc_final: 0.7066 (ttm) REVERT: B 314 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7686 (tt) REVERT: B 331 ARG cc_start: 0.7149 (mpp80) cc_final: 0.5799 (mmm160) REVERT: B 332 ARG cc_start: 0.5937 (ttp-110) cc_final: 0.5159 (ttt90) REVERT: C 264 ARG cc_start: 0.6834 (mtm-85) cc_final: 0.6321 (ttp-110) REVERT: C 267 PHE cc_start: 0.7741 (t80) cc_final: 0.7476 (t80) REVERT: C 272 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6747 (mtt180) REVERT: C 331 ARG cc_start: 0.7012 (mtm-85) cc_final: 0.5682 (mmm160) REVERT: C 482 ARG cc_start: 0.7402 (ttm170) cc_final: 0.7144 (ttm-80) REVERT: C 501 VAL cc_start: 0.7287 (m) cc_final: 0.7075 (t) REVERT: C 505 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6198 (mt) outliers start: 13 outliers final: 0 residues processed: 121 average time/residue: 1.1657 time to fit residues: 149.3358 Evaluate side-chains 103 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN C 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7452 Z= 0.186 Angle : 0.562 8.561 10173 Z= 0.271 Chirality : 0.037 0.123 1185 Planarity : 0.004 0.025 1215 Dihedral : 16.589 150.475 1163 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.18 % Allowed : 24.75 % Favored : 73.07 % 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: -0.56 (0.29), residues: 936 helix: -0.14 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -0.60 (0.47), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 455 HIS 0.003 0.001 HIS A 303 PHE 0.015 0.001 PHE A 421 TYR 0.019 0.001 TYR A 259 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7127 (mpp80) cc_final: 0.5686 (mmm160) REVERT: A 332 ARG cc_start: 0.6248 (ttp-110) cc_final: 0.5488 (ttt90) REVERT: A 491 MET cc_start: 0.7162 (ttm) cc_final: 0.6946 (ttm) REVERT: A 505 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6163 (mp) REVERT: B 331 ARG cc_start: 0.7113 (mpp80) cc_final: 0.5780 (mmm160) REVERT: B 332 ARG cc_start: 0.6014 (ttp-110) cc_final: 0.5285 (ttt90) REVERT: C 264 ARG cc_start: 0.6663 (mtm-85) cc_final: 0.6385 (ttp-110) REVERT: C 267 PHE cc_start: 0.7711 (t80) cc_final: 0.7467 (t80) REVERT: C 272 ARG cc_start: 0.6999 (mtt180) cc_final: 0.6584 (mtt180) REVERT: C 331 ARG cc_start: 0.7036 (mtm-85) cc_final: 0.5661 (mmm160) REVERT: C 501 VAL cc_start: 0.7272 (m) cc_final: 0.7025 (t) REVERT: C 505 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5992 (mp) outliers start: 12 outliers final: 1 residues processed: 111 average time/residue: 1.1990 time to fit residues: 140.5766 Evaluate side-chains 103 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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: 0.7205 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7452 Z= 0.154 Angle : 0.532 6.106 10173 Z= 0.256 Chirality : 0.037 0.122 1185 Planarity : 0.004 0.027 1215 Dihedral : 16.062 154.096 1163 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.04 % Allowed : 25.62 % Favored : 72.34 % 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: -0.06 (0.29), residues: 936 helix: 0.28 (0.21), residues: 663 sheet: None (None), residues: 0 loop : -0.55 (0.44), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 455 HIS 0.003 0.001 HIS A 303 PHE 0.011 0.001 PHE B 421 TYR 0.017 0.001 TYR C 259 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7049 (mpp80) cc_final: 0.5733 (mmm160) REVERT: A 332 ARG cc_start: 0.6295 (ttp-110) cc_final: 0.5492 (ttt90) REVERT: A 431 MET cc_start: 0.6990 (ttm) cc_final: 0.6698 (mtp) REVERT: A 437 MET cc_start: 0.7585 (mtp) cc_final: 0.7357 (mtp) REVERT: A 490 LEU cc_start: 0.7429 (tp) cc_final: 0.7033 (mm) REVERT: A 491 MET cc_start: 0.7045 (ttm) cc_final: 0.6776 (ttm) REVERT: A 505 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6195 (mp) REVERT: B 314 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7727 (tt) REVERT: B 331 ARG cc_start: 0.7085 (mpp80) cc_final: 0.5824 (mmm160) REVERT: B 332 ARG cc_start: 0.6036 (ttp-110) cc_final: 0.5311 (ttt90) REVERT: C 224 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.6212 (mmm) REVERT: C 264 ARG cc_start: 0.6640 (mtm-85) cc_final: 0.6342 (ttp-110) REVERT: C 331 ARG cc_start: 0.7009 (mtm-85) cc_final: 0.5638 (mmm160) REVERT: C 505 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.6006 (mp) outliers start: 11 outliers final: 1 residues processed: 110 average time/residue: 1.2862 time to fit residues: 149.0967 Evaluate side-chains 106 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.0060 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 0.0470 overall best weight: 0.5094 ------------------------------------------------------------------------------- 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: 0.7194 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7452 Z= 0.146 Angle : 0.520 5.997 10173 Z= 0.252 Chirality : 0.037 0.124 1185 Planarity : 0.004 0.027 1215 Dihedral : 15.812 153.255 1163 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.20 % Allowed : 25.91 % Favored : 70.89 % 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: 0.44 (0.30), residues: 936 helix: 0.51 (0.21), residues: 654 sheet: None (None), residues: 0 loop : 0.09 (0.45), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 455 HIS 0.003 0.001 HIS A 303 PHE 0.013 0.001 PHE C 267 TYR 0.018 0.001 TYR C 259 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.752 Fit side-chains REVERT: A 331 ARG cc_start: 0.7030 (mpp80) cc_final: 0.5688 (mmm160) REVERT: A 332 ARG cc_start: 0.6301 (ttp-110) cc_final: 0.5519 (ttt90) REVERT: A 421 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: A 431 MET cc_start: 0.6963 (ttm) cc_final: 0.6608 (mtp) REVERT: A 437 MET cc_start: 0.7596 (mtp) cc_final: 0.7371 (mtp) REVERT: A 490 LEU cc_start: 0.7475 (tp) cc_final: 0.7124 (mm) REVERT: A 491 MET cc_start: 0.6992 (ttm) cc_final: 0.6750 (ttm) REVERT: A 505 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6198 (mp) REVERT: B 224 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6414 (mtm) REVERT: B 314 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7750 (tt) REVERT: B 331 ARG cc_start: 0.7067 (mpp80) cc_final: 0.5810 (mmm160) REVERT: B 332 ARG cc_start: 0.6033 (ttp-110) cc_final: 0.5334 (ttt90) REVERT: C 224 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.6174 (mmm) REVERT: C 272 ARG cc_start: 0.7132 (mtp85) cc_final: 0.6904 (mtt180) REVERT: C 331 ARG cc_start: 0.6981 (mtm-85) cc_final: 0.5626 (mmm160) REVERT: C 505 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5948 (mp) outliers start: 19 outliers final: 5 residues processed: 112 average time/residue: 1.1218 time to fit residues: 133.2584 Evaluate side-chains 113 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.0020 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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: 0.7206 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7452 Z= 0.167 Angle : 0.532 5.870 10173 Z= 0.258 Chirality : 0.037 0.127 1185 Planarity : 0.004 0.028 1215 Dihedral : 15.642 151.020 1163 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.47 % Allowed : 27.37 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.30), residues: 936 helix: 0.62 (0.21), residues: 666 sheet: None (None), residues: 0 loop : 0.06 (0.46), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 455 HIS 0.003 0.001 HIS A 303 PHE 0.024 0.001 PHE B 479 TYR 0.006 0.001 TYR B 436 ARG 0.004 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.755 Fit side-chains REVERT: A 331 ARG cc_start: 0.7016 (mpp80) cc_final: 0.5727 (mmm160) REVERT: A 332 ARG cc_start: 0.6289 (ttp-110) cc_final: 0.5499 (ttt90) REVERT: A 421 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: A 437 MET cc_start: 0.7566 (mtp) cc_final: 0.7340 (mtp) REVERT: A 490 LEU cc_start: 0.7476 (tp) cc_final: 0.7149 (mm) REVERT: A 491 MET cc_start: 0.6962 (ttm) cc_final: 0.6746 (ttm) REVERT: A 505 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6213 (mp) REVERT: B 224 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.6508 (mtm) REVERT: B 249 SER cc_start: 0.8171 (t) cc_final: 0.7952 (m) REVERT: B 314 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7717 (tt) REVERT: B 331 ARG cc_start: 0.7067 (mpp80) cc_final: 0.5896 (mmm160) REVERT: B 332 ARG cc_start: 0.6108 (ttp-110) cc_final: 0.5375 (ttt90) REVERT: C 331 ARG cc_start: 0.6967 (mtm-85) cc_final: 0.5609 (mmm160) REVERT: C 505 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5959 (mp) outliers start: 14 outliers final: 5 residues processed: 107 average time/residue: 1.1127 time to fit residues: 126.2248 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.4980 chunk 10 optimal weight: 0.0270 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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: 0.7184 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7452 Z= 0.149 Angle : 0.522 5.856 10173 Z= 0.253 Chirality : 0.037 0.125 1185 Planarity : 0.003 0.028 1215 Dihedral : 15.448 149.700 1163 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.47 % Allowed : 27.37 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.30), residues: 936 helix: 0.77 (0.21), residues: 666 sheet: None (None), residues: 0 loop : 0.11 (0.45), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 455 HIS 0.003 0.001 HIS A 303 PHE 0.025 0.001 PHE C 479 TYR 0.006 0.001 TYR A 436 ARG 0.003 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.676 Fit side-chains REVERT: A 331 ARG cc_start: 0.6969 (mpp80) cc_final: 0.5717 (mmm160) REVERT: A 332 ARG cc_start: 0.6300 (ttp-110) cc_final: 0.5506 (ttt90) REVERT: A 421 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: A 490 LEU cc_start: 0.7474 (tp) cc_final: 0.7160 (mm) REVERT: A 491 MET cc_start: 0.6946 (ttm) cc_final: 0.6708 (ttm) REVERT: A 505 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6196 (mp) REVERT: B 224 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6452 (mtm) REVERT: B 249 SER cc_start: 0.8145 (t) cc_final: 0.7928 (m) REVERT: B 314 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7706 (tt) REVERT: B 331 ARG cc_start: 0.7007 (mpp80) cc_final: 0.5856 (mmm160) REVERT: B 332 ARG cc_start: 0.6142 (ttp-110) cc_final: 0.5412 (ttt90) REVERT: C 249 SER cc_start: 0.7991 (t) cc_final: 0.7750 (m) REVERT: C 302 MET cc_start: 0.7852 (tmm) cc_final: 0.6354 (tpp) REVERT: C 331 ARG cc_start: 0.6949 (mtm-85) cc_final: 0.5599 (mmm160) outliers start: 14 outliers final: 4 residues processed: 108 average time/residue: 1.1202 time to fit residues: 128.3044 Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 474 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7452 Z= 0.157 Angle : 0.520 6.157 10173 Z= 0.253 Chirality : 0.037 0.126 1185 Planarity : 0.003 0.028 1215 Dihedral : 15.235 147.353 1161 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.33 % Allowed : 27.95 % Favored : 69.72 % 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: 0.82 (0.30), residues: 936 helix: 0.80 (0.21), residues: 669 sheet: None (None), residues: 0 loop : 0.18 (0.45), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 455 HIS 0.003 0.001 HIS A 303 PHE 0.022 0.001 PHE C 479 TYR 0.005 0.001 TYR C 252 ARG 0.003 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.868 Fit side-chains REVERT: A 331 ARG cc_start: 0.6960 (mpp80) cc_final: 0.5706 (mmm160) REVERT: A 332 ARG cc_start: 0.6232 (ttp-110) cc_final: 0.5466 (ttt90) REVERT: A 421 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: A 490 LEU cc_start: 0.7403 (tp) cc_final: 0.7074 (mm) REVERT: A 505 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6207 (mp) REVERT: B 224 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6545 (mtm) REVERT: B 249 SER cc_start: 0.8169 (t) cc_final: 0.7944 (m) REVERT: B 314 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7733 (tt) REVERT: B 331 ARG cc_start: 0.7016 (mpp80) cc_final: 0.5822 (mmm160) REVERT: B 332 ARG cc_start: 0.6189 (ttp-110) cc_final: 0.5393 (ttt90) REVERT: C 249 SER cc_start: 0.7997 (t) cc_final: 0.7745 (m) REVERT: C 302 MET cc_start: 0.7916 (tmm) cc_final: 0.6587 (tpp) REVERT: C 331 ARG cc_start: 0.6945 (mtm-85) cc_final: 0.5598 (mmm160) outliers start: 13 outliers final: 5 residues processed: 108 average time/residue: 1.1415 time to fit residues: 130.6256 Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 474 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7452 Z= 0.151 Angle : 0.517 6.709 10173 Z= 0.252 Chirality : 0.037 0.124 1185 Planarity : 0.004 0.036 1215 Dihedral : 15.131 146.227 1161 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.47 % Allowed : 27.66 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.29), residues: 936 helix: 0.89 (0.21), residues: 669 sheet: None (None), residues: 0 loop : 0.19 (0.44), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 455 HIS 0.003 0.001 HIS A 303 PHE 0.022 0.001 PHE C 479 TYR 0.005 0.001 TYR C 252 ARG 0.003 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.783 Fit side-chains REVERT: A 331 ARG cc_start: 0.6941 (mpp80) cc_final: 0.5689 (mmm160) REVERT: A 332 ARG cc_start: 0.6246 (ttp-110) cc_final: 0.5455 (ttt90) REVERT: A 421 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: A 490 LEU cc_start: 0.7427 (tp) cc_final: 0.7091 (mm) REVERT: A 491 MET cc_start: 0.6962 (ttm) cc_final: 0.6743 (ttm) REVERT: A 505 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6197 (mp) REVERT: B 224 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6459 (mtm) REVERT: B 249 SER cc_start: 0.8160 (t) cc_final: 0.7949 (m) REVERT: B 314 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7716 (tt) REVERT: B 331 ARG cc_start: 0.7023 (mpp80) cc_final: 0.5843 (mmm160) REVERT: B 332 ARG cc_start: 0.6198 (ttp-110) cc_final: 0.5394 (ttt90) REVERT: C 224 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.6569 (mtm) REVERT: C 302 MET cc_start: 0.7881 (tmm) cc_final: 0.6613 (tpp) REVERT: C 331 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.5592 (mmm160) REVERT: C 498 LEU cc_start: 0.6952 (mp) cc_final: 0.6701 (pp) outliers start: 14 outliers final: 5 residues processed: 108 average time/residue: 1.1667 time to fit residues: 133.4213 Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 0.0070 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 45 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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: 0.7143 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7452 Z= 0.130 Angle : 0.508 6.548 10173 Z= 0.246 Chirality : 0.036 0.122 1185 Planarity : 0.003 0.032 1215 Dihedral : 15.014 145.007 1161 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.18 % Allowed : 27.80 % Favored : 70.01 % 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: 0.98 (0.29), residues: 936 helix: 0.94 (0.21), residues: 684 sheet: None (None), residues: 0 loop : 0.12 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 455 HIS 0.002 0.001 HIS A 303 PHE 0.022 0.001 PHE C 479 TYR 0.005 0.001 TYR B 418 ARG 0.003 0.000 ARG C 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.695 Fit side-chains REVERT: A 331 ARG cc_start: 0.6879 (mpp80) cc_final: 0.5646 (mmm160) REVERT: A 332 ARG cc_start: 0.6344 (ttp-110) cc_final: 0.5519 (ttt90) REVERT: A 490 LEU cc_start: 0.7393 (tp) cc_final: 0.7079 (mm) REVERT: A 491 MET cc_start: 0.6949 (ttm) cc_final: 0.6716 (ttm) REVERT: A 505 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6097 (mp) REVERT: B 224 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6558 (mtm) REVERT: B 314 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7715 (tt) REVERT: B 331 ARG cc_start: 0.6908 (mpp80) cc_final: 0.5849 (mmm160) REVERT: B 332 ARG cc_start: 0.6180 (ttp-110) cc_final: 0.5367 (ttt90) REVERT: C 224 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6570 (mtm) REVERT: C 331 ARG cc_start: 0.6957 (mtm-85) cc_final: 0.5583 (mmm160) outliers start: 12 outliers final: 2 residues processed: 109 average time/residue: 1.1416 time to fit residues: 131.7332 Evaluate side-chains 110 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.159672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113791 restraints weight = 23745.583| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.16 r_work: 0.2924 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7452 Z= 0.160 Angle : 0.526 6.543 10173 Z= 0.255 Chirality : 0.037 0.127 1185 Planarity : 0.004 0.033 1215 Dihedral : 14.971 142.920 1161 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.75 % Allowed : 28.24 % Favored : 70.01 % 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: 0.96 (0.29), residues: 936 helix: 0.91 (0.21), residues: 687 sheet: None (None), residues: 0 loop : 0.16 (0.45), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 455 HIS 0.003 0.001 HIS A 303 PHE 0.021 0.001 PHE C 479 TYR 0.005 0.001 TYR C 252 ARG 0.003 0.000 ARG C 442 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2839.59 seconds wall clock time: 51 minutes 23.30 seconds (3083.30 seconds total)