Starting phenix.real_space_refine on Sun Aug 24 08:37:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sly_40583/08_2025/8sly_40583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sly_40583/08_2025/8sly_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_40583/08_2025/8sly_40583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sly_40583/08_2025/8sly_40583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sly_40583/08_2025/8sly_40583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sly_40583/08_2025/8sly_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18257 Number of models: 1 Model: "" Number of chains: 9 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: "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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} 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} Restraints were copied for chains: B, C, D Time building chain proxies: 4.86, per 1000 atoms: 0.27 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: 1.33 Conformation dependent library (CDL) restraints added in 661.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.37 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: 3.09 Time building geometry restraints manager: 1.62 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: 1.670 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.510 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.310 ------------------------------------------------------------------------------- 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 aren 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 : 0.548 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: 0.0954 time to fit residues: 36.1622 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 : 0.615 ------------------------------------------------------------------------------- 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: 4.92 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 aren 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 : 0.555 Fit side-chains REVERT: A 349 ASP cc_start: 0.9307 (t70) cc_final: 0.9037 (t0) REVERT: A 645 MET cc_start: 0.9434 (mmm) cc_final: 0.9233 (mmt) REVERT: B 349 ASP cc_start: 0.9331 (t70) cc_final: 0.9094 (t0) REVERT: B 454 TRP cc_start: 0.8642 (t60) cc_final: 0.8439 (t60) REVERT: B 645 MET cc_start: 0.9410 (mmm) cc_final: 0.9123 (mmt) REVERT: C 349 ASP cc_start: 0.9300 (t70) cc_final: 0.9075 (t0) REVERT: C 645 MET cc_start: 0.9506 (mmm) cc_final: 0.9082 (mmt) REVERT: D 349 ASP cc_start: 0.9307 (t70) cc_final: 0.9036 (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: 0.1045 time to fit residues: 35.3183 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 : 0.787 ------------------------------------------------------------------------------- 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: 3.9990 chunk 190 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 138 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.093588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.076501 restraints weight = 39330.054| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.28 r_work: 0.2895 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18704 Z= 0.170 Angle : 0.532 7.510 25504 Z= 0.257 Chirality : 0.037 0.257 2976 Planarity : 0.003 0.038 3100 Dihedral : 7.736 72.742 2800 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.10 % Allowed : 9.38 % Favored : 89.53 % 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 aren not related in a simple way. whole: 2.12 (0.18), residues: 2316 helix: 2.51 (0.14), residues: 1388 sheet: 0.50 (0.53), residues: 112 loop : -0.44 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 459 TYR 0.016 0.001 TYR A 471 PHE 0.012 0.001 PHE C 407 TRP 0.024 0.001 TRP C 454 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00405 (18704) covalent geometry : angle 0.53163 (25504) hydrogen bonds : bond 0.03712 ( 1080) hydrogen bonds : angle 3.39101 ( 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 178 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.672 Fit side-chains REVERT: A 349 ASP cc_start: 0.9348 (t70) cc_final: 0.9049 (t0) REVERT: B 349 ASP cc_start: 0.9348 (t70) cc_final: 0.9070 (t0) REVERT: B 645 MET cc_start: 0.9371 (mmm) cc_final: 0.9125 (mmt) REVERT: C 349 ASP cc_start: 0.9337 (t70) cc_final: 0.9059 (t0) REVERT: C 645 MET cc_start: 0.9428 (mmm) cc_final: 0.9176 (mmt) REVERT: D 349 ASP cc_start: 0.9329 (t70) cc_final: 0.9056 (t0) REVERT: D 645 MET cc_start: 0.9408 (mmm) cc_final: 0.9188 (mmt) outliers start: 19 outliers final: 16 residues processed: 173 average time/residue: 0.0987 time to fit residues: 29.6169 Evaluate side-chains 163 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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: 0.9990 chunk 170 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.095763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078695 restraints weight = 38787.982| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.28 r_work: 0.2935 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18704 Z= 0.106 Angle : 0.473 7.178 25504 Z= 0.229 Chirality : 0.035 0.118 2976 Planarity : 0.003 0.038 3100 Dihedral : 7.201 69.579 2800 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.74 % Allowed : 10.07 % Favored : 88.19 % 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 aren not related in a simple way. whole: 2.21 (0.18), residues: 2316 helix: 2.61 (0.14), residues: 1388 sheet: 0.63 (0.53), residues: 112 loop : -0.46 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 459 TYR 0.010 0.001 TYR A 471 PHE 0.015 0.001 PHE B 407 TRP 0.025 0.001 TRP D 454 HIS 0.002 0.000 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00246 (18704) covalent geometry : angle 0.47334 (25504) hydrogen bonds : bond 0.03173 ( 1080) hydrogen bonds : angle 3.23510 ( 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 194 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.759 Fit side-chains REVERT: A 349 ASP cc_start: 0.9310 (t70) cc_final: 0.9012 (t0) REVERT: B 349 ASP cc_start: 0.9286 (t70) cc_final: 0.9007 (t0) REVERT: B 645 MET cc_start: 0.9309 (mmm) cc_final: 0.8978 (mmt) REVERT: C 349 ASP cc_start: 0.9299 (t70) cc_final: 0.9004 (t0) REVERT: D 349 ASP cc_start: 0.9292 (t70) cc_final: 0.8997 (t0) REVERT: D 638 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9167 (tp) outliers start: 30 outliers final: 19 residues processed: 185 average time/residue: 0.1052 time to fit residues: 33.5539 Evaluate side-chains 169 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 624 LEU Chi-restraints excluded: chain B residue 632 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 C residue 632 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 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: 1.9990 chunk 25 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 170 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 HIS C 438 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078940 restraints weight = 38639.037| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.27 r_work: 0.2941 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 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 : 0.002 0.031 18704 Z= 0.103 Angle : 0.480 7.563 25504 Z= 0.229 Chirality : 0.035 0.131 2976 Planarity : 0.003 0.038 3100 Dihedral : 6.870 68.163 2800 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.20 % Allowed : 10.71 % Favored : 87.09 % 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 aren not related in a simple way. whole: 2.34 (0.18), residues: 2316 helix: 2.73 (0.14), residues: 1384 sheet: 0.57 (0.52), residues: 112 loop : -0.41 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 459 TYR 0.010 0.001 TYR A 471 PHE 0.012 0.001 PHE C 407 TRP 0.029 0.001 TRP B 454 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00241 (18704) covalent geometry : angle 0.47992 (25504) hydrogen bonds : bond 0.03049 ( 1080) hydrogen bonds : angle 3.14293 ( 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 201 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.680 Fit side-chains REVERT: A 349 ASP cc_start: 0.9304 (t70) cc_final: 0.8995 (t0) REVERT: B 349 ASP cc_start: 0.9294 (t70) cc_final: 0.9001 (t0) REVERT: B 526 SER cc_start: 0.8818 (t) cc_final: 0.8600 (p) REVERT: B 638 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9170 (tp) REVERT: C 349 ASP cc_start: 0.9295 (t70) cc_final: 0.9000 (t0) REVERT: C 526 SER cc_start: 0.8817 (t) cc_final: 0.8590 (p) REVERT: D 349 ASP cc_start: 0.9297 (t70) cc_final: 0.9006 (t0) REVERT: D 638 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9197 (tt) outliers start: 38 outliers final: 23 residues processed: 192 average time/residue: 0.1073 time to fit residues: 34.9043 Evaluate side-chains 187 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 632 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 502 VAL 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 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 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: 0.0980 chunk 161 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 233 optimal weight: 0.8980 chunk 213 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 438 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080727 restraints weight = 38392.024| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.25 r_work: 0.2983 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18704 Z= 0.083 Angle : 0.460 7.417 25504 Z= 0.216 Chirality : 0.035 0.111 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.425 66.284 2800 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.68 % Allowed : 11.40 % Favored : 86.92 % 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 aren not related in a simple way. whole: 2.46 (0.18), residues: 2316 helix: 2.88 (0.14), residues: 1376 sheet: 0.61 (0.52), residues: 112 loop : -0.44 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.007 0.001 TYR A 471 PHE 0.012 0.001 PHE A 407 TRP 0.028 0.001 TRP B 454 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00186 (18704) covalent geometry : angle 0.46010 (25504) hydrogen bonds : bond 0.02761 ( 1080) hydrogen bonds : angle 3.06473 ( 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 220 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.745 Fit side-chains REVERT: A 349 ASP cc_start: 0.9269 (t70) cc_final: 0.8974 (t0) REVERT: A 638 LEU cc_start: 0.9374 (tt) cc_final: 0.9074 (tt) REVERT: B 349 ASP cc_start: 0.9247 (t70) cc_final: 0.8958 (t0) REVERT: C 349 ASP cc_start: 0.9263 (t70) cc_final: 0.8980 (t0) REVERT: D 349 ASP cc_start: 0.9251 (t70) cc_final: 0.8978 (t0) outliers start: 29 outliers final: 20 residues processed: 210 average time/residue: 0.1021 time to fit residues: 36.1643 Evaluate side-chains 193 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 502 VAL 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 542 LEU 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: 0.0050 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.098325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081397 restraints weight = 38331.233| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.25 r_work: 0.2992 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2586 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= 0.081 Angle : 0.455 7.742 25504 Z= 0.214 Chirality : 0.035 0.256 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.204 63.762 2800 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.68 % Allowed : 11.75 % 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 aren not related in a simple way. whole: 2.51 (0.18), residues: 2316 helix: 2.93 (0.14), residues: 1376 sheet: 0.59 (0.52), residues: 112 loop : -0.42 (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 0.012 0.001 PHE B 407 TRP 0.029 0.001 TRP D 454 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00180 (18704) covalent geometry : angle 0.45470 (25504) hydrogen bonds : bond 0.02754 ( 1080) hydrogen bonds : angle 3.02251 ( 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 217 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.9269 (t70) cc_final: 0.8969 (t0) REVERT: A 638 LEU cc_start: 0.9391 (tt) cc_final: 0.9074 (tt) REVERT: B 349 ASP cc_start: 0.9254 (t70) cc_final: 0.8972 (t0) REVERT: C 349 ASP cc_start: 0.9251 (t70) cc_final: 0.8976 (t0) REVERT: D 349 ASP cc_start: 0.9256 (t70) cc_final: 0.8970 (t0) REVERT: D 452 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.7955 (mp10) outliers start: 29 outliers final: 19 residues processed: 208 average time/residue: 0.0989 time to fit residues: 35.3921 Evaluate side-chains 192 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 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 624 LEU Chi-restraints excluded: chain D residue 632 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 228 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 211 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.097880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.080814 restraints weight = 38620.518| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.30 r_work: 0.2981 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18704 Z= 0.091 Angle : 0.477 8.889 25504 Z= 0.220 Chirality : 0.035 0.120 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.136 60.852 2800 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 12.27 % Favored : 85.94 % 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 aren not related in a simple way. whole: 2.54 (0.18), residues: 2316 helix: 2.93 (0.14), residues: 1380 sheet: 0.63 (0.53), residues: 112 loop : -0.39 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.008 0.001 TYR A 471 PHE 0.012 0.001 PHE A 407 TRP 0.032 0.001 TRP A 454 HIS 0.002 0.000 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00211 (18704) covalent geometry : angle 0.47699 (25504) hydrogen bonds : bond 0.02759 ( 1080) hydrogen bonds : angle 3.01307 ( 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 211 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.720 Fit side-chains REVERT: A 349 ASP cc_start: 0.9271 (t70) cc_final: 0.8987 (t0) REVERT: B 349 ASP cc_start: 0.9264 (t70) cc_final: 0.8986 (t0) REVERT: B 452 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: C 349 ASP cc_start: 0.9265 (t70) cc_final: 0.8996 (t0) REVERT: C 640 MET cc_start: 0.9038 (tpp) cc_final: 0.8827 (tpp) REVERT: D 349 ASP cc_start: 0.9262 (t70) cc_final: 0.8987 (t0) REVERT: D 452 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.7902 (mp10) outliers start: 31 outliers final: 24 residues processed: 201 average time/residue: 0.0952 time to fit residues: 33.1221 Evaluate side-chains 197 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 440 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 158 THR 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 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 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: 10.0000 chunk 1 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 230 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 70 optimal weight: 0.0050 chunk 160 optimal weight: 0.3980 chunk 173 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080958 restraints weight = 38421.698| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.27 r_work: 0.2983 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 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 0.041 18704 Z= 0.089 Angle : 0.489 10.069 25504 Z= 0.224 Chirality : 0.035 0.152 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.010 57.911 2800 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.82 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 aren not related in a simple way. whole: 2.55 (0.18), residues: 2316 helix: 2.94 (0.14), residues: 1380 sheet: 0.70 (0.53), 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 0.008 0.001 TYR A 471 PHE 0.013 0.001 PHE D 209 TRP 0.036 0.001 TRP A 454 HIS 0.002 0.000 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00207 (18704) covalent geometry : angle 0.48892 (25504) hydrogen bonds : bond 0.02738 ( 1080) hydrogen bonds : angle 2.98662 ( 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 215 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.9274 (t70) cc_final: 0.8992 (t0) REVERT: A 452 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: A 645 MET cc_start: 0.9170 (tpp) cc_final: 0.8618 (ttp) REVERT: B 349 ASP cc_start: 0.9255 (t70) cc_final: 0.8982 (t0) REVERT: C 349 ASP cc_start: 0.9256 (t70) cc_final: 0.8981 (t0) REVERT: C 452 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: C 640 MET cc_start: 0.9047 (tpp) cc_final: 0.8838 (tpp) REVERT: D 349 ASP cc_start: 0.9268 (t70) cc_final: 0.8991 (t0) REVERT: D 452 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.7914 (mp10) outliers start: 31 outliers final: 25 residues processed: 205 average time/residue: 0.0933 time to fit residues: 32.7239 Evaluate side-chains 204 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 440 LEU 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 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 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: 6.9990 chunk 73 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 110 optimal weight: 0.0970 chunk 175 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.094279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.077209 restraints weight = 38841.990| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.26 r_work: 0.2904 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18704 Z= 0.155 Angle : 0.549 10.397 25504 Z= 0.255 Chirality : 0.037 0.164 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.449 58.969 2800 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.56 % Allowed : 12.62 % 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 aren not related in a simple way. whole: 2.37 (0.18), residues: 2316 helix: 2.77 (0.14), residues: 1380 sheet: 0.56 (0.52), residues: 112 loop : -0.42 (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 A 471 PHE 0.016 0.001 PHE D 407 TRP 0.046 0.001 TRP A 454 HIS 0.004 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00372 (18704) covalent geometry : angle 0.54858 (25504) hydrogen bonds : bond 0.03270 ( 1080) hydrogen bonds : angle 3.16286 ( 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 201 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.700 Fit side-chains REVERT: A 349 ASP cc_start: 0.9292 (t70) cc_final: 0.9009 (t0) REVERT: A 536 ASP cc_start: 0.9176 (m-30) cc_final: 0.8942 (m-30) REVERT: B 349 ASP cc_start: 0.9287 (t70) cc_final: 0.8993 (t0) REVERT: B 536 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8929 (m-30) REVERT: C 349 ASP cc_start: 0.9292 (t70) cc_final: 0.9004 (t0) REVERT: C 536 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8911 (m-30) REVERT: D 349 ASP cc_start: 0.9289 (t70) cc_final: 0.9007 (t0) outliers start: 27 outliers final: 25 residues processed: 195 average time/residue: 0.1169 time to fit residues: 38.2203 Evaluate side-chains 195 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 440 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 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 440 LEU 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 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 440 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 110 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 179 optimal weight: 0.0060 chunk 133 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN C 452 GLN D 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080528 restraints weight = 38547.064| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.26 r_work: 0.2970 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18704 Z= 0.088 Angle : 0.497 10.293 25504 Z= 0.230 Chirality : 0.035 0.154 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.015 59.778 2800 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.79 % Allowed : 12.44 % 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 aren not related in a simple way. whole: 2.52 (0.18), residues: 2316 helix: 2.90 (0.14), residues: 1380 sheet: 0.69 (0.53), residues: 112 loop : -0.39 (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 0.016 0.001 PHE A 209 TRP 0.045 0.001 TRP B 454 HIS 0.002 0.000 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00201 (18704) covalent geometry : angle 0.49703 (25504) hydrogen bonds : bond 0.02821 ( 1080) hydrogen bonds : angle 3.04205 ( 3072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3868.93 seconds wall clock time: 67 minutes 9.74 seconds (4029.74 seconds total)