Starting phenix.real_space_refine on Sun Feb 18 07:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lgp_0882/02_2024/6lgp_0882_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lgp_0882/02_2024/6lgp_0882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lgp_0882/02_2024/6lgp_0882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lgp_0882/02_2024/6lgp_0882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lgp_0882/02_2024/6lgp_0882_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lgp_0882/02_2024/6lgp_0882_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.015 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 20 5.49 5 S 120 5.16 5 C 13940 2.51 5 N 3348 2.21 5 O 3784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A GLU 679": "OE1" <-> "OE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ASP 725": "OD1" <-> "OD2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ASP 752": "OD1" <-> "OD2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ASP 618": "OD1" <-> "OD2" Residue "B GLU 679": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ASP 725": "OD1" <-> "OD2" Residue "B GLU 726": "OE1" <-> "OE2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B GLU 741": "OE1" <-> "OE2" Residue "B ASP 752": "OD1" <-> "OD2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ASP 618": "OD1" <-> "OD2" Residue "C GLU 679": "OE1" <-> "OE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ASP 725": "OD1" <-> "OD2" Residue "C GLU 726": "OE1" <-> "OE2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C GLU 741": "OE1" <-> "OE2" Residue "C ASP 752": "OD1" <-> "OD2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D GLU 355": "OE1" <-> "OE2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ASP 618": "OD1" <-> "OD2" Residue "D GLU 679": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ASP 725": "OD1" <-> "OD2" Residue "D GLU 726": "OE1" <-> "OE2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D GLU 741": "OE1" <-> "OE2" Residue "D ASP 752": "OD1" <-> "OD2" 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: 21212 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5061 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 15, 'TRANS': 606} Chain breaks: 1 Chain: "B" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5061 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 15, 'TRANS': 606} Chain breaks: 1 Chain: "C" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5061 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 15, 'TRANS': 606} Chain breaks: 1 Chain: "D" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5061 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 15, 'TRANS': 606} Chain breaks: 1 Chain: "A" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PLC': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PLC': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PLC': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PLC': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 11.52, per 1000 atoms: 0.54 Number of scatterers: 21212 At special positions: 0 Unit cell: (152.25, 152.25, 130.5, 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 120 16.00 P 20 15.00 O 3784 8.00 N 3348 7.00 C 13940 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: 8.39 Conformation dependent library (CDL) restraints added in 3.4 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 4 sheets defined 54.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 147 Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 201 through 204 No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.748A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 437 through 460 removed outlier: 3.519A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 521 through 540 Processing helix chain 'A' and resid 548 through 568 removed outlier: 3.578A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLY A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 578 through 585 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 669 through 684 Processing helix chain 'A' and resid 688 through 706 removed outlier: 4.129A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 132 through 147 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 201 through 204 No H-bonds generated for 'chain 'B' and resid 201 through 204' Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 230 through 236 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 344 through 350 removed outlier: 3.748A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 423 through 435 Processing helix chain 'B' and resid 437 through 460 removed outlier: 3.519A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 508 Processing helix chain 'B' and resid 521 through 540 Processing helix chain 'B' and resid 548 through 568 removed outlier: 3.578A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLY B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 575 Processing helix chain 'B' and resid 578 through 585 Processing helix chain 'B' and resid 587 through 608 Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 669 through 684 Processing helix chain 'B' and resid 688 through 706 removed outlier: 4.129A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 132 through 147 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 201 through 204 No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 230 through 236 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 344 through 350 removed outlier: 3.748A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 437 through 460 removed outlier: 3.519A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 508 Processing helix chain 'C' and resid 521 through 540 Processing helix chain 'C' and resid 548 through 568 removed outlier: 3.578A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLY C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 575 Processing helix chain 'C' and resid 578 through 585 Processing helix chain 'C' and resid 587 through 608 Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 669 through 684 Processing helix chain 'C' and resid 688 through 706 removed outlier: 4.129A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 132 through 147 Processing helix chain 'D' and resid 154 through 162 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 201 through 204 No H-bonds generated for 'chain 'D' and resid 201 through 204' Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 230 through 236 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 344 through 350 removed outlier: 3.748A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 423 through 435 Processing helix chain 'D' and resid 437 through 460 removed outlier: 3.519A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 508 Processing helix chain 'D' and resid 521 through 540 Processing helix chain 'D' and resid 548 through 568 removed outlier: 3.578A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLY D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 575 Processing helix chain 'D' and resid 578 through 585 Processing helix chain 'D' and resid 587 through 608 Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 651 through 665 Processing helix chain 'D' and resid 669 through 684 Processing helix chain 'D' and resid 688 through 706 removed outlier: 4.129A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 Processing sheet with id= A, first strand: chain 'A' and resid 376 through 378 Processing sheet with id= B, first strand: chain 'B' and resid 376 through 378 Processing sheet with id= C, first strand: chain 'C' and resid 376 through 378 Processing sheet with id= D, first strand: chain 'D' and resid 376 through 378 892 hydrogen bonds defined for protein. 2664 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: 5.69 Time building geometry restraints manager: 9.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3492 1.32 - 1.44: 5448 1.44 - 1.56: 12436 1.56 - 1.69: 40 1.69 - 1.81: 196 Bond restraints: 21612 Sorted by residual: bond pdb=" CA SER B 576 " pdb=" C SER B 576 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.72e-02 3.38e+03 1.08e+01 bond pdb=" CA SER C 576 " pdb=" C SER C 576 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.72e-02 3.38e+03 1.08e+01 bond pdb=" CA SER A 576 " pdb=" C SER A 576 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.72e-02 3.38e+03 1.08e+01 bond pdb=" CA SER D 576 " pdb=" C SER D 576 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.72e-02 3.38e+03 1.08e+01 bond pdb=" O12 POV C 802 " pdb=" P POV C 802 " ideal model delta sigma weight residual 1.657 1.602 0.055 2.00e-02 2.50e+03 7.58e+00 ... (remaining 21607 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.10: 332 106.10 - 113.08: 11540 113.08 - 120.07: 8476 120.07 - 127.06: 8516 127.06 - 134.05: 184 Bond angle restraints: 29048 Sorted by residual: angle pdb=" N ILE D 199 " pdb=" CA ILE D 199 " pdb=" C ILE D 199 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N ILE B 199 " pdb=" CA ILE B 199 " pdb=" C ILE B 199 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N ILE C 199 " pdb=" CA ILE C 199 " pdb=" C ILE C 199 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N ILE A 199 " pdb=" CA ILE A 199 " pdb=" C ILE A 199 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" O3P PLC D 804 " pdb=" P PLC D 804 " pdb=" O4P PLC D 804 " ideal model delta sigma weight residual 93.62 104.65 -11.03 3.00e+00 1.11e-01 1.35e+01 ... (remaining 29043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 12788 35.49 - 70.98: 308 70.98 - 106.48: 28 106.48 - 141.97: 32 141.97 - 177.46: 8 Dihedral angle restraints: 13164 sinusoidal: 5828 harmonic: 7336 Sorted by residual: dihedral pdb=" C1B PLC A1002 " pdb=" CB PLC A1002 " pdb=" O3 PLC A1002 " pdb=" C3 PLC A1002 " ideal model delta sinusoidal sigma weight residual 181.23 3.77 177.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1B PLC D 804 " pdb=" CB PLC D 804 " pdb=" O3 PLC D 804 " pdb=" C3 PLC D 804 " ideal model delta sinusoidal sigma weight residual 181.23 3.77 177.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1B PLC B 803 " pdb=" CB PLC B 803 " pdb=" O3 PLC B 803 " pdb=" C3 PLC B 803 " ideal model delta sinusoidal sigma weight residual 181.23 3.77 177.46 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2844 0.068 - 0.137: 356 0.137 - 0.205: 8 0.205 - 0.274: 12 0.274 - 0.342: 4 Chirality restraints: 3224 Sorted by residual: chirality pdb=" C2 PLC D 805 " pdb=" C1 PLC D 805 " pdb=" C3 PLC D 805 " pdb=" O2 PLC D 805 " both_signs ideal model delta sigma weight residual False -2.31 -2.65 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C2 PLC A1003 " pdb=" C1 PLC A1003 " pdb=" C3 PLC A1003 " pdb=" O2 PLC A1003 " both_signs ideal model delta sigma weight residual False -2.31 -2.65 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C2 PLC C 804 " pdb=" C1 PLC C 804 " pdb=" C3 PLC C 804 " pdb=" O2 PLC C 804 " both_signs ideal model delta sigma weight residual False -2.31 -2.65 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 3221 not shown) Planarity restraints: 3536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1006 " 0.094 2.00e-02 2.50e+03 9.17e-02 8.40e+01 pdb=" C29 POV A1006 " -0.106 2.00e-02 2.50e+03 pdb="C210 POV A1006 " -0.076 2.00e-02 2.50e+03 pdb="C211 POV A1006 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 801 " -0.094 2.00e-02 2.50e+03 9.17e-02 8.40e+01 pdb=" C29 POV D 801 " 0.106 2.00e-02 2.50e+03 pdb="C210 POV D 801 " 0.076 2.00e-02 2.50e+03 pdb="C211 POV D 801 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 807 " -0.094 2.00e-02 2.50e+03 9.17e-02 8.40e+01 pdb=" C29 POV C 807 " 0.106 2.00e-02 2.50e+03 pdb="C210 POV C 807 " 0.076 2.00e-02 2.50e+03 pdb="C211 POV C 807 " -0.088 2.00e-02 2.50e+03 ... (remaining 3533 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 224 2.63 - 3.20: 19484 3.20 - 3.77: 30196 3.77 - 4.33: 43916 4.33 - 4.90: 73662 Nonbonded interactions: 167482 Sorted by model distance: nonbonded pdb=" OH TYR C 213 " pdb=" O PRO D 753 " model vdw 2.065 2.440 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR D 213 " model vdw 2.065 2.440 nonbonded pdb=" OH TYR B 213 " pdb=" O PRO C 753 " model vdw 2.065 2.440 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO B 753 " model vdw 2.065 2.440 nonbonded pdb=" O GLN B 514 " pdb=" OG SER B 518 " model vdw 2.184 2.440 ... (remaining 167477 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 118 through 756 or (resid 1006 and (name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 310 or name C311 or name C312 or name C313 or name C314)))) selection = (chain 'B' and (resid 118 through 756 or resid 806)) selection = (chain 'C' and (resid 118 through 756 or resid 806)) selection = (chain 'D' and (resid 118 through 756 or resid 806)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 2.110 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 55.040 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.140 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.008 0.056 21612 Z= 0.548 Angle : 0.852 11.035 29048 Z= 0.462 Chirality : 0.048 0.342 3224 Planarity : 0.005 0.092 3536 Dihedral : 18.349 177.458 8404 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.65 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % 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: -4.33 (0.13), residues: 2472 helix: -2.16 (0.10), residues: 1572 sheet: -3.19 (0.45), residues: 84 loop : -4.07 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 380 HIS 0.008 0.001 HIS A 301 PHE 0.017 0.002 PHE A 316 TYR 0.024 0.002 TYR B 260 ARG 0.004 0.000 ARG D 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.251 Fit side-chains REVERT: A 138 LEU cc_start: 0.7991 (mt) cc_final: 0.7690 (mt) REVERT: A 173 MET cc_start: 0.8576 (mtm) cc_final: 0.8205 (mtp) REVERT: A 211 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7793 (mp0) REVERT: A 655 LEU cc_start: 0.8535 (mm) cc_final: 0.8310 (mt) REVERT: A 687 GLU cc_start: 0.8438 (pp20) cc_final: 0.8060 (pp20) REVERT: A 714 ARG cc_start: 0.7561 (ttt-90) cc_final: 0.7106 (ttm170) REVERT: A 738 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8525 (mtpp) REVERT: B 138 LEU cc_start: 0.7987 (mt) cc_final: 0.7686 (mt) REVERT: B 173 MET cc_start: 0.8574 (mtm) cc_final: 0.8206 (mtp) REVERT: B 211 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7791 (mp0) REVERT: B 655 LEU cc_start: 0.8537 (mm) cc_final: 0.8313 (mt) REVERT: B 687 GLU cc_start: 0.8434 (pp20) cc_final: 0.8061 (pp20) REVERT: B 714 ARG cc_start: 0.7561 (ttt-90) cc_final: 0.7107 (ttm170) REVERT: B 738 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8523 (mtpp) REVERT: C 138 LEU cc_start: 0.7994 (mt) cc_final: 0.7691 (mt) REVERT: C 173 MET cc_start: 0.8576 (mtm) cc_final: 0.8207 (mtp) REVERT: C 211 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7796 (mp0) REVERT: C 655 LEU cc_start: 0.8539 (mm) cc_final: 0.8313 (mt) REVERT: C 687 GLU cc_start: 0.8433 (pp20) cc_final: 0.8057 (pp20) REVERT: C 714 ARG cc_start: 0.7559 (ttt-90) cc_final: 0.7106 (ttm170) REVERT: C 738 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8520 (mtpp) REVERT: D 138 LEU cc_start: 0.7992 (mt) cc_final: 0.7687 (mt) REVERT: D 173 MET cc_start: 0.8570 (mtm) cc_final: 0.8195 (mtp) REVERT: D 211 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7793 (mp0) REVERT: D 655 LEU cc_start: 0.8540 (mm) cc_final: 0.8315 (mt) REVERT: D 687 GLU cc_start: 0.8438 (pp20) cc_final: 0.8059 (pp20) REVERT: D 714 ARG cc_start: 0.7558 (ttt-90) cc_final: 0.7103 (ttm170) REVERT: D 738 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8522 (mtpp) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.4066 time to fit residues: 198.2627 Evaluate side-chains 260 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 194 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 216 GLN A 279 GLN A 297 ASN A 671 ASN A 683 ASN B 197 ASN B 216 GLN B 279 GLN B 297 ASN B 671 ASN B 683 ASN C 197 ASN C 216 GLN C 279 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN C 683 ASN D 197 ASN D 216 GLN D 279 GLN D 297 ASN D 671 ASN D 683 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21612 Z= 0.164 Angle : 0.574 7.882 29048 Z= 0.286 Chirality : 0.037 0.123 3224 Planarity : 0.003 0.026 3536 Dihedral : 15.112 134.121 3520 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 1.08 % Allowed : 13.18 % Favored : 85.74 % 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: -2.42 (0.16), residues: 2472 helix: -0.44 (0.12), residues: 1608 sheet: -2.84 (0.45), residues: 84 loop : -3.94 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 380 HIS 0.004 0.001 HIS C 301 PHE 0.024 0.001 PHE A 193 TYR 0.010 0.001 TYR B 321 ARG 0.003 0.000 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 325 time to evaluate : 2.369 Fit side-chains REVERT: A 122 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6319 (mtp180) REVERT: A 138 LEU cc_start: 0.8153 (mt) cc_final: 0.7874 (mt) REVERT: A 173 MET cc_start: 0.8462 (mtm) cc_final: 0.8172 (mtp) REVERT: A 174 LYS cc_start: 0.8596 (tttt) cc_final: 0.8193 (tttm) REVERT: A 211 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7681 (mp0) REVERT: A 327 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.6797 (tmt-80) REVERT: A 687 GLU cc_start: 0.8458 (pp20) cc_final: 0.7808 (pp20) REVERT: A 704 GLU cc_start: 0.7312 (tt0) cc_final: 0.6934 (tt0) REVERT: A 714 ARG cc_start: 0.7582 (ttt-90) cc_final: 0.7100 (ttm170) REVERT: B 122 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6312 (mtp180) REVERT: B 138 LEU cc_start: 0.8151 (mt) cc_final: 0.7871 (mt) REVERT: B 173 MET cc_start: 0.8465 (mtm) cc_final: 0.8177 (mtp) REVERT: B 174 LYS cc_start: 0.8595 (tttt) cc_final: 0.8191 (tttm) REVERT: B 211 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7675 (mp0) REVERT: B 327 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.6790 (tmt-80) REVERT: B 687 GLU cc_start: 0.8454 (pp20) cc_final: 0.7810 (pp20) REVERT: B 704 GLU cc_start: 0.7314 (tt0) cc_final: 0.6937 (tt0) REVERT: B 714 ARG cc_start: 0.7581 (ttt-90) cc_final: 0.7099 (ttm170) REVERT: C 122 ARG cc_start: 0.7095 (mtt180) cc_final: 0.6314 (mtp180) REVERT: C 138 LEU cc_start: 0.8153 (mt) cc_final: 0.7870 (mt) REVERT: C 173 MET cc_start: 0.8464 (mtm) cc_final: 0.8173 (mtp) REVERT: C 174 LYS cc_start: 0.8590 (tttt) cc_final: 0.8189 (tttm) REVERT: C 211 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7676 (mp0) REVERT: C 327 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6797 (tmt-80) REVERT: C 687 GLU cc_start: 0.8455 (pp20) cc_final: 0.7807 (pp20) REVERT: C 704 GLU cc_start: 0.7321 (tt0) cc_final: 0.6939 (tt0) REVERT: C 714 ARG cc_start: 0.7581 (ttt-90) cc_final: 0.7098 (ttm170) REVERT: D 122 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6312 (mtp180) REVERT: D 138 LEU cc_start: 0.8150 (mt) cc_final: 0.7871 (mt) REVERT: D 173 MET cc_start: 0.8460 (mtm) cc_final: 0.8166 (mtp) REVERT: D 174 LYS cc_start: 0.8594 (tttt) cc_final: 0.8190 (tttm) REVERT: D 211 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7678 (mp0) REVERT: D 327 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.6793 (tmt-80) REVERT: D 687 GLU cc_start: 0.8457 (pp20) cc_final: 0.7806 (pp20) REVERT: D 704 GLU cc_start: 0.7319 (tt0) cc_final: 0.6941 (tt0) REVERT: D 714 ARG cc_start: 0.7582 (ttt-90) cc_final: 0.7097 (ttm170) outliers start: 24 outliers final: 16 residues processed: 341 average time/residue: 0.3646 time to fit residues: 187.4170 Evaluate side-chains 304 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 288 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 243 optimal weight: 0.0270 chunk 200 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 256 HIS A 745 HIS B 244 HIS B 256 HIS B 745 HIS C 244 HIS C 256 HIS C 297 ASN C 745 HIS D 244 HIS D 256 HIS D 745 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21612 Z= 0.259 Angle : 0.591 9.417 29048 Z= 0.294 Chirality : 0.040 0.136 3224 Planarity : 0.003 0.028 3536 Dihedral : 14.281 127.028 3520 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.53 % Allowed : 16.79 % Favored : 80.69 % 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: -1.59 (0.17), residues: 2472 helix: 0.27 (0.13), residues: 1608 sheet: -2.58 (0.47), residues: 84 loop : -3.80 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 380 HIS 0.005 0.001 HIS D 301 PHE 0.018 0.002 PHE C 506 TYR 0.020 0.002 TYR A 260 ARG 0.001 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 293 time to evaluate : 2.756 Fit side-chains REVERT: A 174 LYS cc_start: 0.8527 (tttt) cc_final: 0.8128 (tttm) REVERT: A 179 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6220 (tp) REVERT: A 211 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7784 (mp0) REVERT: A 327 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.6849 (tpt170) REVERT: A 677 MET cc_start: 0.8475 (mtm) cc_final: 0.8116 (mtp) REVERT: A 687 GLU cc_start: 0.8439 (pp20) cc_final: 0.8141 (pp20) REVERT: A 704 GLU cc_start: 0.7249 (tt0) cc_final: 0.6943 (tt0) REVERT: A 714 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.7004 (ttm170) REVERT: B 174 LYS cc_start: 0.8525 (tttt) cc_final: 0.8125 (tttm) REVERT: B 179 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6214 (tp) REVERT: B 211 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7780 (mp0) REVERT: B 327 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.6846 (tpt170) REVERT: B 677 MET cc_start: 0.8475 (mtm) cc_final: 0.8128 (mtp) REVERT: B 687 GLU cc_start: 0.8435 (pp20) cc_final: 0.8139 (pp20) REVERT: B 704 GLU cc_start: 0.7249 (tt0) cc_final: 0.6946 (tt0) REVERT: B 714 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.7002 (ttm170) REVERT: C 174 LYS cc_start: 0.8521 (tttt) cc_final: 0.8126 (tttm) REVERT: C 179 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6210 (tp) REVERT: C 211 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7778 (mp0) REVERT: C 327 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.6850 (tpt170) REVERT: C 677 MET cc_start: 0.8481 (mtm) cc_final: 0.8149 (mtp) REVERT: C 687 GLU cc_start: 0.8435 (pp20) cc_final: 0.8137 (pp20) REVERT: C 704 GLU cc_start: 0.7251 (tt0) cc_final: 0.6944 (tt0) REVERT: C 714 ARG cc_start: 0.7521 (ttt-90) cc_final: 0.7002 (ttm170) REVERT: D 174 LYS cc_start: 0.8525 (tttt) cc_final: 0.8126 (tttm) REVERT: D 179 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6207 (tp) REVERT: D 211 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7782 (mp0) REVERT: D 327 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.6845 (tpt170) REVERT: D 677 MET cc_start: 0.8480 (mtm) cc_final: 0.8132 (mtp) REVERT: D 687 GLU cc_start: 0.8438 (pp20) cc_final: 0.8138 (pp20) REVERT: D 704 GLU cc_start: 0.7249 (tt0) cc_final: 0.6941 (tt0) REVERT: D 714 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.7001 (ttm170) outliers start: 56 outliers final: 36 residues processed: 345 average time/residue: 0.3410 time to fit residues: 177.4679 Evaluate side-chains 333 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 293 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 239 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 197 ASN C 197 ASN D 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21612 Z= 0.234 Angle : 0.572 9.157 29048 Z= 0.286 Chirality : 0.040 0.310 3224 Planarity : 0.003 0.028 3536 Dihedral : 13.967 109.988 3520 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.89 % Allowed : 17.69 % Favored : 79.42 % 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: -1.21 (0.17), residues: 2472 helix: 0.56 (0.13), residues: 1612 sheet: -2.38 (0.49), residues: 84 loop : -3.66 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 380 HIS 0.005 0.001 HIS D 301 PHE 0.014 0.001 PHE C 506 TYR 0.017 0.002 TYR A 260 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 317 time to evaluate : 2.294 Fit side-chains REVERT: A 122 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6457 (mtp-110) REVERT: A 174 LYS cc_start: 0.8484 (tttt) cc_final: 0.8034 (tttm) REVERT: A 179 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6108 (tp) REVERT: A 211 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7782 (mp0) REVERT: A 327 ARG cc_start: 0.7543 (mmm-85) cc_final: 0.6801 (tpt170) REVERT: A 687 GLU cc_start: 0.8407 (pp20) cc_final: 0.8049 (pp20) REVERT: A 704 GLU cc_start: 0.7258 (tt0) cc_final: 0.6940 (tt0) REVERT: A 714 ARG cc_start: 0.7473 (ttt-90) cc_final: 0.6966 (ttm170) REVERT: B 122 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6455 (mtp-110) REVERT: B 174 LYS cc_start: 0.8482 (tttt) cc_final: 0.8032 (tttm) REVERT: B 179 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.6105 (tp) REVERT: B 211 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7776 (mp0) REVERT: B 327 ARG cc_start: 0.7542 (mmm-85) cc_final: 0.6797 (tpt170) REVERT: B 687 GLU cc_start: 0.8405 (pp20) cc_final: 0.8048 (pp20) REVERT: B 704 GLU cc_start: 0.7256 (tt0) cc_final: 0.6940 (tt0) REVERT: B 714 ARG cc_start: 0.7474 (ttt-90) cc_final: 0.6965 (ttm170) REVERT: C 122 ARG cc_start: 0.7386 (mtt180) cc_final: 0.6456 (mtp-110) REVERT: C 174 LYS cc_start: 0.8478 (tttt) cc_final: 0.8030 (tttm) REVERT: C 179 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.6098 (tp) REVERT: C 211 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7777 (mp0) REVERT: C 327 ARG cc_start: 0.7543 (mmm-85) cc_final: 0.6799 (tpt170) REVERT: C 687 GLU cc_start: 0.8406 (pp20) cc_final: 0.8047 (pp20) REVERT: C 704 GLU cc_start: 0.7266 (tt0) cc_final: 0.6941 (tt0) REVERT: C 714 ARG cc_start: 0.7472 (ttt-90) cc_final: 0.6964 (ttm170) REVERT: D 122 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6456 (mtp-110) REVERT: D 174 LYS cc_start: 0.8480 (tttt) cc_final: 0.8030 (tttm) REVERT: D 179 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6104 (tp) REVERT: D 211 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7781 (mp0) REVERT: D 327 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.6798 (tpt170) REVERT: D 687 GLU cc_start: 0.8408 (pp20) cc_final: 0.8049 (pp20) REVERT: D 704 GLU cc_start: 0.7263 (tt0) cc_final: 0.6941 (tt0) REVERT: D 714 ARG cc_start: 0.7474 (ttt-90) cc_final: 0.6964 (ttm170) outliers start: 64 outliers final: 46 residues processed: 373 average time/residue: 0.3494 time to fit residues: 195.4113 Evaluate side-chains 343 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 293 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 6.9990 chunk 136 optimal weight: 0.0570 chunk 3 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.6102 ------------------------------------------------------------------------------- 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: 0.7740 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21612 Z= 0.206 Angle : 0.581 9.420 29048 Z= 0.282 Chirality : 0.040 0.312 3224 Planarity : 0.003 0.030 3536 Dihedral : 13.720 106.921 3520 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 2.89 % Allowed : 19.86 % Favored : 77.26 % 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 (0.17), residues: 2472 helix: 0.77 (0.13), residues: 1612 sheet: -2.21 (0.50), residues: 84 loop : -3.64 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 380 HIS 0.004 0.001 HIS A 301 PHE 0.019 0.001 PHE C 506 TYR 0.016 0.001 TYR A 260 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 300 time to evaluate : 2.409 Fit side-chains REVERT: A 174 LYS cc_start: 0.8429 (tttt) cc_final: 0.8050 (tttm) REVERT: A 179 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6020 (tp) REVERT: A 199 ILE cc_start: 0.7248 (tp) cc_final: 0.7007 (tp) REVERT: A 327 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.6826 (tpt170) REVERT: A 488 MET cc_start: 0.6752 (ptm) cc_final: 0.4937 (mmt) REVERT: A 677 MET cc_start: 0.8750 (mtm) cc_final: 0.8330 (mtp) REVERT: A 687 GLU cc_start: 0.8396 (pp20) cc_final: 0.8043 (pp20) REVERT: A 704 GLU cc_start: 0.7247 (tt0) cc_final: 0.6939 (tt0) REVERT: A 714 ARG cc_start: 0.7468 (ttt-90) cc_final: 0.7007 (ttm170) REVERT: B 174 LYS cc_start: 0.8427 (tttt) cc_final: 0.8046 (tttm) REVERT: B 179 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6021 (tp) REVERT: B 199 ILE cc_start: 0.7239 (tp) cc_final: 0.7001 (tp) REVERT: B 327 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.6822 (tpt170) REVERT: B 488 MET cc_start: 0.6882 (ptm) cc_final: 0.5142 (mmt) REVERT: B 677 MET cc_start: 0.8738 (mtm) cc_final: 0.8341 (mtp) REVERT: B 687 GLU cc_start: 0.8394 (pp20) cc_final: 0.8045 (pp20) REVERT: B 704 GLU cc_start: 0.7245 (tt0) cc_final: 0.6941 (tt0) REVERT: B 714 ARG cc_start: 0.7467 (ttt-90) cc_final: 0.7006 (ttm170) REVERT: C 174 LYS cc_start: 0.8427 (tttt) cc_final: 0.8053 (tttm) REVERT: C 179 ILE cc_start: 0.6518 (OUTLIER) cc_final: 0.6013 (tp) REVERT: C 199 ILE cc_start: 0.7232 (tp) cc_final: 0.6998 (tp) REVERT: C 327 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.6823 (tpt170) REVERT: C 488 MET cc_start: 0.6887 (ptm) cc_final: 0.5142 (mmt) REVERT: C 677 MET cc_start: 0.8755 (mtm) cc_final: 0.8364 (mtp) REVERT: C 687 GLU cc_start: 0.8398 (pp20) cc_final: 0.8042 (pp20) REVERT: C 704 GLU cc_start: 0.7254 (tt0) cc_final: 0.6941 (tt0) REVERT: C 714 ARG cc_start: 0.7466 (ttt-90) cc_final: 0.7005 (ttm170) REVERT: D 174 LYS cc_start: 0.8428 (tttt) cc_final: 0.8047 (tttm) REVERT: D 179 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6033 (tp) REVERT: D 199 ILE cc_start: 0.7236 (tp) cc_final: 0.6999 (tp) REVERT: D 327 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.6824 (tpt170) REVERT: D 488 MET cc_start: 0.6758 (ptm) cc_final: 0.4943 (mmt) REVERT: D 677 MET cc_start: 0.8766 (mtm) cc_final: 0.8352 (mtp) REVERT: D 687 GLU cc_start: 0.8399 (pp20) cc_final: 0.8043 (pp20) REVERT: D 704 GLU cc_start: 0.7252 (tt0) cc_final: 0.6939 (tt0) REVERT: D 714 ARG cc_start: 0.7468 (ttt-90) cc_final: 0.7005 (ttm170) outliers start: 64 outliers final: 52 residues processed: 350 average time/residue: 0.3428 time to fit residues: 181.9160 Evaluate side-chains 348 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 292 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.9980 chunk 215 optimal weight: 0.0070 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 239 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 79 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 251 ASN A 745 HIS B 227 GLN B 251 ASN B 745 HIS C 227 GLN C 251 ASN C 745 HIS D 227 GLN D 251 ASN D 745 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21612 Z= 0.139 Angle : 0.503 7.616 29048 Z= 0.251 Chirality : 0.037 0.248 3224 Planarity : 0.002 0.029 3536 Dihedral : 13.102 100.566 3520 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.90 % Allowed : 22.11 % Favored : 75.99 % 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: -0.69 (0.17), residues: 2472 helix: 1.03 (0.13), residues: 1608 sheet: -2.09 (0.51), residues: 84 loop : -3.61 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 380 HIS 0.004 0.001 HIS A 745 PHE 0.018 0.001 PHE C 506 TYR 0.011 0.001 TYR B 321 ARG 0.001 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 310 time to evaluate : 2.376 Fit side-chains REVERT: A 160 HIS cc_start: 0.7156 (t-90) cc_final: 0.6795 (t-90) REVERT: A 174 LYS cc_start: 0.8395 (tttt) cc_final: 0.8027 (tttm) REVERT: A 193 PHE cc_start: 0.8334 (t80) cc_final: 0.8133 (t80) REVERT: A 327 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.6717 (tpt170) REVERT: A 488 MET cc_start: 0.6546 (ptm) cc_final: 0.4813 (mmt) REVERT: A 677 MET cc_start: 0.8633 (mtm) cc_final: 0.8337 (mtp) REVERT: A 687 GLU cc_start: 0.8381 (pp20) cc_final: 0.8054 (pp20) REVERT: A 714 ARG cc_start: 0.7526 (ttt-90) cc_final: 0.7047 (ttm170) REVERT: B 160 HIS cc_start: 0.7155 (t-90) cc_final: 0.6790 (t-90) REVERT: B 174 LYS cc_start: 0.8391 (tttt) cc_final: 0.8022 (tttm) REVERT: B 327 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.6713 (tpt170) REVERT: B 488 MET cc_start: 0.6630 (ptm) cc_final: 0.4940 (mmt) REVERT: B 677 MET cc_start: 0.8625 (mtm) cc_final: 0.8343 (mtp) REVERT: B 687 GLU cc_start: 0.8377 (pp20) cc_final: 0.8053 (pp20) REVERT: B 714 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.7044 (ttm170) REVERT: C 160 HIS cc_start: 0.7157 (t-90) cc_final: 0.6791 (t-90) REVERT: C 174 LYS cc_start: 0.8389 (tttt) cc_final: 0.8025 (tttm) REVERT: C 327 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.6716 (tpt170) REVERT: C 488 MET cc_start: 0.6632 (ptm) cc_final: 0.4937 (mmt) REVERT: C 677 MET cc_start: 0.8639 (mtm) cc_final: 0.8364 (mtp) REVERT: C 687 GLU cc_start: 0.8378 (pp20) cc_final: 0.8047 (pp20) REVERT: C 714 ARG cc_start: 0.7523 (ttt-90) cc_final: 0.7044 (ttm170) REVERT: D 160 HIS cc_start: 0.7161 (t-90) cc_final: 0.6796 (t-90) REVERT: D 174 LYS cc_start: 0.8389 (tttt) cc_final: 0.8020 (tttm) REVERT: D 327 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.6715 (tpt170) REVERT: D 488 MET cc_start: 0.6551 (ptm) cc_final: 0.4821 (mmt) REVERT: D 677 MET cc_start: 0.8651 (mtm) cc_final: 0.8357 (mtp) REVERT: D 687 GLU cc_start: 0.8382 (pp20) cc_final: 0.8051 (pp20) REVERT: D 714 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.7041 (ttm170) outliers start: 42 outliers final: 40 residues processed: 334 average time/residue: 0.3783 time to fit residues: 187.3100 Evaluate side-chains 336 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 296 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 745 HIS B 412 ASN B 745 HIS C 412 ASN D 412 ASN D 745 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21612 Z= 0.153 Angle : 0.517 7.844 29048 Z= 0.255 Chirality : 0.038 0.206 3224 Planarity : 0.002 0.033 3536 Dihedral : 12.960 100.486 3520 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.89 % Allowed : 22.16 % Favored : 74.95 % 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: -0.61 (0.17), residues: 2472 helix: 1.09 (0.13), residues: 1616 sheet: -1.97 (0.52), residues: 84 loop : -3.63 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 380 HIS 0.004 0.001 HIS D 745 PHE 0.038 0.001 PHE C 193 TYR 0.010 0.001 TYR A 321 ARG 0.003 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 314 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.7300 (t-90) cc_final: 0.7003 (t-90) REVERT: A 174 LYS cc_start: 0.8435 (tttt) cc_final: 0.8024 (tttm) REVERT: A 327 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.6701 (tpt170) REVERT: A 488 MET cc_start: 0.6539 (ptm) cc_final: 0.4817 (mmt) REVERT: A 677 MET cc_start: 0.8648 (mtm) cc_final: 0.8303 (mtp) REVERT: A 687 GLU cc_start: 0.8333 (pp20) cc_final: 0.7992 (pp20) REVERT: A 714 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7029 (ttm170) REVERT: A 752 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7673 (p0) REVERT: B 160 HIS cc_start: 0.7301 (t-90) cc_final: 0.7004 (t-90) REVERT: B 174 LYS cc_start: 0.8425 (tttt) cc_final: 0.8019 (tttm) REVERT: B 327 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.6696 (tpt170) REVERT: B 488 MET cc_start: 0.6626 (ptm) cc_final: 0.4944 (mmt) REVERT: B 677 MET cc_start: 0.8640 (mtm) cc_final: 0.8312 (mtp) REVERT: B 687 GLU cc_start: 0.8328 (pp20) cc_final: 0.7989 (pp20) REVERT: B 714 ARG cc_start: 0.7497 (ttt-90) cc_final: 0.7026 (ttm170) REVERT: B 752 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7671 (p0) REVERT: C 160 HIS cc_start: 0.7305 (t-90) cc_final: 0.7005 (t-90) REVERT: C 174 LYS cc_start: 0.8428 (tttt) cc_final: 0.8024 (tttm) REVERT: C 327 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.6693 (tpt170) REVERT: C 488 MET cc_start: 0.6629 (ptm) cc_final: 0.4944 (mmt) REVERT: C 677 MET cc_start: 0.8653 (mtm) cc_final: 0.8330 (mtp) REVERT: C 687 GLU cc_start: 0.8328 (pp20) cc_final: 0.7986 (pp20) REVERT: C 714 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7026 (ttm170) REVERT: C 752 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7670 (p0) REVERT: D 160 HIS cc_start: 0.7307 (t-90) cc_final: 0.7008 (t-90) REVERT: D 174 LYS cc_start: 0.8428 (tttt) cc_final: 0.8019 (tttm) REVERT: D 327 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.6699 (tpt170) REVERT: D 488 MET cc_start: 0.6546 (ptm) cc_final: 0.4825 (mmt) REVERT: D 677 MET cc_start: 0.8665 (mtm) cc_final: 0.8322 (mtp) REVERT: D 687 GLU cc_start: 0.8332 (pp20) cc_final: 0.7986 (pp20) REVERT: D 714 ARG cc_start: 0.7496 (ttt-90) cc_final: 0.7024 (ttm170) REVERT: D 752 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7668 (p0) outliers start: 64 outliers final: 47 residues processed: 358 average time/residue: 0.3525 time to fit residues: 187.8995 Evaluate side-chains 345 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 294 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 752 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 752 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 217 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 412 ASN C 412 ASN C 745 HIS D 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21612 Z= 0.214 Angle : 0.569 9.566 29048 Z= 0.277 Chirality : 0.039 0.153 3224 Planarity : 0.004 0.072 3536 Dihedral : 13.069 101.890 3520 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.98 % Allowed : 22.11 % Favored : 74.91 % 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: -0.69 (0.17), residues: 2472 helix: 1.01 (0.13), residues: 1616 sheet: -1.92 (0.52), residues: 84 loop : -3.62 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 380 HIS 0.004 0.001 HIS C 745 PHE 0.030 0.001 PHE C 193 TYR 0.011 0.001 TYR C 260 ARG 0.003 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 292 time to evaluate : 2.354 Fit side-chains REVERT: A 160 HIS cc_start: 0.7276 (t-90) cc_final: 0.7030 (t-90) REVERT: A 174 LYS cc_start: 0.8457 (tttt) cc_final: 0.8015 (tttm) REVERT: A 193 PHE cc_start: 0.8292 (t80) cc_final: 0.7819 (t80) REVERT: A 327 ARG cc_start: 0.7516 (mmm-85) cc_final: 0.6708 (tpt170) REVERT: A 488 MET cc_start: 0.6544 (ptm) cc_final: 0.4838 (mmt) REVERT: A 677 MET cc_start: 0.8654 (mtm) cc_final: 0.8266 (mtp) REVERT: A 687 GLU cc_start: 0.8396 (pp20) cc_final: 0.8031 (pp20) REVERT: A 714 ARG cc_start: 0.7497 (ttt-90) cc_final: 0.7026 (ttm170) REVERT: A 752 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7766 (p0) REVERT: B 157 PHE cc_start: 0.7881 (t80) cc_final: 0.7385 (t80) REVERT: B 160 HIS cc_start: 0.7273 (t-90) cc_final: 0.7024 (t-90) REVERT: B 174 LYS cc_start: 0.8452 (tttt) cc_final: 0.8017 (tttm) REVERT: B 327 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.6705 (tpt170) REVERT: B 488 MET cc_start: 0.6625 (ptm) cc_final: 0.4963 (mmt) REVERT: B 677 MET cc_start: 0.8649 (mtm) cc_final: 0.8279 (mtp) REVERT: B 687 GLU cc_start: 0.8392 (pp20) cc_final: 0.8029 (pp20) REVERT: B 714 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7024 (ttm170) REVERT: B 752 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7766 (p0) REVERT: C 157 PHE cc_start: 0.7881 (t80) cc_final: 0.7386 (t80) REVERT: C 160 HIS cc_start: 0.7275 (t-90) cc_final: 0.7021 (t-90) REVERT: C 174 LYS cc_start: 0.8450 (tttt) cc_final: 0.8017 (tttm) REVERT: C 327 ARG cc_start: 0.7516 (mmm-85) cc_final: 0.6707 (tpt170) REVERT: C 488 MET cc_start: 0.6628 (ptm) cc_final: 0.4962 (mmt) REVERT: C 677 MET cc_start: 0.8662 (mtm) cc_final: 0.8297 (mtp) REVERT: C 687 GLU cc_start: 0.8393 (pp20) cc_final: 0.8023 (pp20) REVERT: C 714 ARG cc_start: 0.7496 (ttt-90) cc_final: 0.7022 (ttm170) REVERT: C 752 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7765 (p0) REVERT: D 157 PHE cc_start: 0.7882 (t80) cc_final: 0.7387 (t80) REVERT: D 160 HIS cc_start: 0.7274 (t-90) cc_final: 0.7025 (t-90) REVERT: D 174 LYS cc_start: 0.8449 (tttt) cc_final: 0.8013 (tttm) REVERT: D 327 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.6708 (tpt170) REVERT: D 488 MET cc_start: 0.6547 (ptm) cc_final: 0.4843 (mmt) REVERT: D 677 MET cc_start: 0.8671 (mtm) cc_final: 0.8288 (mtp) REVERT: D 687 GLU cc_start: 0.8393 (pp20) cc_final: 0.8025 (pp20) REVERT: D 714 ARG cc_start: 0.7495 (ttt-90) cc_final: 0.7020 (ttm170) REVERT: D 752 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7766 (p0) outliers start: 66 outliers final: 48 residues processed: 339 average time/residue: 0.3626 time to fit residues: 182.5236 Evaluate side-chains 341 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 289 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 752 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 752 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 201 optimal weight: 0.0000 chunk 210 optimal weight: 0.2980 chunk 221 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN B 745 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21612 Z= 0.173 Angle : 0.541 9.346 29048 Z= 0.263 Chirality : 0.038 0.164 3224 Planarity : 0.003 0.064 3536 Dihedral : 12.868 100.678 3520 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.66 % Allowed : 22.70 % Favored : 74.64 % 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: -0.63 (0.17), residues: 2472 helix: 1.06 (0.13), residues: 1616 sheet: -1.85 (0.52), residues: 84 loop : -3.61 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 380 HIS 0.004 0.001 HIS C 745 PHE 0.010 0.001 PHE A 506 TYR 0.010 0.001 TYR C 260 ARG 0.004 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 295 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.7867 (t80) cc_final: 0.7420 (t80) REVERT: A 160 HIS cc_start: 0.7241 (t-90) cc_final: 0.6992 (t-90) REVERT: A 174 LYS cc_start: 0.8445 (tttt) cc_final: 0.8008 (tttm) REVERT: A 193 PHE cc_start: 0.8223 (t80) cc_final: 0.7992 (t80) REVERT: A 202 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8482 (mtm110) REVERT: A 327 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.6690 (tpt170) REVERT: A 488 MET cc_start: 0.6502 (ptm) cc_final: 0.4830 (mmt) REVERT: A 514 GLN cc_start: 0.4760 (tp40) cc_final: 0.4374 (tp40) REVERT: A 677 MET cc_start: 0.8644 (mtm) cc_final: 0.8253 (mtp) REVERT: A 687 GLU cc_start: 0.8392 (pp20) cc_final: 0.8033 (pp20) REVERT: A 714 ARG cc_start: 0.7496 (ttt-90) cc_final: 0.7026 (ttm170) REVERT: A 752 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7756 (p0) REVERT: B 157 PHE cc_start: 0.7739 (t80) cc_final: 0.7398 (t80) REVERT: B 160 HIS cc_start: 0.7274 (t-90) cc_final: 0.7035 (t-90) REVERT: B 174 LYS cc_start: 0.8437 (tttt) cc_final: 0.8001 (tttm) REVERT: B 193 PHE cc_start: 0.8235 (t80) cc_final: 0.8028 (t80) REVERT: B 202 ARG cc_start: 0.8726 (mtp85) cc_final: 0.8472 (mtm110) REVERT: B 327 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.6686 (tpt170) REVERT: B 488 MET cc_start: 0.6585 (ptm) cc_final: 0.4954 (mmt) REVERT: B 514 GLN cc_start: 0.4771 (tp40) cc_final: 0.4382 (tp40) REVERT: B 677 MET cc_start: 0.8642 (mtm) cc_final: 0.8265 (mtp) REVERT: B 687 GLU cc_start: 0.8387 (pp20) cc_final: 0.8031 (pp20) REVERT: B 714 ARG cc_start: 0.7496 (ttt-90) cc_final: 0.7024 (ttm170) REVERT: B 752 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7758 (p0) REVERT: C 157 PHE cc_start: 0.7739 (t80) cc_final: 0.7398 (t80) REVERT: C 160 HIS cc_start: 0.7276 (t-90) cc_final: 0.7033 (t-90) REVERT: C 174 LYS cc_start: 0.8439 (tttt) cc_final: 0.8006 (tttm) REVERT: C 193 PHE cc_start: 0.8229 (t80) cc_final: 0.8023 (t80) REVERT: C 202 ARG cc_start: 0.8726 (mtp85) cc_final: 0.8475 (mtm110) REVERT: C 327 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.6691 (tpt170) REVERT: C 488 MET cc_start: 0.6591 (ptm) cc_final: 0.4955 (mmt) REVERT: C 514 GLN cc_start: 0.4768 (tp40) cc_final: 0.4414 (tp40) REVERT: C 677 MET cc_start: 0.8652 (mtm) cc_final: 0.8283 (mtp) REVERT: C 687 GLU cc_start: 0.8389 (pp20) cc_final: 0.8028 (pp20) REVERT: C 714 ARG cc_start: 0.7494 (ttt-90) cc_final: 0.7023 (ttm170) REVERT: C 752 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7752 (p0) REVERT: D 157 PHE cc_start: 0.7742 (t80) cc_final: 0.7398 (t80) REVERT: D 160 HIS cc_start: 0.7275 (t-90) cc_final: 0.7034 (t-90) REVERT: D 174 LYS cc_start: 0.8439 (tttt) cc_final: 0.8001 (tttm) REVERT: D 193 PHE cc_start: 0.8234 (t80) cc_final: 0.8027 (t80) REVERT: D 202 ARG cc_start: 0.8725 (mtp85) cc_final: 0.8474 (mtm110) REVERT: D 327 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.6690 (tpt170) REVERT: D 488 MET cc_start: 0.6509 (ptm) cc_final: 0.4835 (mmt) REVERT: D 514 GLN cc_start: 0.4759 (tp40) cc_final: 0.4367 (tp40) REVERT: D 677 MET cc_start: 0.8664 (mtm) cc_final: 0.8274 (mtp) REVERT: D 687 GLU cc_start: 0.8391 (pp20) cc_final: 0.8030 (pp20) REVERT: D 714 ARG cc_start: 0.7491 (ttt-90) cc_final: 0.7020 (ttm170) REVERT: D 752 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7754 (p0) outliers start: 59 outliers final: 52 residues processed: 334 average time/residue: 0.3825 time to fit residues: 189.7621 Evaluate side-chains 350 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 294 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 752 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 752 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN C 412 ASN D 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21612 Z= 0.227 Angle : 0.575 9.658 29048 Z= 0.279 Chirality : 0.040 0.159 3224 Planarity : 0.003 0.058 3536 Dihedral : 12.937 101.801 3520 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.71 % Allowed : 22.88 % Favored : 74.41 % 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: -0.71 (0.17), residues: 2472 helix: 0.96 (0.13), residues: 1624 sheet: -1.88 (0.52), residues: 84 loop : -3.61 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 380 HIS 0.004 0.001 HIS C 301 PHE 0.013 0.001 PHE A 316 TYR 0.014 0.002 TYR A 565 ARG 0.005 0.000 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 294 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.7772 (t80) cc_final: 0.7406 (t80) REVERT: A 160 HIS cc_start: 0.7440 (t-90) cc_final: 0.7176 (t-90) REVERT: A 174 LYS cc_start: 0.8467 (tttt) cc_final: 0.8023 (tttm) REVERT: A 193 PHE cc_start: 0.8247 (t80) cc_final: 0.7989 (t80) REVERT: A 327 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.6814 (tpt170) REVERT: A 488 MET cc_start: 0.6497 (ptm) cc_final: 0.4842 (mmt) REVERT: A 514 GLN cc_start: 0.4832 (tp40) cc_final: 0.4459 (tp40) REVERT: A 677 MET cc_start: 0.8668 (mtm) cc_final: 0.8237 (mtp) REVERT: A 687 GLU cc_start: 0.8398 (pp20) cc_final: 0.8024 (pp20) REVERT: A 714 ARG cc_start: 0.7494 (ttt-90) cc_final: 0.7022 (ttm170) REVERT: A 752 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7799 (p0) REVERT: B 157 PHE cc_start: 0.7794 (t80) cc_final: 0.7433 (t80) REVERT: B 160 HIS cc_start: 0.7445 (t-90) cc_final: 0.7186 (t-90) REVERT: B 174 LYS cc_start: 0.8456 (tttt) cc_final: 0.8018 (tttm) REVERT: B 193 PHE cc_start: 0.8248 (t80) cc_final: 0.7995 (t80) REVERT: B 327 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.6812 (tpt170) REVERT: B 488 MET cc_start: 0.6581 (ptm) cc_final: 0.4969 (mmt) REVERT: B 514 GLN cc_start: 0.4836 (tp40) cc_final: 0.4463 (tp40) REVERT: B 677 MET cc_start: 0.8664 (mtm) cc_final: 0.8250 (mtp) REVERT: B 687 GLU cc_start: 0.8394 (pp20) cc_final: 0.8024 (pp20) REVERT: B 714 ARG cc_start: 0.7494 (ttt-90) cc_final: 0.7021 (ttm170) REVERT: B 752 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7799 (p0) REVERT: C 157 PHE cc_start: 0.7795 (t80) cc_final: 0.7434 (t80) REVERT: C 160 HIS cc_start: 0.7447 (t-90) cc_final: 0.7187 (t-90) REVERT: C 174 LYS cc_start: 0.8457 (tttt) cc_final: 0.8020 (tttm) REVERT: C 193 PHE cc_start: 0.8243 (t80) cc_final: 0.7992 (t80) REVERT: C 327 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.6810 (tpt170) REVERT: C 488 MET cc_start: 0.6585 (ptm) cc_final: 0.4968 (mmt) REVERT: C 514 GLN cc_start: 0.4835 (tp40) cc_final: 0.4459 (tp40) REVERT: C 677 MET cc_start: 0.8671 (mtm) cc_final: 0.8267 (mtp) REVERT: C 687 GLU cc_start: 0.8394 (pp20) cc_final: 0.8019 (pp20) REVERT: C 714 ARG cc_start: 0.7493 (ttt-90) cc_final: 0.7021 (ttm170) REVERT: C 752 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7795 (p0) REVERT: D 157 PHE cc_start: 0.7796 (t80) cc_final: 0.7432 (t80) REVERT: D 160 HIS cc_start: 0.7445 (t-90) cc_final: 0.7187 (t-90) REVERT: D 174 LYS cc_start: 0.8456 (tttt) cc_final: 0.8015 (tttm) REVERT: D 193 PHE cc_start: 0.8249 (t80) cc_final: 0.7998 (t80) REVERT: D 327 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.6814 (tpt170) REVERT: D 488 MET cc_start: 0.6508 (ptm) cc_final: 0.4852 (mmt) REVERT: D 514 GLN cc_start: 0.4829 (tp40) cc_final: 0.4454 (tp40) REVERT: D 677 MET cc_start: 0.8682 (mtm) cc_final: 0.8257 (mtp) REVERT: D 687 GLU cc_start: 0.8396 (pp20) cc_final: 0.8020 (pp20) REVERT: D 714 ARG cc_start: 0.7491 (ttt-90) cc_final: 0.7018 (ttm170) REVERT: D 752 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7797 (p0) outliers start: 60 outliers final: 56 residues processed: 338 average time/residue: 0.3614 time to fit residues: 181.6398 Evaluate side-chains 354 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 294 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 512 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 752 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 752 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.0010 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 202 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.149044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114501 restraints weight = 24153.400| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.74 r_work: 0.3034 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21612 Z= 0.139 Angle : 0.520 9.216 29048 Z= 0.254 Chirality : 0.037 0.145 3224 Planarity : 0.003 0.056 3536 Dihedral : 12.420 99.421 3520 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.53 % Allowed : 22.97 % Favored : 74.50 % 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: -0.55 (0.17), residues: 2472 helix: 1.13 (0.13), residues: 1616 sheet: -1.82 (0.51), residues: 84 loop : -3.59 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 380 HIS 0.004 0.001 HIS C 745 PHE 0.007 0.001 PHE C 449 TYR 0.010 0.001 TYR D 321 ARG 0.003 0.000 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4484.09 seconds wall clock time: 83 minutes 22.67 seconds (5002.67 seconds total)