Starting phenix.real_space_refine on Thu Feb 5 15:07:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sly_40583/02_2026/8sly_40583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sly_40583/02_2026/8sly_40583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sly_40583/02_2026/8sly_40583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sly_40583/02_2026/8sly_40583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sly_40583/02_2026/8sly_40583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sly_40583/02_2026/8sly_40583.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 Na 1 4.78 5 C 12092 2.51 5 N 3028 2.21 5 O 3044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18257 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 11, 'GLU:plan': 19, 'TRP:plan': 2, 'GLN:plan1': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 227 Chain: "B" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 11, 'GLU:plan': 19, 'TRP:plan': 2, 'GLN:plan1': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 227 Chain: "C" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 11, 'GLU:plan': 19, 'TRP:plan': 2, 'GLN:plan1': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 227 Chain: "D" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 12, 'ARG:plan': 11, 'GLU:plan': 19, 'TRP:plan': 2, 'GLN:plan1': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 227 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {' NA': 1, 'P0T': 2, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'P0T': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'P0T': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'P0T': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.79, per 1000 atoms: 0.21 Number of scatterers: 18257 At special positions: 0 Unit cell: (156.04, 156.04, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 4 15.00 Na 1 11.00 O 3044 8.00 N 3028 7.00 C 12092 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 - 3.00 Amino acid : True - 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: 1.25 Conformation dependent library (CDL) restraints added in 655.0 milliseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 65.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.666A pdb=" N LYS A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.657A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.677A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 369 through 374 removed outlier: 4.025A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 374' Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.506A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 433 through 459 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.698A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.903A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.129A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 527 through 560 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.671A pdb=" N ALA A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.690A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 672 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.666A pdb=" N LYS B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.657A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.676A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 369 through 374 removed outlier: 4.025A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 375 through 389 removed outlier: 3.505A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 433 through 459 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.698A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.903A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.129A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 527 through 560 Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.671A pdb=" N ALA B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.690A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 672 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.666A pdb=" N LYS C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.657A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.676A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.025A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 374' Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.506A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 433 through 459 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.698A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.904A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.129A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'C' and resid 527 through 560 Processing helix chain 'C' and resid 592 through 602 removed outlier: 3.671A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.690A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 672 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.666A pdb=" N LYS D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.657A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.677A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 369 through 374 removed outlier: 4.025A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 374' Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.506A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 383 " --> pdb=" O ASN D 379 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 433 through 459 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.698A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.903A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.129A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 519 Processing helix chain 'D' and resid 527 through 560 Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.671A pdb=" N ALA D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.690A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 672 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 7.299A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.298A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 7.299A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 7.299A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3072 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: 2.68 Time building geometry restraints manager: 1.63 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: 2949 1.32 - 1.45: 5167 1.45 - 1.57: 10428 1.57 - 1.69: 32 1.69 - 1.82: 128 Bond restraints: 18704 Sorted by residual: bond pdb=" C05 P0T C 801 " pdb=" C06 P0T C 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C05 P0T D 801 " pdb=" C06 P0T D 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C05 P0T A 801 " pdb=" C06 P0T A 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" C05 P0T B 801 " pdb=" C06 P0T B 801 " ideal model delta sigma weight residual 1.521 1.656 -0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C03 P0T C 801 " pdb=" C04 P0T C 801 " ideal model delta sigma weight residual 1.548 1.679 -0.131 2.00e-02 2.50e+03 4.30e+01 ... (remaining 18699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 24966 1.99 - 3.98: 382 3.98 - 5.98: 112 5.98 - 7.97: 28 7.97 - 9.96: 16 Bond angle restraints: 25504 Sorted by residual: angle pdb=" N ILE A 605 " pdb=" CA ILE A 605 " pdb=" C ILE A 605 " ideal model delta sigma weight residual 112.98 108.73 4.25 1.25e+00 6.40e-01 1.15e+01 angle pdb=" N ILE D 605 " pdb=" CA ILE D 605 " pdb=" C ILE D 605 " ideal model delta sigma weight residual 112.98 108.74 4.24 1.25e+00 6.40e-01 1.15e+01 angle pdb=" N ILE B 605 " pdb=" CA ILE B 605 " pdb=" C ILE B 605 " ideal model delta sigma weight residual 112.98 108.76 4.22 1.25e+00 6.40e-01 1.14e+01 angle pdb=" N ILE C 605 " pdb=" CA ILE C 605 " pdb=" C ILE C 605 " ideal model delta sigma weight residual 112.98 108.76 4.22 1.25e+00 6.40e-01 1.14e+01 angle pdb=" C22 POV D 803 " pdb=" C21 POV D 803 " pdb=" O21 POV D 803 " ideal model delta sigma weight residual 111.03 120.99 -9.96 3.00e+00 1.11e-01 1.10e+01 ... (remaining 25499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 10448 27.39 - 54.78: 396 54.78 - 82.17: 40 82.17 - 109.55: 4 109.55 - 136.94: 8 Dihedral angle restraints: 10896 sinusoidal: 3980 harmonic: 6916 Sorted by residual: dihedral pdb=" C18 P0T B 801 " pdb=" C20 P0T B 801 " pdb=" C21 P0T B 801 " pdb=" C22 P0T B 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.35 136.94 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C18 P0T C 801 " pdb=" C20 P0T C 801 " pdb=" C21 P0T C 801 " pdb=" C22 P0T C 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.36 136.93 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C18 P0T A 801 " pdb=" C20 P0T A 801 " pdb=" C21 P0T A 801 " pdb=" C22 P0T A 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.36 136.93 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 10893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2949 0.112 - 0.223: 19 0.223 - 0.335: 0 0.335 - 0.447: 0 0.447 - 0.559: 8 Chirality restraints: 2976 Sorted by residual: chirality pdb=" C03 P0T C 802 " pdb=" C04 P0T C 802 " pdb=" C05 P0T C 802 " pdb=" C10 P0T C 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C03 P0T A 802 " pdb=" C04 P0T A 802 " pdb=" C05 P0T A 802 " pdb=" C10 P0T A 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C03 P0T B 802 " pdb=" C04 P0T B 802 " pdb=" C05 P0T B 802 " pdb=" C10 P0T B 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 ... (remaining 2973 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 604 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C THR C 604 " 0.029 2.00e-02 2.50e+03 pdb=" O THR C 604 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 605 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 604 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR A 604 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 604 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 605 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 604 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C THR B 604 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 604 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 605 " 0.010 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1759 2.74 - 3.28: 18065 3.28 - 3.82: 30255 3.82 - 4.36: 35197 4.36 - 4.90: 60802 Nonbonded interactions: 146078 Sorted by model distance: nonbonded pdb=" OH TYR C 544 " pdb=" OG1 THR C 604 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 544 " pdb=" OG1 THR A 604 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR D 544 " pdb=" OG1 THR D 604 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR B 544 " pdb=" OG1 THR B 604 " model vdw 2.206 3.040 nonbonded pdb=" O ALA D 361 " pdb=" NH1 ARG D 369 " model vdw 2.302 3.120 ... (remaining 146073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 75 through 802) selection = (chain 'B' and resid 75 through 802) selection = (chain 'C' and resid 75 through 802) selection = (chain 'D' and resid 75 through 802) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.980 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 18704 Z= 0.320 Angle : 0.665 9.959 25504 Z= 0.297 Chirality : 0.046 0.559 2976 Planarity : 0.003 0.047 3100 Dihedral : 15.008 136.942 6416 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.18), residues: 2316 helix: 1.76 (0.14), residues: 1376 sheet: 0.44 (0.50), residues: 112 loop : -0.50 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 459 TYR 0.016 0.001 TYR B 162 PHE 0.023 0.001 PHE C 362 TRP 0.024 0.001 TRP C 454 HIS 0.001 0.000 HIS D 413 Details of bonding type rmsd covalent geometry : bond 0.00627 (18704) covalent geometry : angle 0.66479 (25504) hydrogen bonds : bond 0.24036 ( 1080) hydrogen bonds : angle 6.01926 ( 3072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.749 Fit side-chains REVERT: A 349 ASP cc_start: 0.8840 (t70) cc_final: 0.8586 (t0) REVERT: B 349 ASP cc_start: 0.8910 (t70) cc_final: 0.8687 (t0) REVERT: C 349 ASP cc_start: 0.8862 (t70) cc_final: 0.8649 (t0) REVERT: D 349 ASP cc_start: 0.8880 (t70) cc_final: 0.8628 (t0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1066 time to fit residues: 39.9682 Evaluate side-chains 166 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 127 ASN C 127 ASN D 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082430 restraints weight = 38641.248| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.24 r_work: 0.3005 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18704 Z= 0.102 Angle : 0.493 8.243 25504 Z= 0.241 Chirality : 0.036 0.171 2976 Planarity : 0.003 0.035 3100 Dihedral : 8.780 91.686 2800 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.98 % Allowed : 5.56 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.18), residues: 2316 helix: 2.39 (0.14), residues: 1380 sheet: 0.81 (0.52), residues: 112 loop : -0.48 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 560 TYR 0.014 0.001 TYR A 471 PHE 0.014 0.001 PHE C 407 TRP 0.028 0.001 TRP B 454 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00220 (18704) covalent geometry : angle 0.49256 (25504) hydrogen bonds : bond 0.03591 ( 1080) hydrogen bonds : angle 3.61268 ( 3072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.507 Fit side-chains REVERT: A 349 ASP cc_start: 0.9308 (t70) cc_final: 0.9038 (t0) REVERT: A 645 MET cc_start: 0.9434 (mmm) cc_final: 0.9233 (mmt) REVERT: B 349 ASP cc_start: 0.9332 (t70) cc_final: 0.9096 (t0) REVERT: B 454 TRP cc_start: 0.8644 (t60) cc_final: 0.8441 (t60) REVERT: B 645 MET cc_start: 0.9409 (mmm) cc_final: 0.9121 (mmt) REVERT: C 349 ASP cc_start: 0.9301 (t70) cc_final: 0.9076 (t0) REVERT: C 645 MET cc_start: 0.9505 (mmm) cc_final: 0.9083 (mmt) REVERT: D 349 ASP cc_start: 0.9310 (t70) cc_final: 0.9038 (t0) REVERT: D 638 LEU cc_start: 0.9295 (tt) cc_final: 0.9042 (tt) outliers start: 17 outliers final: 8 residues processed: 198 average time/residue: 0.0941 time to fit residues: 31.8500 Evaluate side-chains 173 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS B 413 HIS D 413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.075937 restraints weight = 39438.914| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.28 r_work: 0.2883 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18704 Z= 0.194 Angle : 0.545 7.416 25504 Z= 0.264 Chirality : 0.037 0.149 2976 Planarity : 0.004 0.038 3100 Dihedral : 7.806 72.816 2800 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.04 % Allowed : 9.61 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.18), residues: 2316 helix: 2.46 (0.14), residues: 1388 sheet: 0.47 (0.52), residues: 112 loop : -0.44 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 459 TYR 0.017 0.001 TYR A 471 PHE 0.013 0.001 PHE C 407 TRP 0.025 0.001 TRP A 454 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00462 (18704) covalent geometry : angle 0.54499 (25504) hydrogen bonds : bond 0.03796 ( 1080) hydrogen bonds : angle 3.44174 ( 3072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.746 Fit side-chains REVERT: A 349 ASP cc_start: 0.9355 (t70) cc_final: 0.9060 (t0) REVERT: B 349 ASP cc_start: 0.9349 (t70) cc_final: 0.9057 (t0) REVERT: C 349 ASP cc_start: 0.9336 (t70) cc_final: 0.9043 (t0) REVERT: C 645 MET cc_start: 0.9443 (mmm) cc_final: 0.9127 (mmt) REVERT: D 349 ASP cc_start: 0.9337 (t70) cc_final: 0.9045 (t0) REVERT: D 454 TRP cc_start: 0.8965 (t60) cc_final: 0.8754 (t60) outliers start: 18 outliers final: 16 residues processed: 169 average time/residue: 0.1070 time to fit residues: 31.6239 Evaluate side-chains 159 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 632 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 66 optimal weight: 0.5980 chunk 170 optimal weight: 0.0770 chunk 200 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.096574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.079553 restraints weight = 38718.993| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.26 r_work: 0.2951 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18704 Z= 0.090 Angle : 0.466 7.279 25504 Z= 0.225 Chirality : 0.035 0.111 2976 Planarity : 0.003 0.037 3100 Dihedral : 7.145 69.309 2800 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.74 % Allowed : 9.95 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.18), residues: 2316 helix: 2.62 (0.14), residues: 1388 sheet: 0.68 (0.53), residues: 112 loop : -0.48 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 459 TYR 0.009 0.001 TYR A 471 PHE 0.016 0.001 PHE B 407 TRP 0.025 0.001 TRP C 454 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00201 (18704) covalent geometry : angle 0.46611 (25504) hydrogen bonds : bond 0.03106 ( 1080) hydrogen bonds : angle 3.23979 ( 3072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.575 Fit side-chains REVERT: A 349 ASP cc_start: 0.9299 (t70) cc_final: 0.8991 (t0) REVERT: A 638 LEU cc_start: 0.9406 (tt) cc_final: 0.9184 (tt) REVERT: B 349 ASP cc_start: 0.9284 (t70) cc_final: 0.8993 (t0) REVERT: C 349 ASP cc_start: 0.9280 (t70) cc_final: 0.8994 (t0) REVERT: D 349 ASP cc_start: 0.9277 (t70) cc_final: 0.8992 (t0) REVERT: D 638 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9153 (tt) outliers start: 30 outliers final: 19 residues processed: 192 average time/residue: 0.1077 time to fit residues: 35.7615 Evaluate side-chains 173 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 638 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 438 HIS C 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.095094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.078024 restraints weight = 38793.917| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.28 r_work: 0.2923 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18704 Z= 0.123 Angle : 0.494 7.687 25504 Z= 0.237 Chirality : 0.036 0.125 2976 Planarity : 0.003 0.038 3100 Dihedral : 6.950 68.633 2800 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.31 % Allowed : 11.05 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.18), residues: 2316 helix: 2.71 (0.14), residues: 1384 sheet: 0.63 (0.53), residues: 112 loop : -0.48 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 459 TYR 0.011 0.001 TYR A 471 PHE 0.012 0.001 PHE C 407 TRP 0.028 0.001 TRP B 454 HIS 0.003 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00291 (18704) covalent geometry : angle 0.49370 (25504) hydrogen bonds : bond 0.03173 ( 1080) hydrogen bonds : angle 3.17677 ( 3072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.724 Fit side-chains REVERT: A 349 ASP cc_start: 0.9321 (t70) cc_final: 0.9029 (t0) REVERT: A 638 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9211 (tt) REVERT: B 349 ASP cc_start: 0.9305 (t70) cc_final: 0.9001 (t0) REVERT: B 526 SER cc_start: 0.8872 (t) cc_final: 0.8630 (p) REVERT: B 638 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9197 (tt) REVERT: C 349 ASP cc_start: 0.9306 (t70) cc_final: 0.9020 (t0) REVERT: C 485 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9364 (tt) REVERT: C 645 MET cc_start: 0.9427 (mmm) cc_final: 0.8996 (mmt) REVERT: D 349 ASP cc_start: 0.9309 (t70) cc_final: 0.9016 (t0) REVERT: D 638 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9225 (tp) outliers start: 40 outliers final: 25 residues processed: 195 average time/residue: 0.1154 time to fit residues: 37.9385 Evaluate side-chains 187 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 638 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 235 optimal weight: 9.9990 chunk 21 optimal weight: 0.0060 chunk 161 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 233 optimal weight: 0.0980 chunk 213 optimal weight: 0.4980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 HIS D 438 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081879 restraints weight = 38455.891| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.25 r_work: 0.2998 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18704 Z= 0.080 Angle : 0.456 7.249 25504 Z= 0.215 Chirality : 0.035 0.112 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.359 65.695 2800 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.85 % Allowed : 11.57 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.18), residues: 2316 helix: 2.88 (0.14), residues: 1376 sheet: 0.70 (0.53), residues: 112 loop : -0.45 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 280 TYR 0.006 0.001 TYR A 471 PHE 0.011 0.001 PHE B 407 TRP 0.027 0.001 TRP B 454 HIS 0.002 0.000 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00174 (18704) covalent geometry : angle 0.45632 (25504) hydrogen bonds : bond 0.02701 ( 1080) hydrogen bonds : angle 3.05811 ( 3072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.806 Fit side-chains REVERT: A 349 ASP cc_start: 0.9264 (t70) cc_final: 0.8976 (t0) REVERT: B 349 ASP cc_start: 0.9260 (t70) cc_final: 0.8973 (t0) REVERT: C 349 ASP cc_start: 0.9250 (t70) cc_final: 0.8974 (t0) REVERT: D 349 ASP cc_start: 0.9248 (t70) cc_final: 0.8962 (t0) REVERT: D 372 MET cc_start: 0.9275 (mtt) cc_final: 0.9070 (mtt) outliers start: 32 outliers final: 19 residues processed: 223 average time/residue: 0.1105 time to fit residues: 41.4639 Evaluate side-chains 200 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 150 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 109 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080965 restraints weight = 38435.555| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.25 r_work: 0.2981 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18704 Z= 0.087 Angle : 0.466 8.121 25504 Z= 0.219 Chirality : 0.035 0.112 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.232 64.011 2800 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.27 % Allowed : 12.44 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.18), residues: 2316 helix: 2.93 (0.14), residues: 1376 sheet: 0.66 (0.52), residues: 112 loop : -0.43 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 280 TYR 0.008 0.001 TYR A 471 PHE 0.013 0.001 PHE B 407 TRP 0.031 0.001 TRP D 454 HIS 0.002 0.000 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00201 (18704) covalent geometry : angle 0.46583 (25504) hydrogen bonds : bond 0.02779 ( 1080) hydrogen bonds : angle 3.00783 ( 3072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.9275 (t70) cc_final: 0.8984 (t0) REVERT: A 638 LEU cc_start: 0.9401 (tt) cc_final: 0.9083 (tt) REVERT: B 349 ASP cc_start: 0.9256 (t70) cc_final: 0.8972 (t0) REVERT: B 452 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: C 349 ASP cc_start: 0.9256 (t70) cc_final: 0.8986 (t0) REVERT: D 349 ASP cc_start: 0.9255 (t70) cc_final: 0.8987 (t0) REVERT: D 372 MET cc_start: 0.9383 (mtt) cc_final: 0.9025 (mtt) REVERT: D 452 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.7936 (mp10) outliers start: 22 outliers final: 19 residues processed: 198 average time/residue: 0.1113 time to fit residues: 37.7559 Evaluate side-chains 196 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 228 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.097530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080456 restraints weight = 38601.332| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.27 r_work: 0.2972 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18704 Z= 0.093 Angle : 0.466 8.796 25504 Z= 0.219 Chirality : 0.035 0.114 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.177 61.728 2800 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 12.21 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.18), residues: 2316 helix: 2.96 (0.14), residues: 1376 sheet: 0.63 (0.52), residues: 112 loop : -0.41 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.009 0.001 TYR A 471 PHE 0.013 0.001 PHE B 407 TRP 0.035 0.001 TRP D 454 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00219 (18704) covalent geometry : angle 0.46587 (25504) hydrogen bonds : bond 0.02792 ( 1080) hydrogen bonds : angle 3.00182 ( 3072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.9276 (t70) cc_final: 0.9000 (t0) REVERT: A 452 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: A 638 LEU cc_start: 0.9410 (tt) cc_final: 0.9062 (tt) REVERT: B 349 ASP cc_start: 0.9263 (t70) cc_final: 0.8986 (t0) REVERT: B 452 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: C 349 ASP cc_start: 0.9263 (t70) cc_final: 0.8989 (t0) REVERT: D 349 ASP cc_start: 0.9268 (t70) cc_final: 0.8987 (t0) REVERT: D 372 MET cc_start: 0.9376 (mtt) cc_final: 0.9020 (mtt) REVERT: D 452 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.7906 (mp10) outliers start: 31 outliers final: 21 residues processed: 204 average time/residue: 0.1038 time to fit residues: 36.2822 Evaluate side-chains 198 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 65 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 235 optimal weight: 0.0030 chunk 230 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 70 optimal weight: 0.0070 chunk 160 optimal weight: 2.9990 chunk 173 optimal weight: 0.3980 overall best weight: 1.4812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078538 restraints weight = 38601.413| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.26 r_work: 0.2934 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18704 Z= 0.118 Angle : 0.495 8.804 25504 Z= 0.232 Chirality : 0.035 0.125 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.249 60.118 2800 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.91 % Allowed : 12.33 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.18), residues: 2316 helix: 2.91 (0.14), residues: 1380 sheet: 0.66 (0.52), residues: 112 loop : -0.39 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 280 TYR 0.010 0.001 TYR A 471 PHE 0.014 0.001 PHE D 407 TRP 0.041 0.001 TRP B 454 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00283 (18704) covalent geometry : angle 0.49471 (25504) hydrogen bonds : bond 0.02982 ( 1080) hydrogen bonds : angle 3.05262 ( 3072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.723 Fit side-chains REVERT: A 349 ASP cc_start: 0.9294 (t70) cc_final: 0.9015 (t0) REVERT: A 452 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: B 349 ASP cc_start: 0.9287 (t70) cc_final: 0.8997 (t0) REVERT: C 349 ASP cc_start: 0.9286 (t70) cc_final: 0.9016 (t0) REVERT: D 349 ASP cc_start: 0.9274 (t70) cc_final: 0.8991 (t0) REVERT: D 372 MET cc_start: 0.9423 (mtt) cc_final: 0.9061 (mtt) outliers start: 33 outliers final: 27 residues processed: 197 average time/residue: 0.1104 time to fit residues: 36.8428 Evaluate side-chains 197 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN C 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.077188 restraints weight = 38750.804| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.26 r_work: 0.2901 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18704 Z= 0.155 Angle : 0.532 10.260 25504 Z= 0.249 Chirality : 0.036 0.134 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.505 60.261 2800 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.74 % Allowed : 12.50 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.18), residues: 2316 helix: 2.83 (0.14), residues: 1380 sheet: 0.53 (0.52), residues: 112 loop : -0.43 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 280 TYR 0.012 0.001 TYR D 228 PHE 0.016 0.001 PHE A 407 TRP 0.049 0.002 TRP B 454 HIS 0.004 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00370 (18704) covalent geometry : angle 0.53248 (25504) hydrogen bonds : bond 0.03251 ( 1080) hydrogen bonds : angle 3.15824 ( 3072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.9302 (t70) cc_final: 0.9014 (t0) REVERT: A 536 ASP cc_start: 0.9160 (m-30) cc_final: 0.8942 (m-30) REVERT: B 349 ASP cc_start: 0.9300 (t70) cc_final: 0.9014 (t0) REVERT: B 536 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8945 (m-30) REVERT: C 349 ASP cc_start: 0.9290 (t70) cc_final: 0.9015 (t0) REVERT: C 452 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.9029 (mm-40) REVERT: C 536 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8954 (m-30) REVERT: D 349 ASP cc_start: 0.9290 (t70) cc_final: 0.9010 (t0) REVERT: D 372 MET cc_start: 0.9431 (mtt) cc_final: 0.9061 (mtt) REVERT: D 452 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: D 536 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8928 (m-30) outliers start: 30 outliers final: 23 residues processed: 196 average time/residue: 0.1052 time to fit residues: 34.6808 Evaluate side-chains 197 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 110 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 95 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN D 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080741 restraints weight = 38360.223| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.24 r_work: 0.2975 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18704 Z= 0.086 Angle : 0.480 10.319 25504 Z= 0.223 Chirality : 0.035 0.116 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.032 60.519 2800 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.62 % Allowed : 12.56 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.18), residues: 2316 helix: 2.96 (0.14), residues: 1380 sheet: 0.73 (0.53), residues: 112 loop : -0.38 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 280 TYR 0.007 0.001 TYR A 471 PHE 0.012 0.001 PHE D 407 TRP 0.051 0.001 TRP C 454 HIS 0.002 0.000 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00188 (18704) covalent geometry : angle 0.48023 (25504) hydrogen bonds : bond 0.02766 ( 1080) hydrogen bonds : angle 3.03278 ( 3072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4264.38 seconds wall clock time: 73 minutes 52.98 seconds (4432.98 seconds total)