Starting phenix.real_space_refine on Mon Apr 6 00:19:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k1s_22629/04_2026/7k1s_22629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k1s_22629/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k1s_22629/04_2026/7k1s_22629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k1s_22629/04_2026/7k1s_22629.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k1s_22629/04_2026/7k1s_22629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k1s_22629/04_2026/7k1s_22629.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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 dihedrals: 18 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 dihedrals: 18 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 dihedrals: 18 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.77, per 1000 atoms: 0.26 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: 1.42 Conformation dependent library (CDL) restraints added in 535.8 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: 0.63 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: 2.76 Time building geometry restraints manager: 1.88 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 - 23.24: 8554 23.24 - 46.48: 464 46.48 - 69.72: 48 69.72 - 92.96: 42 92.96 - 116.20: 6 Dihedral angle restraints: 9114 sinusoidal: 3939 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 9111 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.090 Find NCS groups from input model: 0.290 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 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 : 14.988 116.195 5739 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 covalent geometry : bond 0.00632 (14739) covalent geometry : angle 0.89415 (20016) SS BOND : bond 0.00672 ( 15) SS BOND : angle 1.97098 ( 30) hydrogen bonds : bond 0.14889 ( 552) hydrogen bonds : angle 8.38383 ( 1719) link_ALPHA1-3 : bond 0.00050 ( 6) link_ALPHA1-3 : angle 0.24000 ( 18) link_ALPHA1-4 : bond 0.00278 ( 3) link_ALPHA1-4 : angle 0.84634 ( 9) link_ALPHA1-6 : bond 0.01438 ( 3) link_ALPHA1-6 : angle 6.99781 ( 9) link_BETA1-4 : bond 0.00172 ( 3) link_BETA1-4 : angle 1.02855 ( 9) link_NAG-ASN : bond 0.00377 ( 6) link_NAG-ASN : angle 1.64878 ( 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 : 0.527 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: 0.1456 time to fit residues: 62.6221 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 : 0.562 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 254 HIS A 411 GLN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.156637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121802 restraints weight = 18256.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125528 restraints weight = 11506.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.128278 restraints weight = 8263.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130232 restraints weight = 6410.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.131515 restraints weight = 5313.772| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14775 Z= 0.264 Angle : 0.781 8.556 20109 Z= 0.401 Chirality : 0.049 0.198 2286 Planarity : 0.005 0.043 2541 Dihedral : 8.772 82.725 2391 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.67 % Allowed : 11.77 % Favored : 85.56 % 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: -1.61 (0.19), residues: 1740 helix: 0.26 (0.30), residues: 288 sheet: -1.30 (0.23), residues: 468 loop : -1.34 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 332 TYR 0.027 0.003 TYR A 314 PHE 0.026 0.003 PHE C 148 TRP 0.023 0.003 TRP C 359 HIS 0.008 0.002 HIS C 527 Details of bonding type rmsd covalent geometry : bond 0.00611 (14739) covalent geometry : angle 0.76536 (20016) SS BOND : bond 0.00859 ( 15) SS BOND : angle 2.15258 ( 30) hydrogen bonds : bond 0.04826 ( 552) hydrogen bonds : angle 6.20244 ( 1719) link_ALPHA1-3 : bond 0.00702 ( 6) link_ALPHA1-3 : angle 1.51069 ( 18) link_ALPHA1-4 : bond 0.01148 ( 3) link_ALPHA1-4 : angle 1.95688 ( 9) link_ALPHA1-6 : bond 0.00878 ( 3) link_ALPHA1-6 : angle 2.34952 ( 9) link_BETA1-4 : bond 0.00356 ( 3) link_BETA1-4 : angle 3.93897 ( 9) link_NAG-ASN : bond 0.01074 ( 6) link_NAG-ASN : angle 2.70358 ( 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 215 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.718 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: 0.8217 (tttt) cc_final: 0.7964 (ttpt) REVERT: A 401 ILE cc_start: 0.8285 (tt) cc_final: 0.8053 (tt) REVERT: B 215 SER cc_start: 0.8356 (t) cc_final: 0.8006 (t) REVERT: B 393 MET cc_start: 0.8472 (mtt) cc_final: 0.8210 (mtt) REVERT: B 401 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8139 (tt) REVERT: B 637 MET cc_start: 0.6794 (mtm) cc_final: 0.6464 (mtm) REVERT: B 678 MET cc_start: 0.7946 (tpp) cc_final: 0.7623 (tpp) REVERT: C 215 SER cc_start: 0.8016 (t) cc_final: 0.7679 (t) REVERT: C 657 HIS cc_start: 0.7132 (m-70) cc_final: 0.6874 (t-170) outliers start: 42 outliers final: 22 residues processed: 207 average time/residue: 0.1099 time to fit residues: 34.5775 Evaluate side-chains 163 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 410 ASN 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 566 LEU 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: 1.9990 chunk 118 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 133 optimal weight: 0.0970 chunk 148 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 674 HIS A 724 HIS B 411 GLN B 583 ASN B 674 HIS B 724 HIS C 143 HIS C 411 GLN C 458 GLN C 525 GLN C 583 ASN C 721 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.159603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125515 restraints weight = 17946.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129482 restraints weight = 10987.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132278 restraints weight = 7687.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.134307 restraints weight = 5903.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.135637 restraints weight = 4830.203| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2677 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= 0.136 Angle : 0.619 8.672 20109 Z= 0.315 Chirality : 0.045 0.236 2286 Planarity : 0.004 0.041 2541 Dihedral : 8.288 79.099 2391 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.91 % Allowed : 15.97 % Favored : 82.12 % 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: -1.17 (0.19), residues: 1740 helix: 1.19 (0.32), residues: 270 sheet: -1.10 (0.22), residues: 465 loop : -1.16 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 611 TYR 0.020 0.002 TYR B 659 PHE 0.021 0.002 PHE B 148 TRP 0.013 0.001 TRP C 180 HIS 0.018 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00306 (14739) covalent geometry : angle 0.60362 (20016) SS BOND : bond 0.00405 ( 15) SS BOND : angle 1.77427 ( 30) hydrogen bonds : bond 0.04047 ( 552) hydrogen bonds : angle 5.69953 ( 1719) link_ALPHA1-3 : bond 0.00520 ( 6) link_ALPHA1-3 : angle 1.36571 ( 18) link_ALPHA1-4 : bond 0.01274 ( 3) link_ALPHA1-4 : angle 2.02844 ( 9) link_ALPHA1-6 : bond 0.00210 ( 3) link_ALPHA1-6 : angle 2.76971 ( 9) link_BETA1-4 : bond 0.00528 ( 3) link_BETA1-4 : angle 3.58250 ( 9) link_NAG-ASN : bond 0.00303 ( 6) link_NAG-ASN : angle 1.75694 ( 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 195 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8124 (tttt) cc_final: 0.7853 (ttpt) REVERT: A 401 ILE cc_start: 0.8196 (tt) cc_final: 0.7961 (tt) REVERT: A 596 GLN cc_start: 0.5826 (OUTLIER) cc_final: 0.5300 (mp10) REVERT: A 678 MET cc_start: 0.8188 (tpp) cc_final: 0.7925 (tpp) REVERT: B 198 ILE cc_start: 0.8819 (mt) cc_final: 0.8530 (mt) REVERT: B 401 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8014 (tt) REVERT: C 198 ILE cc_start: 0.8793 (mt) cc_final: 0.8429 (mt) REVERT: C 215 SER cc_start: 0.7975 (t) cc_final: 0.7603 (t) REVERT: C 531 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6603 (mmp) REVERT: C 657 HIS cc_start: 0.7099 (m-70) cc_final: 0.6815 (t-170) outliers start: 30 outliers final: 15 residues processed: 186 average time/residue: 0.1115 time to fit residues: 31.4521 Evaluate side-chains 156 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 67 optimal weight: 0.0470 chunk 126 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 151 optimal weight: 0.0030 chunk 1 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 724 HIS B 458 GLN B 674 HIS B 724 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.159047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.124821 restraints weight = 17841.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.128826 restraints weight = 10802.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.131633 restraints weight = 7526.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.133623 restraints weight = 5753.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.134798 restraints weight = 4707.415| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14775 Z= 0.130 Angle : 0.596 8.637 20109 Z= 0.301 Chirality : 0.044 0.181 2286 Planarity : 0.004 0.040 2541 Dihedral : 7.674 71.647 2391 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.93 % Allowed : 16.48 % Favored : 80.60 % 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: -0.81 (0.19), residues: 1740 helix: 1.62 (0.32), residues: 273 sheet: -0.82 (0.22), residues: 477 loop : -1.00 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 611 TYR 0.022 0.002 TYR C 260 PHE 0.018 0.002 PHE B 148 TRP 0.011 0.001 TRP C 359 HIS 0.010 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00292 (14739) covalent geometry : angle 0.58155 (20016) SS BOND : bond 0.00305 ( 15) SS BOND : angle 1.32189 ( 30) hydrogen bonds : bond 0.03676 ( 552) hydrogen bonds : angle 5.36676 ( 1719) link_ALPHA1-3 : bond 0.00524 ( 6) link_ALPHA1-3 : angle 1.33811 ( 18) link_ALPHA1-4 : bond 0.01034 ( 3) link_ALPHA1-4 : angle 2.31996 ( 9) link_ALPHA1-6 : bond 0.00119 ( 3) link_ALPHA1-6 : angle 2.56283 ( 9) link_BETA1-4 : bond 0.00444 ( 3) link_BETA1-4 : angle 3.81467 ( 9) link_NAG-ASN : bond 0.00303 ( 6) link_NAG-ASN : angle 1.79581 ( 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: 46 poor density : 163 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8064 (tttt) cc_final: 0.7816 (ttpt) REVERT: A 401 ILE cc_start: 0.8122 (tt) cc_final: 0.7873 (tt) REVERT: A 579 ILE cc_start: 0.8601 (mm) cc_final: 0.8328 (mm) REVERT: A 596 GLN cc_start: 0.5906 (OUTLIER) cc_final: 0.5337 (mp10) REVERT: A 678 MET cc_start: 0.8024 (tpp) cc_final: 0.7823 (tpp) REVERT: A 719 ARG cc_start: 0.7125 (mtm110) cc_final: 0.6894 (ttm110) REVERT: B 198 ILE cc_start: 0.8793 (mt) cc_final: 0.8499 (mt) REVERT: B 401 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8003 (tt) REVERT: B 430 TYR cc_start: 0.7103 (t80) cc_final: 0.6847 (t80) REVERT: C 215 SER cc_start: 0.8067 (t) cc_final: 0.7683 (t) REVERT: C 554 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5334 (t80) REVERT: C 579 ILE cc_start: 0.8605 (mm) cc_final: 0.8092 (mt) outliers start: 46 outliers final: 26 residues processed: 200 average time/residue: 0.1200 time to fit residues: 35.6663 Evaluate side-chains 174 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 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 299 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 520 THR 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 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 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 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: 0.5980 chunk 35 optimal weight: 0.0970 chunk 86 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.158672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124901 restraints weight = 18001.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.128788 restraints weight = 11007.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131606 restraints weight = 7677.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.133484 restraints weight = 5881.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.134633 restraints weight = 4845.593| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3260 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= 0.127 Angle : 0.594 8.848 20109 Z= 0.298 Chirality : 0.044 0.192 2286 Planarity : 0.004 0.039 2541 Dihedral : 7.270 66.868 2391 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.35 % Allowed : 18.38 % Favored : 79.26 % 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: -0.62 (0.20), residues: 1740 helix: 1.79 (0.32), residues: 273 sheet: -0.61 (0.23), residues: 477 loop : -0.93 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 440 TYR 0.013 0.001 TYR C 659 PHE 0.015 0.001 PHE C 148 TRP 0.010 0.001 TRP A 359 HIS 0.019 0.001 HIS C 657 Details of bonding type rmsd covalent geometry : bond 0.00288 (14739) covalent geometry : angle 0.57972 (20016) SS BOND : bond 0.00280 ( 15) SS BOND : angle 0.96551 ( 30) hydrogen bonds : bond 0.03578 ( 552) hydrogen bonds : angle 5.23233 ( 1719) link_ALPHA1-3 : bond 0.00485 ( 6) link_ALPHA1-3 : angle 1.35591 ( 18) link_ALPHA1-4 : bond 0.01004 ( 3) link_ALPHA1-4 : angle 2.45152 ( 9) link_ALPHA1-6 : bond 0.00158 ( 3) link_ALPHA1-6 : angle 2.52337 ( 9) link_BETA1-4 : bond 0.00499 ( 3) link_BETA1-4 : angle 3.89119 ( 9) link_NAG-ASN : bond 0.00261 ( 6) link_NAG-ASN : angle 1.73476 ( 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 187 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8183 (tt) cc_final: 0.7906 (tt) REVERT: A 596 GLN cc_start: 0.5878 (OUTLIER) cc_final: 0.5391 (mp10) REVERT: A 678 MET cc_start: 0.7993 (tpp) cc_final: 0.7780 (tpp) REVERT: B 198 ILE cc_start: 0.8786 (mt) cc_final: 0.8557 (mt) REVERT: B 401 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8039 (tt) REVERT: B 596 GLN cc_start: 0.6036 (OUTLIER) cc_final: 0.5709 (mp10) REVERT: B 599 MET cc_start: 0.3699 (mmt) cc_final: 0.3411 (mmt) REVERT: B 678 MET cc_start: 0.8121 (tpp) cc_final: 0.7756 (tpp) REVERT: C 215 SER cc_start: 0.8180 (t) cc_final: 0.7775 (t) outliers start: 37 outliers final: 26 residues processed: 176 average time/residue: 0.1258 time to fit residues: 32.4931 Evaluate side-chains 166 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 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 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 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 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 713 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 152 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 125 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4190 r_free = 0.4190 target = 0.158674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.122515 restraints weight = 17980.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.127073 restraints weight = 10284.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130242 restraints weight = 6878.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.132522 restraints weight = 5126.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.133845 restraints weight = 4122.483| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3434 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= 0.112 Angle : 0.572 8.446 20109 Z= 0.286 Chirality : 0.043 0.175 2286 Planarity : 0.004 0.040 2541 Dihedral : 6.708 62.213 2391 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.61 % Allowed : 19.15 % Favored : 78.24 % 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: -0.47 (0.20), residues: 1740 helix: 2.02 (0.32), residues: 270 sheet: -0.46 (0.23), residues: 465 loop : -0.88 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 611 TYR 0.014 0.001 TYR C 260 PHE 0.014 0.001 PHE C 148 TRP 0.010 0.001 TRP C 359 HIS 0.005 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00254 (14739) covalent geometry : angle 0.55751 (20016) SS BOND : bond 0.00249 ( 15) SS BOND : angle 0.87575 ( 30) hydrogen bonds : bond 0.03450 ( 552) hydrogen bonds : angle 5.08278 ( 1719) link_ALPHA1-3 : bond 0.00460 ( 6) link_ALPHA1-3 : angle 1.37289 ( 18) link_ALPHA1-4 : bond 0.00933 ( 3) link_ALPHA1-4 : angle 2.59726 ( 9) link_ALPHA1-6 : bond 0.00139 ( 3) link_ALPHA1-6 : angle 2.43366 ( 9) link_BETA1-4 : bond 0.00479 ( 3) link_BETA1-4 : angle 3.89788 ( 9) link_NAG-ASN : bond 0.00101 ( 6) link_NAG-ASN : angle 1.52238 ( 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 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8211 (tt) cc_final: 0.7876 (tt) REVERT: A 596 GLN cc_start: 0.5824 (OUTLIER) cc_final: 0.5408 (mp10) REVERT: A 719 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6832 (ttm110) REVERT: B 198 ILE cc_start: 0.8771 (mt) cc_final: 0.8545 (mt) REVERT: B 401 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7933 (tt) REVERT: B 596 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5838 (mp10) REVERT: B 599 MET cc_start: 0.3566 (mmt) cc_final: 0.3274 (mmt) REVERT: C 170 TYR cc_start: 0.7376 (m-80) cc_final: 0.7171 (m-80) REVERT: C 215 SER cc_start: 0.8167 (t) cc_final: 0.7758 (t) REVERT: C 554 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6026 (t80) outliers start: 41 outliers final: 27 residues processed: 184 average time/residue: 0.1109 time to fit residues: 30.7580 Evaluate side-chains 166 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 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 280 GLU Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 520 THR 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 696 MET Chi-restraints excluded: chain C residue 700 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 144 optimal weight: 0.0870 chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 190 ASN B 190 ASN C 190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.151429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117411 restraints weight = 18547.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.120935 restraints weight = 11531.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.123514 restraints weight = 8223.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.125249 restraints weight = 6386.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.126460 restraints weight = 5329.482| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14775 Z= 0.218 Angle : 0.682 8.794 20109 Z= 0.343 Chirality : 0.047 0.236 2286 Planarity : 0.004 0.040 2541 Dihedral : 6.364 53.873 2391 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.44 % Allowed : 19.97 % Favored : 76.59 % 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: -0.72 (0.19), residues: 1740 helix: 1.54 (0.31), residues: 273 sheet: -0.32 (0.23), residues: 483 loop : -1.15 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 719 TYR 0.021 0.002 TYR B 430 PHE 0.020 0.002 PHE B 293 TRP 0.021 0.002 TRP C 359 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00507 (14739) covalent geometry : angle 0.66574 (20016) SS BOND : bond 0.00468 ( 15) SS BOND : angle 1.13572 ( 30) hydrogen bonds : bond 0.03878 ( 552) hydrogen bonds : angle 5.31004 ( 1719) link_ALPHA1-3 : bond 0.00645 ( 6) link_ALPHA1-3 : angle 1.22255 ( 18) link_ALPHA1-4 : bond 0.00869 ( 3) link_ALPHA1-4 : angle 2.99599 ( 9) link_ALPHA1-6 : bond 0.00186 ( 3) link_ALPHA1-6 : angle 2.51926 ( 9) link_BETA1-4 : bond 0.00344 ( 3) link_BETA1-4 : angle 4.23663 ( 9) link_NAG-ASN : bond 0.00518 ( 6) link_NAG-ASN : angle 2.47747 ( 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 188 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 134 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8156 (tt) cc_final: 0.7897 (tt) REVERT: A 554 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.5502 (t80) REVERT: A 596 GLN cc_start: 0.5867 (OUTLIER) cc_final: 0.5453 (mp10) REVERT: A 678 MET cc_start: 0.8299 (tpp) cc_final: 0.8063 (tpp) REVERT: B 401 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7989 (tt) REVERT: B 599 MET cc_start: 0.4035 (mmt) cc_final: 0.3744 (mmt) REVERT: B 678 MET cc_start: 0.8293 (tpp) cc_final: 0.8064 (tpp) REVERT: C 554 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5993 (t80) REVERT: C 637 MET cc_start: 0.6911 (mmp) cc_final: 0.6510 (mtm) outliers start: 54 outliers final: 38 residues processed: 174 average time/residue: 0.1069 time to fit residues: 28.9223 Evaluate side-chains 168 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 356 THR 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 589 SER 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 566 LEU 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 171 TYR 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 509 THR Chi-restraints excluded: chain C residue 520 THR 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 713 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 162 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN B 190 ASN C 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.154874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.120687 restraints weight = 18264.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.124515 restraints weight = 11035.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127197 restraints weight = 7686.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.129136 restraints weight = 5900.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130247 restraints weight = 4857.393| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14775 Z= 0.136 Angle : 0.605 8.925 20109 Z= 0.302 Chirality : 0.044 0.209 2286 Planarity : 0.004 0.039 2541 Dihedral : 5.967 51.613 2391 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.18 % Allowed : 20.42 % Favored : 76.40 % 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: -0.56 (0.20), residues: 1740 helix: 1.75 (0.31), residues: 273 sheet: -0.24 (0.23), residues: 483 loop : -1.06 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 611 TYR 0.024 0.002 TYR B 260 PHE 0.013 0.001 PHE B 148 TRP 0.012 0.001 TRP C 180 HIS 0.005 0.001 HIS C 527 Details of bonding type rmsd covalent geometry : bond 0.00312 (14739) covalent geometry : angle 0.58940 (20016) SS BOND : bond 0.00278 ( 15) SS BOND : angle 1.18575 ( 30) hydrogen bonds : bond 0.03566 ( 552) hydrogen bonds : angle 5.15805 ( 1719) link_ALPHA1-3 : bond 0.00551 ( 6) link_ALPHA1-3 : angle 1.31941 ( 18) link_ALPHA1-4 : bond 0.00918 ( 3) link_ALPHA1-4 : angle 3.04096 ( 9) link_ALPHA1-6 : bond 0.00075 ( 3) link_ALPHA1-6 : angle 2.50999 ( 9) link_BETA1-4 : bond 0.00478 ( 3) link_BETA1-4 : angle 4.04053 ( 9) link_NAG-ASN : bond 0.00142 ( 6) link_NAG-ASN : angle 1.69078 ( 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: 50 poor density : 127 time to evaluate : 0.494 Fit side-chains REVERT: A 401 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7936 (tt) REVERT: A 554 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.5762 (t80) REVERT: A 596 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.5534 (mp10) REVERT: A 678 MET cc_start: 0.8286 (tpp) cc_final: 0.7986 (tpp) REVERT: A 719 ARG cc_start: 0.7207 (mtm110) cc_final: 0.6963 (ttm110) REVERT: B 401 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7965 (tt) REVERT: B 596 GLN cc_start: 0.6092 (OUTLIER) cc_final: 0.5858 (mp10) REVERT: B 678 MET cc_start: 0.8188 (tpp) cc_final: 0.7849 (tpp) REVERT: C 554 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6222 (t80) REVERT: C 637 MET cc_start: 0.6855 (mmp) cc_final: 0.6440 (mtm) outliers start: 50 outliers final: 37 residues processed: 165 average time/residue: 0.1070 time to fit residues: 27.3237 Evaluate side-chains 165 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 323 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 589 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 56 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.154542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120516 restraints weight = 18554.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124216 restraints weight = 11340.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.126880 restraints weight = 7955.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.128469 restraints weight = 6146.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.129930 restraints weight = 5136.532| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3917 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= 0.143 Angle : 0.616 9.066 20109 Z= 0.307 Chirality : 0.045 0.302 2286 Planarity : 0.004 0.039 2541 Dihedral : 5.644 47.464 2391 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.93 % Allowed : 20.74 % Favored : 76.34 % 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: -0.49 (0.20), residues: 1740 helix: 1.79 (0.31), residues: 276 sheet: -0.19 (0.23), residues: 483 loop : -1.03 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 611 TYR 0.018 0.002 TYR B 430 PHE 0.013 0.002 PHE B 148 TRP 0.014 0.001 TRP B 359 HIS 0.005 0.001 HIS C 527 Details of bonding type rmsd covalent geometry : bond 0.00329 (14739) covalent geometry : angle 0.60015 (20016) SS BOND : bond 0.00324 ( 15) SS BOND : angle 1.03538 ( 30) hydrogen bonds : bond 0.03523 ( 552) hydrogen bonds : angle 5.12173 ( 1719) link_ALPHA1-3 : bond 0.00577 ( 6) link_ALPHA1-3 : angle 1.28803 ( 18) link_ALPHA1-4 : bond 0.00864 ( 3) link_ALPHA1-4 : angle 3.14761 ( 9) link_ALPHA1-6 : bond 0.00047 ( 3) link_ALPHA1-6 : angle 2.38702 ( 9) link_BETA1-4 : bond 0.00537 ( 3) link_BETA1-4 : angle 4.11163 ( 9) link_NAG-ASN : bond 0.00154 ( 6) link_NAG-ASN : angle 1.77172 ( 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 169 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 0.647 Fit side-chains REVERT: A 401 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8030 (tt) REVERT: A 554 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5959 (t80) REVERT: A 596 GLN cc_start: 0.5881 (OUTLIER) cc_final: 0.5531 (mp10) REVERT: A 678 MET cc_start: 0.8273 (tpp) cc_final: 0.7969 (tpp) REVERT: B 401 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7969 (tt) REVERT: C 554 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6233 (t80) REVERT: C 637 MET cc_start: 0.6974 (mmp) cc_final: 0.6402 (mtm) outliers start: 46 outliers final: 38 residues processed: 158 average time/residue: 0.1046 time to fit residues: 25.5534 Evaluate side-chains 165 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL 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 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 589 SER 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 589 SER 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 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 110 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 168 optimal weight: 0.2980 chunk 144 optimal weight: 0.8980 chunk 164 optimal weight: 0.0030 chunk 49 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.156247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.122062 restraints weight = 18292.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126042 restraints weight = 11008.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.128808 restraints weight = 7598.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.130782 restraints weight = 5796.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.132039 restraints weight = 4757.165| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14775 Z= 0.115 Angle : 0.603 9.186 20109 Z= 0.300 Chirality : 0.044 0.248 2286 Planarity : 0.004 0.039 2541 Dihedral : 5.405 46.026 2391 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.35 % Allowed : 21.56 % Favored : 76.08 % 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: -0.32 (0.20), residues: 1740 helix: 1.97 (0.31), residues: 276 sheet: -0.05 (0.23), residues: 486 loop : -0.96 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 719 TYR 0.018 0.001 TYR C 260 PHE 0.012 0.001 PHE B 148 TRP 0.013 0.001 TRP C 180 HIS 0.004 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00262 (14739) covalent geometry : angle 0.58849 (20016) SS BOND : bond 0.00207 ( 15) SS BOND : angle 0.83145 ( 30) hydrogen bonds : bond 0.03390 ( 552) hydrogen bonds : angle 5.02004 ( 1719) link_ALPHA1-3 : bond 0.00541 ( 6) link_ALPHA1-3 : angle 1.33882 ( 18) link_ALPHA1-4 : bond 0.00837 ( 3) link_ALPHA1-4 : angle 3.20647 ( 9) link_ALPHA1-6 : bond 0.00059 ( 3) link_ALPHA1-6 : angle 2.26959 ( 9) link_BETA1-4 : bond 0.00608 ( 3) link_BETA1-4 : angle 4.04394 ( 9) link_NAG-ASN : bond 0.00097 ( 6) link_NAG-ASN : angle 1.46918 ( 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 177 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.544 Fit side-chains REVERT: A 401 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7924 (tt) REVERT: A 554 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6341 (t80) REVERT: A 596 GLN cc_start: 0.5866 (OUTLIER) cc_final: 0.5547 (mp10) REVERT: A 678 MET cc_start: 0.8269 (tpp) cc_final: 0.7935 (tpp) REVERT: B 198 ILE cc_start: 0.8773 (mt) cc_final: 0.8525 (mt) REVERT: B 401 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 678 MET cc_start: 0.8250 (tpp) cc_final: 0.7904 (tpp) REVERT: C 554 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6326 (t80) REVERT: C 637 MET cc_start: 0.6959 (mmp) cc_final: 0.6382 (mtm) REVERT: C 678 MET cc_start: 0.8170 (tpp) cc_final: 0.7840 (tpp) outliers start: 37 outliers final: 31 residues processed: 166 average time/residue: 0.1036 time to fit residues: 26.4312 Evaluate side-chains 163 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL 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 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 578 VAL Chi-restraints excluded: chain A residue 589 SER 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 589 SER 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 520 THR 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 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: 4.9990 chunk 131 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.152973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.118969 restraints weight = 18565.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.122738 restraints weight = 11240.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.125376 restraints weight = 7856.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.127115 restraints weight = 6058.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.128486 restraints weight = 5019.368| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14775 Z= 0.174 Angle : 0.650 9.007 20109 Z= 0.326 Chirality : 0.045 0.234 2286 Planarity : 0.004 0.039 2541 Dihedral : 5.324 41.746 2391 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.67 % Allowed : 21.37 % Favored : 75.95 % 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: -0.43 (0.19), residues: 1740 helix: 1.79 (0.31), residues: 276 sheet: -0.05 (0.23), residues: 480 loop : -1.03 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 719 TYR 0.016 0.002 TYR B 260 PHE 0.014 0.002 PHE B 293 TRP 0.017 0.002 TRP B 359 HIS 0.005 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00405 (14739) covalent geometry : angle 0.63508 (20016) SS BOND : bond 0.00338 ( 15) SS BOND : angle 0.99941 ( 30) hydrogen bonds : bond 0.03574 ( 552) hydrogen bonds : angle 5.12663 ( 1719) link_ALPHA1-3 : bond 0.00637 ( 6) link_ALPHA1-3 : angle 1.25488 ( 18) link_ALPHA1-4 : bond 0.00848 ( 3) link_ALPHA1-4 : angle 3.37079 ( 9) link_ALPHA1-6 : bond 0.00142 ( 3) link_ALPHA1-6 : angle 2.24080 ( 9) link_BETA1-4 : bond 0.00447 ( 3) link_BETA1-4 : angle 4.22495 ( 9) link_NAG-ASN : bond 0.00221 ( 6) link_NAG-ASN : angle 1.94328 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.62 seconds wall clock time: 37 minutes 34.13 seconds (2254.13 seconds total)