Starting phenix.real_space_refine on Fri Jul 3 14:25:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k1s_22629/07_2026/7k1s_22629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k1s_22629/07_2026/7k1s_22629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k1s_22629/07_2026/7k1s_22629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k1s_22629/07_2026/7k1s_22629.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k1s_22629/07_2026/7k1s_22629.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k1s_22629/07_2026/7k1s_22629.cif" model { file = "/net/cci-nas-00/data/ceres_data/7k1s_22629/07_2026/7k1s_22629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k1s_22629/07_2026/7k1s_22629.cif" } resolution = 3.9 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 9087 2.51 5 N 2478 2.21 5 O 2778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14409 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.45, per 1000 atoms: 0.24 Number of scatterers: 14409 At special positions: 0 Unit cell: (90.1, 96.46, 178.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2778 8.00 N 2478 7.00 C 9087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 540 " distance=2.02 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 540 " distance=2.02 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 540 " distance=2.02 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 645 " distance=2.03 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 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN E 3 " - " MAN E 6 " " MAN E 4 " - " MAN E 5 " " MAN F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN E 3 " - " MAN E 4 " " MAN F 3 " - " MAN F 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 686 " " NAG B1001 " - " ASN B 686 " " NAG C1001 " - " ASN C 686 " " NAG D 1 " - " ASN A 257 " " NAG E 1 " - " ASN B 257 " " NAG F 1 " - " ASN C 257 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 673.7 milliseconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 33 sheets defined 22.3% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 368' Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.681A pdb=" N ILE A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 554 removed outlier: 4.159A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'B' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 368' Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.682A pdb=" N ILE B 412 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 554 removed outlier: 3.872A pdb=" N GLN B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'C' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 408 through 412 removed outlier: 3.681A pdb=" N ILE C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 554 removed outlier: 4.158A pdb=" N ALA C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 729 Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 574 removed outlier: 4.371A pdb=" N THR A 129 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 130 " --> pdb=" O GLY C 677 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 679 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG A 132 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 403 removed outlier: 6.092A pdb=" N TRP A 374 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 157 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU A 376 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 155 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 378 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA A 153 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 403 removed outlier: 6.092A pdb=" N TRP A 374 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 157 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU A 376 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 155 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 378 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA A 153 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR A 178 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 191 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 176 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 193 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 174 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG A 195 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 172 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR A 170 " --> pdb=" O PRO A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR A 178 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 191 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 176 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 193 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 174 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG A 195 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 172 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR A 170 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS A 166 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN A 360 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA9, first strand: chain 'A' and resid 591 through 595 removed outlier: 3.863A pdb=" N GLN A 628 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 636 " --> pdb=" O GLN A 628 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AB2, first strand: chain 'A' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU A 663 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 677 through 679 removed outlier: 3.828A pdb=" N GLY A 677 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR B 129 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP B 374 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 157 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 376 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 155 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 378 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA B 153 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP B 374 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 157 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 376 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 155 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 378 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA B 153 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR B 178 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 191 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 176 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA B 193 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 174 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 195 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 172 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR B 170 " --> pdb=" O PRO B 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR B 178 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 191 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 176 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA B 193 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 174 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 195 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 172 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR B 170 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS B 166 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN B 360 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 212 through 214 Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AC1, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AC2, first strand: chain 'B' and resid 591 through 595 removed outlier: 3.862A pdb=" N GLN B 628 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 636 " --> pdb=" O GLN B 628 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AC4, first strand: chain 'B' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU B 663 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 677 through 679 removed outlier: 3.750A pdb=" N GLY B 677 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR C 129 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP C 374 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS C 157 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 376 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 155 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU C 378 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA C 153 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP C 374 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS C 157 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 376 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 155 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU C 378 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA C 153 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR C 178 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 191 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 176 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 193 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 174 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG C 195 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS C 172 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR C 170 " --> pdb=" O PRO C 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR C 178 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 191 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 176 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 193 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 174 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG C 195 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS C 172 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR C 170 " --> pdb=" O PRO C 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS C 166 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN C 360 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 212 through 214 Processing sheet with id=AD2, first strand: chain 'C' and resid 216 through 221 Processing sheet with id=AD3, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AD4, first strand: chain 'C' and resid 591 through 595 removed outlier: 3.862A pdb=" N GLN C 628 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 636 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 607 through 609 Processing sheet with id=AD6, first strand: chain 'C' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU C 663 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1719 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: 2.98 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4680 1.34 - 1.46: 3625 1.46 - 1.58: 6332 1.58 - 1.70: 0 1.70 - 1.83: 102 Bond restraints: 14739 Sorted by residual: bond pdb=" N ILE B 679 " pdb=" CA ILE B 679 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 8.98e+00 bond pdb=" N ILE C 679 " pdb=" CA ILE C 679 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.84e+00 bond pdb=" N VAL C 512 " pdb=" CA VAL C 512 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.59e+00 bond pdb=" N ILE A 679 " pdb=" CA ILE A 679 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.19e-02 7.06e+03 8.40e+00 bond pdb=" N MET B 678 " pdb=" CA MET B 678 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.33e+00 ... (remaining 14734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 18553 1.60 - 3.19: 1233 3.19 - 4.79: 191 4.79 - 6.39: 30 6.39 - 7.98: 9 Bond angle restraints: 20016 Sorted by residual: angle pdb=" N VAL A 512 " pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 113.07 107.60 5.47 1.37e+00 5.33e-01 1.59e+01 angle pdb=" N PHE A 514 " pdb=" CA PHE A 514 " pdb=" C PHE A 514 " ideal model delta sigma weight residual 111.71 107.77 3.94 1.15e+00 7.56e-01 1.17e+01 angle pdb=" N PHE C 514 " pdb=" CA PHE C 514 " pdb=" C PHE C 514 " ideal model delta sigma weight residual 112.34 107.98 4.36 1.30e+00 5.92e-01 1.13e+01 angle pdb=" N PHE B 514 " pdb=" CA PHE B 514 " pdb=" C PHE B 514 " ideal model delta sigma weight residual 112.34 108.14 4.20 1.30e+00 5.92e-01 1.04e+01 angle pdb=" C THR B 509 " pdb=" N SER B 510 " pdb=" CA SER B 510 " ideal model delta sigma weight residual 122.83 118.18 4.65 1.54e+00 4.22e-01 9.10e+00 ... (remaining 20011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 7828 17.39 - 34.79: 698 34.79 - 52.18: 117 52.18 - 69.57: 27 69.57 - 86.96: 27 Dihedral angle restraints: 8697 sinusoidal: 3522 harmonic: 5175 Sorted by residual: dihedral pdb=" CB CYS B 608 " pdb=" SG CYS B 608 " pdb=" SG CYS B 645 " pdb=" CB CYS B 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.35 78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS A 608 " pdb=" SG CYS A 608 " pdb=" SG CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.35 78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS C 608 " pdb=" SG CYS C 608 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.34 78.34 1 1.00e+01 1.00e-02 7.66e+01 ... (remaining 8694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 2268 0.184 - 0.368: 15 0.368 - 0.552: 0 0.552 - 0.735: 0 0.735 - 0.919: 3 Chirality restraints: 2286 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 MAN F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.11e+03 chirality pdb=" C1 MAN D 4 " pdb=" O6 MAN D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.90e+03 chirality pdb=" C1 MAN E 4 " pdb=" O6 MAN E 3 " pdb=" C2 MAN E 4 " pdb=" O5 MAN E 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.76e+03 ... (remaining 2283 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.266 2.00e-02 2.50e+03 2.22e-01 6.17e+02 pdb=" C7 NAG F 2 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.373 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.262 2.00e-02 2.50e+03 2.18e-01 5.96e+02 pdb=" C7 NAG E 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.365 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.187 2.00e-02 2.50e+03 1.54e-01 2.97e+02 pdb=" C7 NAG D 2 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.250 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 37 2.30 - 2.95: 6792 2.95 - 3.60: 19460 3.60 - 4.25: 32642 4.25 - 4.90: 55457 Nonbonded interactions: 114388 Sorted by model distance: nonbonded pdb=" OE2 GLU A 513 " pdb=" OE2 GLU B 513 " model vdw 1.647 3.040 nonbonded pdb=" CD2 LEU A 698 " pdb=" CG1 VAL C 512 " model vdw 1.722 3.880 nonbonded pdb=" OE1 GLU A 513 " pdb=" OE1 GLU B 513 " model vdw 1.767 3.040 nonbonded pdb=" OE2 GLU A 513 " pdb=" CD GLU B 513 " model vdw 1.903 3.270 nonbonded pdb=" CD1 LEU A 517 " pdb=" OE2 GLU B 513 " model vdw 2.121 3.460 ... (remaining 114383 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.480 Find NCS groups from input model: 0.300 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 0.064 14775 Z= 0.299 Angle : 0.909 10.470 20109 Z= 0.507 Chirality : 0.064 0.919 2286 Planarity : 0.009 0.222 2541 Dihedral : 13.846 86.964 5322 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.38 % Allowed : 3.05 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.61 (0.18), residues: 1740 helix: -0.57 (0.28), residues: 303 sheet: -2.12 (0.21), residues: 471 loop : -1.91 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 195 TYR 0.031 0.003 TYR A 302 PHE 0.033 0.003 PHE A 453 TRP 0.024 0.003 TRP C 253 HIS 0.011 0.002 HIS C 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.30 (14739) covalent geometry : angle 0.89415 / 0.50 (20016) SS BOND : bond 0.00672 / 0.34 ( 15) SS BOND : angle 1.97098 / 1.22 ( 30) hydrogen bonds : bond 0.14889 / 9.77 ( 552) hydrogen bonds : angle 8.38383 / 5.76 ( 1719) link_ALPHA1-3 : bond 0.00050 / 0.02 ( 6) link_ALPHA1-3 : angle 0.24000 / 0.13 ( 18) link_ALPHA1-4 : bond 0.00278 / 0.13 ( 3) link_ALPHA1-4 : angle 0.84634 / 0.50 ( 9) link_ALPHA1-6 : bond 0.01438 / 0.66 ( 3) link_ALPHA1-6 : angle 6.99781 / 3.90 ( 9) link_BETA1-4 : bond 0.00172 / 0.08 ( 3) link_BETA1-4 : angle 1.02855 / 0.47 ( 9) link_NAG-ASN : bond 0.00377 / 0.20 ( 6) link_NAG-ASN : angle 1.64878 / 0.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 306 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8022 (tttt) cc_final: 0.7765 (ttpt) REVERT: A 246 ASN cc_start: 0.5972 (m-40) cc_final: 0.5107 (p0) REVERT: A 393 MET cc_start: 0.8555 (mtt) cc_final: 0.8081 (mtm) REVERT: A 401 ILE cc_start: 0.8350 (tt) cc_final: 0.8068 (tt) REVERT: A 657 HIS cc_start: 0.6975 (m-70) cc_final: 0.6485 (t-170) REVERT: B 246 ASN cc_start: 0.6086 (m-40) cc_final: 0.5385 (p0) REVERT: B 393 MET cc_start: 0.8650 (mtt) cc_final: 0.8411 (mtt) REVERT: B 531 MET cc_start: 0.6997 (mmp) cc_final: 0.6760 (mmm) REVERT: B 657 HIS cc_start: 0.7096 (m-70) cc_final: 0.6648 (t-90) REVERT: C 216 LYS cc_start: 0.8099 (tttt) cc_final: 0.7813 (ttpt) REVERT: C 246 ASN cc_start: 0.6355 (m-40) cc_final: 0.5458 (p0) REVERT: C 406 GLU cc_start: 0.7748 (mm-30) cc_final: 0.6719 (tp30) REVERT: C 531 MET cc_start: 0.6817 (mmp) cc_final: 0.6517 (mmm) outliers start: 6 outliers final: 0 residues processed: 312 average time/residue: 0.1530 time to fit residues: 66.2534 Evaluate side-chains 167 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 254 HIS A 543 GLN A 649 HIS A 721 ASN A 724 HIS B 223 ASN B 254 HIS B 543 GLN B 583 ASN B 649 HIS B 721 ASN B 724 HIS C 223 ASN C 254 HIS C 543 GLN C 583 ASN C 649 HIS C 721 ASN C 724 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.157090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122231 restraints weight = 18213.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.125966 restraints weight = 11460.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128719 restraints weight = 8213.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130427 restraints weight = 6386.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.131986 restraints weight = 5344.096| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14775 Z= 0.265 Angle : 0.772 9.096 20109 Z= 0.397 Chirality : 0.050 0.243 2286 Planarity : 0.005 0.043 2541 Dihedral : 4.669 17.379 1974 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.61 % Allowed : 11.70 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.61 (0.18), residues: 1740 helix: 0.34 (0.30), residues: 288 sheet: -1.36 (0.23), residues: 459 loop : -1.34 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 332 TYR 0.028 0.003 TYR A 314 PHE 0.027 0.003 PHE C 148 TRP 0.023 0.003 TRP C 359 HIS 0.008 0.002 HIS B 649 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 (14739) covalent geometry : angle 0.75858 / 0.39 (20016) SS BOND : bond 0.00632 / 0.34 ( 15) SS BOND : angle 2.16363 / 1.31 ( 30) hydrogen bonds : bond 0.04802 / 3.23 ( 552) hydrogen bonds : angle 6.20342 / 4.27 ( 1719) link_ALPHA1-3 : bond 0.00767 / 0.39 ( 6) link_ALPHA1-3 : angle 1.36376 / 0.85 ( 18) link_ALPHA1-4 : bond 0.01290 / 0.59 ( 3) link_ALPHA1-4 : angle 2.63188 / 1.54 ( 9) link_ALPHA1-6 : bond 0.00190 / 0.09 ( 3) link_ALPHA1-6 : angle 2.17116 / 1.25 ( 9) link_BETA1-4 : bond 0.00522 / 0.27 ( 3) link_BETA1-4 : angle 2.51469 / 1.42 ( 9) link_NAG-ASN : bond 0.00835 / 0.34 ( 6) link_NAG-ASN : angle 2.59392 / 1.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8197 (tttt) cc_final: 0.7949 (ttpt) REVERT: A 401 ILE cc_start: 0.8304 (tt) cc_final: 0.8087 (tt) REVERT: A 678 MET cc_start: 0.8204 (tpp) cc_final: 0.7997 (tpp) REVERT: B 215 SER cc_start: 0.8385 (t) cc_final: 0.8064 (t) REVERT: B 393 MET cc_start: 0.8469 (mtt) cc_final: 0.8230 (mtt) REVERT: B 401 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 637 MET cc_start: 0.6789 (mtm) cc_final: 0.6462 (mtm) REVERT: C 215 SER cc_start: 0.7990 (t) cc_final: 0.7633 (t) REVERT: C 657 HIS cc_start: 0.7127 (m-70) cc_final: 0.6871 (t-170) outliers start: 41 outliers final: 20 residues processed: 206 average time/residue: 0.1192 time to fit residues: 37.1535 Evaluate side-chains 156 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 8 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 133 optimal weight: 0.0070 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN A 674 HIS B 411 GLN B 583 ASN ** B 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS C 411 GLN C 458 GLN C 583 ASN C 721 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.159568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125340 restraints weight = 17940.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.129412 restraints weight = 11050.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.132215 restraints weight = 7732.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.133919 restraints weight = 5929.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.135562 restraints weight = 4921.502| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14775 Z= 0.140 Angle : 0.615 8.803 20109 Z= 0.316 Chirality : 0.045 0.169 2286 Planarity : 0.004 0.042 2541 Dihedral : 4.434 18.745 1974 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.04 % Allowed : 15.01 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.18 (0.19), residues: 1740 helix: 1.16 (0.31), residues: 270 sheet: -1.09 (0.22), residues: 459 loop : -1.18 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 611 TYR 0.027 0.002 TYR C 260 PHE 0.021 0.002 PHE C 148 TRP 0.014 0.001 TRP B 180 HIS 0.021 0.001 HIS B 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14739) covalent geometry : angle 0.60199 / 0.31 (20016) SS BOND : bond 0.00804 / 0.38 ( 15) SS BOND : angle 1.91251 / 1.13 ( 30) hydrogen bonds : bond 0.04083 / 2.76 ( 552) hydrogen bonds : angle 5.73803 / 3.96 ( 1719) link_ALPHA1-3 : bond 0.00634 / 0.31 ( 6) link_ALPHA1-3 : angle 1.26295 / 0.79 ( 18) link_ALPHA1-4 : bond 0.01169 / 0.54 ( 3) link_ALPHA1-4 : angle 2.17987 / 1.26 ( 9) link_ALPHA1-6 : bond 0.00273 / 0.13 ( 3) link_ALPHA1-6 : angle 2.59735 / 1.54 ( 9) link_BETA1-4 : bond 0.00927 / 0.41 ( 3) link_BETA1-4 : angle 2.20387 / 1.24 ( 9) link_NAG-ASN : bond 0.00221 / 0.10 ( 6) link_NAG-ASN : angle 1.79732 / 1.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8127 (tttt) cc_final: 0.7874 (ttpt) REVERT: A 401 ILE cc_start: 0.8212 (tt) cc_final: 0.7967 (tt) REVERT: A 596 GLN cc_start: 0.5869 (OUTLIER) cc_final: 0.5353 (mp10) REVERT: A 678 MET cc_start: 0.8023 (tpp) cc_final: 0.7787 (tpp) REVERT: B 401 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7991 (tt) REVERT: B 678 MET cc_start: 0.8016 (tpp) cc_final: 0.7790 (tpp) REVERT: C 198 ILE cc_start: 0.8810 (mt) cc_final: 0.8447 (mt) REVERT: C 215 SER cc_start: 0.7965 (t) cc_final: 0.7610 (t) REVERT: C 396 LEU cc_start: 0.9366 (mt) cc_final: 0.9162 (mp) REVERT: C 531 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6623 (mmp) REVERT: C 657 HIS cc_start: 0.7058 (m-70) cc_final: 0.6756 (t-170) outliers start: 32 outliers final: 17 residues processed: 181 average time/residue: 0.1192 time to fit residues: 32.5985 Evaluate side-chains 161 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 67 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 151 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN ** A 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 674 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.158155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124215 restraints weight = 17847.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.128069 restraints weight = 10955.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.130862 restraints weight = 7706.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.132684 restraints weight = 5902.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.134026 restraints weight = 4862.363| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14775 Z= 0.144 Angle : 0.593 9.000 20109 Z= 0.303 Chirality : 0.044 0.196 2286 Planarity : 0.004 0.040 2541 Dihedral : 4.265 15.583 1974 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.24 % Allowed : 16.28 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.89 (0.19), residues: 1740 helix: 1.53 (0.32), residues: 273 sheet: -0.88 (0.23), residues: 465 loop : -1.03 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.019 0.002 TYR C 260 PHE 0.018 0.002 PHE B 148 TRP 0.012 0.002 TRP C 359 HIS 0.011 0.001 HIS B 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14739) covalent geometry : angle 0.58237 / 0.30 (20016) SS BOND : bond 0.00351 / 0.18 ( 15) SS BOND : angle 1.36351 / 0.83 ( 30) hydrogen bonds : bond 0.03763 / 2.55 ( 552) hydrogen bonds : angle 5.42436 / 3.75 ( 1719) link_ALPHA1-3 : bond 0.00622 / 0.30 ( 6) link_ALPHA1-3 : angle 1.24112 / 0.78 ( 18) link_ALPHA1-4 : bond 0.01166 / 0.54 ( 3) link_ALPHA1-4 : angle 2.26502 / 1.31 ( 9) link_ALPHA1-6 : bond 0.00058 / 0.03 ( 3) link_ALPHA1-6 : angle 2.32026 / 1.37 ( 9) link_BETA1-4 : bond 0.00908 / 0.42 ( 3) link_BETA1-4 : angle 2.19863 / 1.22 ( 9) link_NAG-ASN : bond 0.00204 / 0.10 ( 6) link_NAG-ASN : angle 1.87735 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8073 (tttt) cc_final: 0.7841 (ttpt) REVERT: A 401 ILE cc_start: 0.8129 (tt) cc_final: 0.7884 (tt) REVERT: A 579 ILE cc_start: 0.8601 (mm) cc_final: 0.8321 (mm) REVERT: A 596 GLN cc_start: 0.5859 (OUTLIER) cc_final: 0.5410 (mp10) REVERT: A 719 ARG cc_start: 0.7140 (mtm110) cc_final: 0.6900 (ttm110) REVERT: B 401 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8024 (tt) REVERT: B 430 TYR cc_start: 0.7143 (t80) cc_final: 0.6942 (t80) REVERT: C 215 SER cc_start: 0.8123 (t) cc_final: 0.7742 (t) REVERT: C 260 TYR cc_start: 0.5616 (t80) cc_final: 0.5024 (t80) REVERT: C 430 TYR cc_start: 0.7196 (t80) cc_final: 0.6972 (t80) outliers start: 51 outliers final: 30 residues processed: 198 average time/residue: 0.1159 time to fit residues: 34.8828 Evaluate side-chains 174 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 86 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 674 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.158757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124789 restraints weight = 17989.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.128671 restraints weight = 11002.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.131409 restraints weight = 7704.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133325 restraints weight = 5928.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.134551 restraints weight = 4868.489| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14775 Z= 0.123 Angle : 0.573 8.742 20109 Z= 0.292 Chirality : 0.044 0.180 2286 Planarity : 0.004 0.038 2541 Dihedral : 4.102 14.603 1974 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.48 % Allowed : 18.00 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.61 (0.20), residues: 1740 helix: 1.83 (0.32), residues: 273 sheet: -0.63 (0.23), residues: 465 loop : -0.92 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 440 TYR 0.015 0.001 TYR C 659 PHE 0.015 0.001 PHE C 148 TRP 0.010 0.001 TRP C 180 HIS 0.018 0.001 HIS C 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14739) covalent geometry : angle 0.56329 / 0.29 (20016) SS BOND : bond 0.00278 / 0.14 ( 15) SS BOND : angle 0.97391 / 0.61 ( 30) hydrogen bonds : bond 0.03541 / 2.40 ( 552) hydrogen bonds : angle 5.24528 / 3.63 ( 1719) link_ALPHA1-3 : bond 0.00607 / 0.29 ( 6) link_ALPHA1-3 : angle 1.27132 / 0.79 ( 18) link_ALPHA1-4 : bond 0.01201 / 0.55 ( 3) link_ALPHA1-4 : angle 2.19844 / 1.27 ( 9) link_ALPHA1-6 : bond 0.00131 / 0.06 ( 3) link_ALPHA1-6 : angle 2.23240 / 1.32 ( 9) link_BETA1-4 : bond 0.00933 / 0.43 ( 3) link_BETA1-4 : angle 2.15278 / 1.21 ( 9) link_NAG-ASN : bond 0.00102 / 0.04 ( 6) link_NAG-ASN : angle 1.71009 / 1.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8213 (tt) cc_final: 0.7936 (tt) REVERT: A 517 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 596 GLN cc_start: 0.5781 (OUTLIER) cc_final: 0.5376 (mp10) REVERT: B 401 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7988 (tt) REVERT: B 430 TYR cc_start: 0.7096 (t80) cc_final: 0.6874 (t80) REVERT: B 596 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5718 (mp10) REVERT: B 599 MET cc_start: 0.3741 (mmt) cc_final: 0.3460 (mmt) REVERT: B 678 MET cc_start: 0.8125 (tpp) cc_final: 0.7827 (tpp) REVERT: C 198 ILE cc_start: 0.8744 (mt) cc_final: 0.8397 (mt) REVERT: C 215 SER cc_start: 0.8193 (t) cc_final: 0.7753 (t) outliers start: 39 outliers final: 24 residues processed: 181 average time/residue: 0.1192 time to fit residues: 32.5895 Evaluate side-chains 164 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 596 GLN Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 152 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.156207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.122238 restraints weight = 18218.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.126054 restraints weight = 11254.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128720 restraints weight = 7911.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.130619 restraints weight = 6109.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.131728 restraints weight = 5041.742| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14775 Z= 0.155 Angle : 0.598 8.497 20109 Z= 0.303 Chirality : 0.045 0.206 2286 Planarity : 0.004 0.041 2541 Dihedral : 4.106 16.013 1974 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.93 % Allowed : 19.34 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.58 (0.20), residues: 1740 helix: 1.90 (0.31), residues: 270 sheet: -0.38 (0.23), residues: 477 loop : -1.05 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 611 TYR 0.019 0.002 TYR C 430 PHE 0.014 0.002 PHE A 148 TRP 0.014 0.002 TRP C 359 HIS 0.005 0.001 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (14739) covalent geometry : angle 0.58795 / 0.30 (20016) SS BOND : bond 0.00358 / 0.18 ( 15) SS BOND : angle 0.99810 / 0.62 ( 30) hydrogen bonds : bond 0.03590 / 2.45 ( 552) hydrogen bonds : angle 5.20542 / 3.59 ( 1719) link_ALPHA1-3 : bond 0.00659 / 0.31 ( 6) link_ALPHA1-3 : angle 1.21086 / 0.76 ( 18) link_ALPHA1-4 : bond 0.01133 / 0.52 ( 3) link_ALPHA1-4 : angle 2.35769 / 1.36 ( 9) link_ALPHA1-6 : bond 0.00038 / 0.02 ( 3) link_ALPHA1-6 : angle 2.18913 / 1.28 ( 9) link_BETA1-4 : bond 0.00859 / 0.39 ( 3) link_BETA1-4 : angle 2.26404 / 1.25 ( 9) link_NAG-ASN : bond 0.00177 / 0.08 ( 6) link_NAG-ASN : angle 1.98684 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8189 (tt) cc_final: 0.7935 (tt) REVERT: A 554 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.5388 (t80) REVERT: A 596 GLN cc_start: 0.5857 (OUTLIER) cc_final: 0.5435 (mp10) REVERT: A 719 ARG cc_start: 0.7122 (mtm110) cc_final: 0.6877 (ttm110) REVERT: B 401 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7987 (tt) REVERT: B 596 GLN cc_start: 0.6155 (OUTLIER) cc_final: 0.5829 (mp10) REVERT: B 599 MET cc_start: 0.3656 (mmt) cc_final: 0.3383 (mmt) outliers start: 46 outliers final: 34 residues processed: 170 average time/residue: 0.1196 time to fit residues: 30.6492 Evaluate side-chains 168 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 596 GLN Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 118 optimal weight: 0.0070 chunk 164 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.156777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122378 restraints weight = 18002.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.126323 restraints weight = 10813.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.129125 restraints weight = 7494.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.130993 restraints weight = 5720.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.132498 restraints weight = 4692.960| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14775 Z= 0.116 Angle : 0.565 8.870 20109 Z= 0.285 Chirality : 0.044 0.191 2286 Planarity : 0.004 0.040 2541 Dihedral : 3.993 16.220 1974 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.05 % Allowed : 19.53 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.41 (0.20), residues: 1740 helix: 2.12 (0.32), residues: 270 sheet: -0.28 (0.23), residues: 483 loop : -0.95 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 719 TYR 0.015 0.001 TYR C 260 PHE 0.014 0.001 PHE B 148 TRP 0.011 0.001 TRP B 180 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14739) covalent geometry : angle 0.55631 / 0.28 (20016) SS BOND : bond 0.00253 / 0.13 ( 15) SS BOND : angle 0.84895 / 0.55 ( 30) hydrogen bonds : bond 0.03420 / 2.33 ( 552) hydrogen bonds : angle 5.06826 / 3.50 ( 1719) link_ALPHA1-3 : bond 0.00595 / 0.28 ( 6) link_ALPHA1-3 : angle 1.25758 / 0.78 ( 18) link_ALPHA1-4 : bond 0.01178 / 0.54 ( 3) link_ALPHA1-4 : angle 2.20223 / 1.26 ( 9) link_ALPHA1-6 : bond 0.00082 / 0.04 ( 3) link_ALPHA1-6 : angle 2.11794 / 1.24 ( 9) link_BETA1-4 : bond 0.01023 / 0.47 ( 3) link_BETA1-4 : angle 2.19593 / 1.24 ( 9) link_NAG-ASN : bond 0.00059 / 0.03 ( 6) link_NAG-ASN : angle 1.61123 / 0.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.619 Fit side-chains REVERT: A 401 ILE cc_start: 0.8227 (tt) cc_final: 0.7971 (tt) REVERT: A 596 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5519 (mp10) REVERT: A 719 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6883 (mtm110) REVERT: B 401 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7896 (tt) REVERT: B 596 GLN cc_start: 0.6145 (OUTLIER) cc_final: 0.5869 (mp10) REVERT: B 599 MET cc_start: 0.3733 (mmt) cc_final: 0.3478 (mmt) REVERT: B 678 MET cc_start: 0.8166 (tpp) cc_final: 0.7851 (tpp) REVERT: B 719 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6978 (mtm110) REVERT: C 554 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.5890 (t80) REVERT: C 579 ILE cc_start: 0.8488 (mm) cc_final: 0.8107 (mm) REVERT: C 637 MET cc_start: 0.6862 (mmp) cc_final: 0.6505 (mtm) outliers start: 48 outliers final: 32 residues processed: 182 average time/residue: 0.1067 time to fit residues: 30.0040 Evaluate side-chains 162 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 596 GLN Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 705 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 162 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.155887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.121268 restraints weight = 18274.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.125160 restraints weight = 11366.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.127574 restraints weight = 7980.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.129651 restraints weight = 6244.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.130755 restraints weight = 5134.074| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14775 Z= 0.141 Angle : 0.591 9.119 20109 Z= 0.297 Chirality : 0.045 0.207 2286 Planarity : 0.004 0.040 2541 Dihedral : 4.027 15.348 1974 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 20.17 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.41 (0.20), residues: 1740 helix: 1.93 (0.31), residues: 276 sheet: -0.21 (0.23), residues: 483 loop : -0.95 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 719 TYR 0.016 0.001 TYR C 260 PHE 0.013 0.002 PHE C 148 TRP 0.013 0.001 TRP B 359 HIS 0.005 0.001 HIS C 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14739) covalent geometry : angle 0.58148 / 0.30 (20016) SS BOND : bond 0.00290 / 0.14 ( 15) SS BOND : angle 1.17528 / 0.72 ( 30) hydrogen bonds : bond 0.03484 / 2.37 ( 552) hydrogen bonds : angle 5.07335 / 3.50 ( 1719) link_ALPHA1-3 : bond 0.00649 / 0.31 ( 6) link_ALPHA1-3 : angle 1.21735 / 0.76 ( 18) link_ALPHA1-4 : bond 0.01122 / 0.52 ( 3) link_ALPHA1-4 : angle 2.33830 / 1.35 ( 9) link_ALPHA1-6 : bond 0.00044 / 0.02 ( 3) link_ALPHA1-6 : angle 2.08507 / 1.22 ( 9) link_BETA1-4 : bond 0.00941 / 0.44 ( 3) link_BETA1-4 : angle 2.25516 / 1.25 ( 9) link_NAG-ASN : bond 0.00147 / 0.07 ( 6) link_NAG-ASN : angle 1.85336 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7992 (tt) REVERT: A 554 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.5702 (t80) REVERT: A 596 GLN cc_start: 0.5934 (OUTLIER) cc_final: 0.5568 (mp10) REVERT: B 401 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7903 (tt) REVERT: B 596 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5957 (mp10) REVERT: B 599 MET cc_start: 0.4053 (mmt) cc_final: 0.3830 (mmt) REVERT: B 678 MET cc_start: 0.8283 (tpp) cc_final: 0.7900 (tpp) REVERT: C 554 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.5951 (t80) REVERT: C 579 ILE cc_start: 0.8518 (mm) cc_final: 0.8069 (mm) REVERT: C 637 MET cc_start: 0.6905 (mmp) cc_final: 0.6412 (mtm) outliers start: 48 outliers final: 38 residues processed: 164 average time/residue: 0.1136 time to fit residues: 28.1801 Evaluate side-chains 167 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 596 GLN Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.155158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120582 restraints weight = 18556.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.124440 restraints weight = 11198.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.127180 restraints weight = 7811.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.129120 restraints weight = 5977.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.130285 restraints weight = 4928.995| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14775 Z= 0.141 Angle : 0.593 9.034 20109 Z= 0.298 Chirality : 0.044 0.210 2286 Planarity : 0.004 0.040 2541 Dihedral : 4.033 15.291 1974 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.93 % Allowed : 20.42 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.39 (0.20), residues: 1740 helix: 2.01 (0.31), residues: 273 sheet: -0.21 (0.23), residues: 483 loop : -0.94 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 719 TYR 0.018 0.002 TYR C 260 PHE 0.013 0.002 PHE C 695 TRP 0.013 0.001 TRP B 359 HIS 0.005 0.001 HIS C 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (14739) covalent geometry : angle 0.58342 / 0.30 (20016) SS BOND : bond 0.00313 / 0.15 ( 15) SS BOND : angle 1.02408 / 0.63 ( 30) hydrogen bonds : bond 0.03470 / 2.36 ( 552) hydrogen bonds : angle 5.05888 / 3.50 ( 1719) link_ALPHA1-3 : bond 0.00659 / 0.31 ( 6) link_ALPHA1-3 : angle 1.20865 / 0.75 ( 18) link_ALPHA1-4 : bond 0.01116 / 0.52 ( 3) link_ALPHA1-4 : angle 2.35020 / 1.35 ( 9) link_ALPHA1-6 : bond 0.00056 / 0.03 ( 3) link_ALPHA1-6 : angle 2.06658 / 1.21 ( 9) link_BETA1-4 : bond 0.00959 / 0.44 ( 3) link_BETA1-4 : angle 2.28316 / 1.27 ( 9) link_NAG-ASN : bond 0.00114 / 0.06 ( 6) link_NAG-ASN : angle 1.78544 / 1.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.565 Fit side-chains REVERT: A 401 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 554 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.5933 (t80) REVERT: A 596 GLN cc_start: 0.5921 (OUTLIER) cc_final: 0.5554 (mp10) REVERT: B 401 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7893 (tt) REVERT: B 596 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5891 (mp10) REVERT: C 554 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6111 (t80) REVERT: C 579 ILE cc_start: 0.8536 (mm) cc_final: 0.8079 (mm) REVERT: C 637 MET cc_start: 0.6913 (mmp) cc_final: 0.6367 (mtm) outliers start: 46 outliers final: 38 residues processed: 158 average time/residue: 0.1037 time to fit residues: 24.8706 Evaluate side-chains 167 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 596 GLN Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 705 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 110 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 168 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS B 143 HIS B 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.156321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.122019 restraints weight = 18252.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.125773 restraints weight = 11171.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128479 restraints weight = 7859.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.130408 restraints weight = 6089.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.131531 restraints weight = 5022.864| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14775 Z= 0.126 Angle : 0.587 9.069 20109 Z= 0.295 Chirality : 0.044 0.203 2286 Planarity : 0.004 0.040 2541 Dihedral : 3.996 16.704 1974 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.86 % Allowed : 20.42 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.33 (0.20), residues: 1740 helix: 2.06 (0.31), residues: 273 sheet: -0.14 (0.23), residues: 483 loop : -0.92 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 719 TYR 0.019 0.001 TYR C 260 PHE 0.012 0.001 PHE B 148 TRP 0.012 0.001 TRP B 359 HIS 0.004 0.001 HIS C 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14739) covalent geometry : angle 0.57854 / 0.29 (20016) SS BOND : bond 0.00262 / 0.13 ( 15) SS BOND : angle 0.87853 / 0.56 ( 30) hydrogen bonds : bond 0.03406 / 2.31 ( 552) hydrogen bonds : angle 5.02005 / 3.47 ( 1719) link_ALPHA1-3 : bond 0.00644 / 0.30 ( 6) link_ALPHA1-3 : angle 1.22115 / 0.76 ( 18) link_ALPHA1-4 : bond 0.01113 / 0.51 ( 3) link_ALPHA1-4 : angle 2.33876 / 1.34 ( 9) link_ALPHA1-6 : bond 0.00020 / 0.01 ( 3) link_ALPHA1-6 : angle 2.02477 / 1.18 ( 9) link_BETA1-4 : bond 0.00971 / 0.45 ( 3) link_BETA1-4 : angle 2.27424 / 1.27 ( 9) link_NAG-ASN : bond 0.00058 / 0.03 ( 6) link_NAG-ASN : angle 1.66599 / 0.98 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7986 (tt) REVERT: A 554 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6172 (t80) REVERT: A 596 GLN cc_start: 0.5937 (OUTLIER) cc_final: 0.5597 (mp10) REVERT: A 719 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6983 (ttp-110) REVERT: B 401 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7762 (tt) REVERT: B 678 MET cc_start: 0.8287 (tpp) cc_final: 0.7896 (tpp) REVERT: C 554 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6158 (t80) REVERT: C 579 ILE cc_start: 0.8512 (mm) cc_final: 0.8060 (mm) REVERT: C 637 MET cc_start: 0.6914 (mmp) cc_final: 0.6344 (mtm) REVERT: C 678 MET cc_start: 0.8135 (tpp) cc_final: 0.7793 (tpp) outliers start: 45 outliers final: 33 residues processed: 160 average time/residue: 0.1122 time to fit residues: 27.0791 Evaluate side-chains 164 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 148 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.120021 restraints weight = 18493.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.123824 restraints weight = 11239.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.126508 restraints weight = 7892.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128280 restraints weight = 6112.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.129650 restraints weight = 5062.350| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14775 Z= 0.149 Angle : 0.609 8.979 20109 Z= 0.306 Chirality : 0.045 0.243 2286 Planarity : 0.004 0.040 2541 Dihedral : 4.041 16.138 1974 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.67 % Allowed : 20.42 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.33 (0.20), residues: 1740 helix: 1.91 (0.31), residues: 276 sheet: -0.10 (0.23), residues: 483 loop : -0.91 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 719 TYR 0.020 0.002 TYR C 260 PHE 0.013 0.002 PHE C 695 TRP 0.015 0.002 TRP B 359 HIS 0.005 0.001 HIS C 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (14739) covalent geometry : angle 0.59980 / 0.30 (20016) SS BOND : bond 0.00288 / 0.13 ( 15) SS BOND : angle 0.93057 / 0.59 ( 30) hydrogen bonds : bond 0.03446 / 2.35 ( 552) hydrogen bonds : angle 5.06725 / 3.51 ( 1719) link_ALPHA1-3 : bond 0.00683 / 0.32 ( 6) link_ALPHA1-3 : angle 1.18261 / 0.73 ( 18) link_ALPHA1-4 : bond 0.01069 / 0.49 ( 3) link_ALPHA1-4 : angle 2.44458 / 1.40 ( 9) link_ALPHA1-6 : bond 0.00121 / 0.06 ( 3) link_ALPHA1-6 : angle 2.02217 / 1.18 ( 9) link_BETA1-4 : bond 0.00956 / 0.44 ( 3) link_BETA1-4 : angle 2.37549 / 1.31 ( 9) link_NAG-ASN : bond 0.00164 / 0.08 ( 6) link_NAG-ASN : angle 1.83686 / 1.09 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2202.23 seconds wall clock time: 39 minutes 19.86 seconds (2359.86 seconds total)