Starting phenix.real_space_refine on Thu Aug 6 08:16:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yik_72993/08_2026/9yik_72993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yik_72993/08_2026/9yik_72993.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/9yik_72993/08_2026/9yik_72993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yik_72993/08_2026/9yik_72993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yik_72993/08_2026/9yik_72993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yik_72993/08_2026/9yik_72993.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= 0.011 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 105 5.16 5 C 8703 2.51 5 N 2361 2.21 5 O 2757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13926 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Chain: "G" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Restraints were copied for chains: B, A, F, E, I, K, J, L Time building chain proxies: 3.32, per 1000 atoms: 0.24 Number of scatterers: 13926 At special positions: 0 Unit cell: (125.28, 127.02, 115.71, 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 105 16.00 O 2757 8.00 N 2361 7.00 C 8703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=2.05 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG D 1 " - " ASN G 262 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 234 " " NAG E 607 " - " ASN E 276 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 301 " " NAG E 610 " - " ASN E 332 " " NAG E 611 " - " ASN E 339 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 234 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 295 " " NAG F 609 " - " ASN F 301 " " NAG F 610 " - " ASN F 332 " " NAG F 611 " - " ASN F 339 " " NAG F 612 " - " ASN F 392 " " NAG F 613 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 160 " " NAG G 605 " - " ASN G 197 " " NAG G 606 " - " ASN G 234 " " NAG G 607 " - " ASN G 276 " " NAG G 608 " - " ASN G 295 " " NAG G 609 " - " ASN G 301 " " NAG G 610 " - " ASN G 332 " " NAG G 611 " - " ASN G 339 " " NAG G 612 " - " ASN G 392 " " NAG G 613 " - " ASN G 448 " " NAG H 1 " - " ASN G 386 " " NAG I 1 " - " ASN F 262 " " NAG J 1 " - " ASN F 386 " " NAG K 1 " - " ASN E 262 " " NAG L 1 " - " ASN E 386 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 611.5 milliseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 27 sheets defined 26.9% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.560A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.694A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 651 Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.676A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.526A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 354 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.676A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 474 through 483 removed outlier: 4.024A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.560A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.694A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.678A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.526A pdb=" N LEU F 125 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 126' Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 354 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.676A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 474 through 483 removed outlier: 4.024A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.559A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 removed outlier: 3.695A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 651 Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.677A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.526A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.677A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.024A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 603 through 609 removed outlier: 7.288A pdb=" N THR C 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL G 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL C 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.719A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.623A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER G 56 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'G' and resid 169 through 174 Processing sheet with id=AA6, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.290A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.980A pdb=" N ILE G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N LEU G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.371A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 274 removed outlier: 11.371A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N LEU G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.980A pdb=" N ILE G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 302 through 308 removed outlier: 5.489A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.282A pdb=" N THR B 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL F 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL B 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.719A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.624A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER F 56 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'F' and resid 169 through 174 Processing sheet with id=AB6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.290A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 271 through 274 removed outlier: 11.370A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.489A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC1, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.284A pdb=" N THR A 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL E 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL A 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.720A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.624A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER E 56 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.290A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.980A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.371A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 274 removed outlier: 11.371A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.980A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 302 through 308 removed outlier: 5.489A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 423 through 424 501 hydrogen bonds defined for protein. 1359 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: 2.34 Time building geometry restraints manager: 1.44 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: 4447 1.34 - 1.46: 2678 1.46 - 1.58: 6927 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 14190 Sorted by residual: bond pdb=" C3 NAG B 701 " pdb=" O3 NAG B 701 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C3 NAG F 613 " pdb=" O3 NAG F 613 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C3 NAG F 601 " pdb=" O3 NAG F 601 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C3 NAG E 611 " pdb=" O3 NAG E 611 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C3 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 14185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 18744 1.64 - 3.27: 458 3.27 - 4.91: 58 4.91 - 6.54: 0 6.54 - 8.18: 3 Bond angle restraints: 19263 Sorted by residual: angle pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 118.82 110.64 8.18 3.00e+00 1.11e-01 7.43e+00 angle pdb=" C1 BMA I 3 " pdb=" O5 BMA I 3 " pdb=" C5 BMA I 3 " ideal model delta sigma weight residual 118.82 110.68 8.14 3.00e+00 1.11e-01 7.37e+00 angle pdb=" C1 BMA K 3 " pdb=" O5 BMA K 3 " pdb=" C5 BMA K 3 " ideal model delta sigma weight residual 118.82 110.72 8.10 3.00e+00 1.11e-01 7.28e+00 angle pdb=" N THR F 297 " pdb=" CA THR F 297 " pdb=" C THR F 297 " ideal model delta sigma weight residual 108.55 112.75 -4.20 1.62e+00 3.81e-01 6.74e+00 angle pdb=" N THR E 297 " pdb=" CA THR E 297 " pdb=" C THR E 297 " ideal model delta sigma weight residual 108.55 112.72 -4.17 1.62e+00 3.81e-01 6.62e+00 ... (remaining 19258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 8515 21.66 - 43.33: 629 43.33 - 64.99: 123 64.99 - 86.66: 33 86.66 - 108.32: 15 Dihedral angle restraints: 9315 sinusoidal: 4512 harmonic: 4803 Sorted by residual: dihedral pdb=" CB CYS B 605 " pdb=" SG CYS B 605 " pdb=" SG CYS F 501 " pdb=" CB CYS F 501 " ideal model delta sinusoidal sigma weight residual 93.00 14.07 78.93 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS A 605 " pdb=" SG CYS A 605 " pdb=" SG CYS E 501 " pdb=" CB CYS E 501 " ideal model delta sinusoidal sigma weight residual 93.00 14.28 78.72 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" CB CYS C 605 " pdb=" SG CYS C 605 " pdb=" SG CYS G 501 " pdb=" CB CYS G 501 " ideal model delta sinusoidal sigma weight residual 93.00 14.41 78.59 1 1.00e+01 1.00e-02 7.70e+01 ... (remaining 9312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1811 0.051 - 0.102: 370 0.102 - 0.153: 141 0.153 - 0.204: 9 0.204 - 0.255: 6 Chirality restraints: 2337 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2334 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 75 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO E 76 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 75 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO G 76 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 76 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 76 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 75 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.03e+00 pdb=" N PRO F 76 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 76 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 76 " -0.020 5.00e-02 4.00e+02 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 9716 3.10 - 3.55: 13641 3.55 - 4.00: 21221 4.00 - 4.45: 25508 4.45 - 4.90: 39450 Nonbonded interactions: 109536 Sorted by model distance: nonbonded pdb=" N GLY F 380 " pdb=" N GLU F 381 " model vdw 2.651 2.560 nonbonded pdb=" N GLY E 380 " pdb=" N GLU E 381 " model vdw 2.651 2.560 nonbonded pdb=" N GLY G 380 " pdb=" N GLU G 381 " model vdw 2.651 2.560 nonbonded pdb=" N VAL E 127 " pdb=" O VAL E 127 " model vdw 2.652 2.496 nonbonded pdb=" N VAL G 127 " pdb=" O VAL G 127 " model vdw 2.652 2.496 ... (remaining 109531 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 'C' selection = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 4.390 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: 0.030 Process input model: 14.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.004 0.030 14283 Z= 0.213 Angle : 0.590 8.179 19506 Z= 0.275 Chirality : 0.049 0.255 2337 Planarity : 0.003 0.036 2391 Dihedral : 15.734 108.324 6093 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.01 % Allowed : 6.88 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1620 helix: 1.64 (0.28), residues: 387 sheet: 0.64 (0.30), residues: 270 loop : -0.86 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 143 TYR 0.006 0.001 TYR E 191 PHE 0.012 0.001 PHE G 53 TRP 0.006 0.001 TRP B 631 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (14190) covalent geometry : angle 0.57353 / 0.27 (19263) SS BOND : bond 0.00353 / 0.15 ( 36) SS BOND : angle 0.46609 / 0.32 ( 72) hydrogen bonds : bond 0.11545 / 7.46 ( 489) hydrogen bonds : angle 5.52128 / 4.10 ( 1359) link_BETA1-4 : bond 0.00344 / 0.21 ( 9) link_BETA1-4 : angle 1.20835 / 0.66 ( 27) link_NAG-ASN : bond 0.00304 / 0.19 ( 48) link_NAG-ASN : angle 1.65608 / 1.23 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 445 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 634 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7319 (mt-10) REVERT: G 191 TYR cc_start: 0.8605 (m-80) cc_final: 0.8200 (m-80) REVERT: B 612 SER cc_start: 0.7670 (t) cc_final: 0.7392 (t) REVERT: F 50 THR cc_start: 0.9042 (t) cc_final: 0.8829 (p) REVERT: F 125 LEU cc_start: 0.9210 (tp) cc_final: 0.9004 (tp) REVERT: E 486 TYR cc_start: 0.9022 (m-80) cc_final: 0.8820 (m-80) outliers start: 15 outliers final: 6 residues processed: 460 average time/residue: 0.1157 time to fit residues: 77.6994 Evaluate side-chains 247 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 241 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain E residue 433 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN C 650 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 HIS ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN G 283 ASN G 330 HIS G 344 ASN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 650 GLN B 652 GLN F 130 GLN F 283 ASN F 330 HIS F 344 ASN ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN A 630 GLN E 85 HIS E 130 GLN E 283 ASN E 330 HIS ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125062 restraints weight = 20531.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128311 restraints weight = 13458.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130686 restraints weight = 9944.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132370 restraints weight = 7885.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133540 restraints weight = 6591.065| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 14283 Z= 0.198 Angle : 0.635 8.457 19506 Z= 0.318 Chirality : 0.048 0.310 2337 Planarity : 0.004 0.052 2391 Dihedral : 7.775 59.221 2963 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.18 % Allowed : 15.11 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.21), residues: 1620 helix: 1.35 (0.27), residues: 393 sheet: -0.19 (0.25), residues: 372 loop : -0.82 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 360 TYR 0.013 0.001 TYR G 177 PHE 0.016 0.002 PHE F 53 TRP 0.014 0.002 TRP G 427 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (14190) covalent geometry : angle 0.60355 / 0.31 (19263) SS BOND : bond 0.00331 / 0.19 ( 36) SS BOND : angle 1.46233 / 0.83 ( 72) hydrogen bonds : bond 0.03628 / 2.42 ( 489) hydrogen bonds : angle 4.48555 / 3.23 ( 1359) link_BETA1-4 : bond 0.00461 / 0.29 ( 9) link_BETA1-4 : angle 2.24284 / 1.34 ( 27) link_NAG-ASN : bond 0.00384 / 0.24 ( 48) link_NAG-ASN : angle 1.96552 / 1.42 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 247 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 617 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.6112 (mtt-85) REVERT: C 641 ILE cc_start: 0.8287 (mm) cc_final: 0.8082 (mt) REVERT: G 104 MET cc_start: 0.9018 (tpp) cc_final: 0.8619 (tpt) REVERT: G 161 MET cc_start: 0.8800 (tpp) cc_final: 0.8319 (tpt) REVERT: B 617 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.6254 (mtt-85) REVERT: A 542 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7409 (ttp80) REVERT: E 161 MET cc_start: 0.8843 (tpp) cc_final: 0.8319 (tpt) REVERT: E 492 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8263 (mt-10) outliers start: 62 outliers final: 38 residues processed: 285 average time/residue: 0.0988 time to fit residues: 42.6392 Evaluate side-chains 257 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 443 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 146 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 HIS G 425 ASN B 630 GLN ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS E 344 ASN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117009 restraints weight = 20782.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120157 restraints weight = 13821.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122303 restraints weight = 10286.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124026 restraints weight = 8288.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125161 restraints weight = 6957.191| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14283 Z= 0.206 Angle : 0.623 8.169 19506 Z= 0.315 Chirality : 0.046 0.214 2337 Planarity : 0.004 0.055 2391 Dihedral : 6.586 55.780 2958 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.72 % Allowed : 18.15 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1620 helix: 1.38 (0.27), residues: 390 sheet: 0.03 (0.25), residues: 372 loop : -0.93 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 273 TYR 0.014 0.001 TYR G 486 PHE 0.025 0.002 PHE G 53 TRP 0.017 0.002 TRP F 427 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (14190) covalent geometry : angle 0.58339 / 0.31 (19263) SS BOND : bond 0.00479 / 0.24 ( 36) SS BOND : angle 1.91128 / 1.10 ( 72) hydrogen bonds : bond 0.03888 / 2.63 ( 489) hydrogen bonds : angle 4.33169 / 3.10 ( 1359) link_BETA1-4 : bond 0.00317 / 0.18 ( 9) link_BETA1-4 : angle 1.82793 / 1.02 ( 27) link_NAG-ASN : bond 0.00421 / 0.23 ( 48) link_NAG-ASN : angle 2.13826 / 1.52 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 232 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8100 (t0) cc_final: 0.7835 (t0) REVERT: G 104 MET cc_start: 0.8955 (tpp) cc_final: 0.8566 (tpt) REVERT: G 161 MET cc_start: 0.8840 (tpp) cc_final: 0.8573 (tpt) REVERT: G 180 ASP cc_start: 0.9014 (m-30) cc_final: 0.8783 (t0) REVERT: G 356 ASN cc_start: 0.7332 (p0) cc_final: 0.7066 (p0) REVERT: G 492 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8154 (mt-10) REVERT: B 617 ARG cc_start: 0.6574 (mtt180) cc_final: 0.6279 (mtt-85) REVERT: F 180 ASP cc_start: 0.9010 (m-30) cc_final: 0.8772 (t0) REVERT: F 356 ASN cc_start: 0.7350 (p0) cc_final: 0.7123 (p0) REVERT: E 161 MET cc_start: 0.8814 (tpp) cc_final: 0.8199 (tpt) REVERT: E 356 ASN cc_start: 0.7454 (p0) cc_final: 0.7113 (p0) REVERT: E 447 SER cc_start: 0.8710 (t) cc_final: 0.8500 (p) REVERT: E 492 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8297 (mt-10) outliers start: 70 outliers final: 48 residues processed: 283 average time/residue: 0.0916 time to fit residues: 39.9275 Evaluate side-chains 258 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain E residue 494 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.115830 restraints weight = 20692.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118936 restraints weight = 13764.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121163 restraints weight = 10235.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122733 restraints weight = 8212.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123668 restraints weight = 6948.402| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14283 Z= 0.167 Angle : 0.570 7.632 19506 Z= 0.287 Chirality : 0.046 0.316 2337 Planarity : 0.004 0.054 2391 Dihedral : 6.076 55.984 2958 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.32 % Allowed : 20.04 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.21), residues: 1620 helix: 1.55 (0.27), residues: 393 sheet: 0.06 (0.25), residues: 372 loop : -0.96 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 273 TYR 0.010 0.001 TYR E 173 PHE 0.014 0.001 PHE E 53 TRP 0.012 0.001 TRP E 427 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (14190) covalent geometry : angle 0.53828 / 0.28 (19263) SS BOND : bond 0.00235 / 0.15 ( 36) SS BOND : angle 1.40354 / 0.79 ( 72) hydrogen bonds : bond 0.03433 / 2.31 ( 489) hydrogen bonds : angle 4.24386 / 3.03 ( 1359) link_BETA1-4 : bond 0.00228 / 0.15 ( 9) link_BETA1-4 : angle 1.61110 / 0.90 ( 27) link_NAG-ASN : bond 0.00349 / 0.21 ( 48) link_NAG-ASN : angle 1.92569 / 1.38 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 237 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8154 (t0) cc_final: 0.7876 (t0) REVERT: G 104 MET cc_start: 0.8963 (tpp) cc_final: 0.8548 (tpt) REVERT: G 161 MET cc_start: 0.8815 (tpp) cc_final: 0.8591 (tpt) REVERT: G 180 ASP cc_start: 0.9030 (m-30) cc_final: 0.8779 (t0) REVERT: G 356 ASN cc_start: 0.7575 (p0) cc_final: 0.7297 (p0) REVERT: G 447 SER cc_start: 0.8952 (t) cc_final: 0.8736 (p) REVERT: G 492 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8185 (mt-10) REVERT: B 584 GLU cc_start: 0.8348 (tp30) cc_final: 0.8125 (tp30) REVERT: B 617 ARG cc_start: 0.6623 (mtt180) cc_final: 0.6372 (mtt-85) REVERT: F 107 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: F 180 ASP cc_start: 0.8984 (m-30) cc_final: 0.8734 (t0) REVERT: F 356 ASN cc_start: 0.7449 (p0) cc_final: 0.7221 (p0) REVERT: A 627 THR cc_start: 0.8635 (p) cc_final: 0.8229 (p) REVERT: A 630 GLN cc_start: 0.8051 (mt0) cc_final: 0.7806 (mt0) REVERT: E 161 MET cc_start: 0.8841 (tpp) cc_final: 0.8591 (tpt) REVERT: E 356 ASN cc_start: 0.7530 (p0) cc_final: 0.7079 (p0) REVERT: E 492 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8292 (mt-10) outliers start: 64 outliers final: 52 residues processed: 278 average time/residue: 0.0926 time to fit residues: 39.0014 Evaluate side-chains 270 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 363 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 160 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 37 optimal weight: 0.0000 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN A 650 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119067 restraints weight = 20701.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122015 restraints weight = 13900.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124214 restraints weight = 10435.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125640 restraints weight = 8366.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126825 restraints weight = 7099.661| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14283 Z= 0.108 Angle : 0.525 7.094 19506 Z= 0.265 Chirality : 0.044 0.299 2337 Planarity : 0.003 0.031 2391 Dihedral : 5.763 54.741 2958 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.91 % Allowed : 21.32 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1620 helix: 1.80 (0.27), residues: 393 sheet: 0.19 (0.25), residues: 372 loop : -0.91 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 273 TYR 0.009 0.001 TYR E 173 PHE 0.014 0.001 PHE G 53 TRP 0.010 0.001 TRP G 427 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (14190) covalent geometry : angle 0.49718 / 0.26 (19263) SS BOND : bond 0.00175 / 0.11 ( 36) SS BOND : angle 1.21628 / 0.69 ( 72) hydrogen bonds : bond 0.03075 / 2.06 ( 489) hydrogen bonds : angle 4.12630 / 2.94 ( 1359) link_BETA1-4 : bond 0.00374 / 0.22 ( 9) link_BETA1-4 : angle 1.43604 / 0.78 ( 27) link_NAG-ASN : bond 0.00352 / 0.21 ( 48) link_NAG-ASN : angle 1.77529 / 1.28 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8182 (t0) cc_final: 0.7839 (t0) REVERT: C 647 GLU cc_start: 0.6975 (tt0) cc_final: 0.6689 (tt0) REVERT: G 104 MET cc_start: 0.8931 (tpp) cc_final: 0.8517 (tpt) REVERT: G 161 MET cc_start: 0.8808 (tpp) cc_final: 0.8394 (tpt) REVERT: G 180 ASP cc_start: 0.8935 (m-30) cc_final: 0.8706 (t0) REVERT: G 356 ASN cc_start: 0.7427 (p0) cc_final: 0.7131 (p0) REVERT: G 447 SER cc_start: 0.8941 (t) cc_final: 0.8721 (p) REVERT: B 584 GLU cc_start: 0.8298 (tp30) cc_final: 0.8077 (tp30) REVERT: B 617 ARG cc_start: 0.6638 (mtt180) cc_final: 0.6409 (mtt-85) REVERT: B 639 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7603 (m) REVERT: F 107 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: F 180 ASP cc_start: 0.8926 (m-30) cc_final: 0.8698 (t0) REVERT: F 356 ASN cc_start: 0.7303 (p0) cc_final: 0.7069 (p0) REVERT: A 584 GLU cc_start: 0.8301 (tp30) cc_final: 0.7946 (tp30) REVERT: E 161 MET cc_start: 0.8844 (tpp) cc_final: 0.8487 (tpt) REVERT: E 356 ASN cc_start: 0.7414 (p0) cc_final: 0.6959 (p0) outliers start: 58 outliers final: 38 residues processed: 281 average time/residue: 0.0980 time to fit residues: 42.0042 Evaluate side-chains 267 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 494 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN A 652 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115748 restraints weight = 20789.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118824 restraints weight = 13724.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121130 restraints weight = 10216.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122741 restraints weight = 8124.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123759 restraints weight = 6822.537| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14283 Z= 0.155 Angle : 0.558 9.193 19506 Z= 0.281 Chirality : 0.045 0.288 2337 Planarity : 0.003 0.033 2391 Dihedral : 5.614 55.969 2952 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.32 % Allowed : 21.32 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1620 helix: 1.83 (0.28), residues: 390 sheet: -0.05 (0.24), residues: 417 loop : -0.91 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 166 TYR 0.009 0.001 TYR E 173 PHE 0.014 0.001 PHE E 53 TRP 0.009 0.001 TRP C 631 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (14190) covalent geometry : angle 0.53001 / 0.27 (19263) SS BOND : bond 0.00272 / 0.17 ( 36) SS BOND : angle 1.34734 / 0.79 ( 72) hydrogen bonds : bond 0.03261 / 2.19 ( 489) hydrogen bonds : angle 4.11026 / 2.93 ( 1359) link_BETA1-4 : bond 0.00259 / 0.16 ( 9) link_BETA1-4 : angle 1.55720 / 0.87 ( 27) link_NAG-ASN : bond 0.00327 / 0.19 ( 48) link_NAG-ASN : angle 1.81322 / 1.31 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8211 (t0) cc_final: 0.7836 (t0) REVERT: G 104 MET cc_start: 0.8970 (tpp) cc_final: 0.8589 (tpt) REVERT: G 161 MET cc_start: 0.8831 (tpp) cc_final: 0.8380 (tpt) REVERT: G 180 ASP cc_start: 0.9012 (m-30) cc_final: 0.8745 (t0) REVERT: G 356 ASN cc_start: 0.7568 (p0) cc_final: 0.7038 (p0) REVERT: B 584 GLU cc_start: 0.8321 (tp30) cc_final: 0.8064 (tp30) REVERT: B 617 ARG cc_start: 0.6789 (mtt180) cc_final: 0.6467 (mtt-85) REVERT: F 107 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: F 180 ASP cc_start: 0.8969 (m-30) cc_final: 0.8746 (t0) REVERT: F 356 ASN cc_start: 0.7348 (p0) cc_final: 0.6958 (p0) REVERT: F 422 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7418 (mm-40) REVERT: A 584 GLU cc_start: 0.8318 (tp30) cc_final: 0.7983 (tp30) REVERT: A 632 ASP cc_start: 0.8544 (t70) cc_final: 0.8335 (t70) REVERT: E 161 MET cc_start: 0.8861 (tpp) cc_final: 0.8450 (tpt) REVERT: E 356 ASN cc_start: 0.7440 (p0) cc_final: 0.7010 (p0) outliers start: 64 outliers final: 47 residues processed: 271 average time/residue: 0.0940 time to fit residues: 38.4126 Evaluate side-chains 264 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116535 restraints weight = 20699.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119641 restraints weight = 13585.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121955 restraints weight = 10067.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123566 restraints weight = 7988.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124670 restraints weight = 6687.697| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14283 Z= 0.123 Angle : 0.537 7.091 19506 Z= 0.271 Chirality : 0.044 0.290 2337 Planarity : 0.003 0.035 2391 Dihedral : 5.496 55.219 2952 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.25 % Allowed : 21.73 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1620 helix: 1.85 (0.28), residues: 393 sheet: 0.07 (0.24), residues: 411 loop : -0.88 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 166 TYR 0.025 0.001 TYR A 638 PHE 0.013 0.001 PHE G 53 TRP 0.011 0.001 TRP C 631 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14190) covalent geometry : angle 0.51061 / 0.26 (19263) SS BOND : bond 0.00262 / 0.14 ( 36) SS BOND : angle 1.21495 / 0.68 ( 72) hydrogen bonds : bond 0.03093 / 2.08 ( 489) hydrogen bonds : angle 4.05866 / 2.90 ( 1359) link_BETA1-4 : bond 0.00288 / 0.18 ( 9) link_BETA1-4 : angle 1.46452 / 0.81 ( 27) link_NAG-ASN : bond 0.00322 / 0.19 ( 48) link_NAG-ASN : angle 1.75252 / 1.27 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8207 (t0) cc_final: 0.7809 (t0) REVERT: G 104 MET cc_start: 0.8968 (tpp) cc_final: 0.8526 (tpt) REVERT: G 107 ASP cc_start: 0.8547 (m-30) cc_final: 0.8107 (t70) REVERT: G 161 MET cc_start: 0.8776 (tpp) cc_final: 0.8179 (tpt) REVERT: G 279 ASN cc_start: 0.8762 (t0) cc_final: 0.8507 (t0) REVERT: G 356 ASN cc_start: 0.7515 (p0) cc_final: 0.7005 (p0) REVERT: B 584 GLU cc_start: 0.8338 (tp30) cc_final: 0.8073 (tp30) REVERT: B 606 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 617 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6469 (mtt-85) REVERT: B 639 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7603 (m) REVERT: F 107 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: F 114 GLN cc_start: 0.8261 (mt0) cc_final: 0.7721 (mm-40) REVERT: F 180 ASP cc_start: 0.8946 (m-30) cc_final: 0.8692 (t0) REVERT: F 356 ASN cc_start: 0.7285 (p0) cc_final: 0.6897 (p0) REVERT: F 422 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7389 (mm-40) REVERT: A 584 GLU cc_start: 0.8310 (tp30) cc_final: 0.7959 (tp30) REVERT: E 161 MET cc_start: 0.8876 (tpp) cc_final: 0.8462 (tpt) REVERT: E 356 ASN cc_start: 0.7427 (p0) cc_final: 0.7000 (p0) outliers start: 63 outliers final: 53 residues processed: 266 average time/residue: 0.0985 time to fit residues: 39.5656 Evaluate side-chains 272 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112792 restraints weight = 20754.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115735 restraints weight = 13780.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117965 restraints weight = 10292.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119528 restraints weight = 8201.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120594 restraints weight = 6900.267| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14283 Z= 0.141 Angle : 0.547 7.845 19506 Z= 0.276 Chirality : 0.045 0.285 2337 Planarity : 0.003 0.038 2391 Dihedral : 5.544 55.699 2952 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.59 % Allowed : 21.46 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.05 (0.21), residues: 1620 helix: 1.83 (0.28), residues: 393 sheet: -0.07 (0.25), residues: 399 loop : -0.93 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 166 TYR 0.027 0.001 TYR A 638 PHE 0.013 0.001 PHE G 53 TRP 0.010 0.001 TRP C 631 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14190) covalent geometry : angle 0.52033 / 0.27 (19263) SS BOND : bond 0.00228 / 0.14 ( 36) SS BOND : angle 1.24572 / 0.68 ( 72) hydrogen bonds : bond 0.03155 / 2.12 ( 489) hydrogen bonds : angle 4.04565 / 2.89 ( 1359) link_BETA1-4 : bond 0.00265 / 0.16 ( 9) link_BETA1-4 : angle 1.48377 / 0.83 ( 27) link_NAG-ASN : bond 0.00311 / 0.18 ( 48) link_NAG-ASN : angle 1.75932 / 1.28 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8260 (t0) cc_final: 0.7830 (t0) REVERT: G 104 MET cc_start: 0.8975 (tpp) cc_final: 0.8537 (tpt) REVERT: G 107 ASP cc_start: 0.8544 (m-30) cc_final: 0.8114 (t70) REVERT: G 161 MET cc_start: 0.8803 (tpp) cc_final: 0.8220 (tpt) REVERT: G 279 ASN cc_start: 0.8803 (t0) cc_final: 0.8550 (t0) REVERT: G 356 ASN cc_start: 0.7543 (p0) cc_final: 0.7066 (p0) REVERT: B 584 GLU cc_start: 0.8384 (tp30) cc_final: 0.8104 (tp30) REVERT: B 606 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8336 (p) REVERT: B 617 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6502 (mtt-85) REVERT: B 639 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7647 (m) REVERT: F 107 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: F 114 GLN cc_start: 0.8283 (mt0) cc_final: 0.7729 (mm-40) REVERT: F 180 ASP cc_start: 0.8982 (m-30) cc_final: 0.8710 (t0) REVERT: F 356 ASN cc_start: 0.7211 (p0) cc_final: 0.6826 (p0) REVERT: F 422 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7427 (mm-40) REVERT: A 584 GLU cc_start: 0.8339 (tp30) cc_final: 0.7972 (tp30) REVERT: E 161 MET cc_start: 0.8886 (tpp) cc_final: 0.8456 (tpt) REVERT: E 356 ASN cc_start: 0.7482 (p0) cc_final: 0.7064 (p0) outliers start: 68 outliers final: 54 residues processed: 263 average time/residue: 0.1011 time to fit residues: 40.0890 Evaluate side-chains 267 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 104 optimal weight: 0.0060 chunk 132 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113869 restraints weight = 20748.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116949 restraints weight = 13651.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119161 restraints weight = 10102.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120662 restraints weight = 8039.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121889 restraints weight = 6770.308| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14283 Z= 0.120 Angle : 0.537 9.300 19506 Z= 0.270 Chirality : 0.044 0.287 2337 Planarity : 0.003 0.040 2391 Dihedral : 5.434 55.198 2952 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.85 % Allowed : 22.33 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1620 helix: 1.88 (0.28), residues: 393 sheet: 0.06 (0.25), residues: 393 loop : -0.92 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 166 TYR 0.029 0.001 TYR A 638 PHE 0.013 0.001 PHE G 53 TRP 0.013 0.001 TRP C 631 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14190) covalent geometry : angle 0.51232 / 0.27 (19263) SS BOND : bond 0.00218 / 0.14 ( 36) SS BOND : angle 1.10846 / 0.62 ( 72) hydrogen bonds : bond 0.03050 / 2.06 ( 489) hydrogen bonds : angle 4.01594 / 2.86 ( 1359) link_BETA1-4 : bond 0.00302 / 0.19 ( 9) link_BETA1-4 : angle 1.41862 / 0.79 ( 27) link_NAG-ASN : bond 0.00313 / 0.18 ( 48) link_NAG-ASN : angle 1.69929 / 1.23 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8265 (t0) cc_final: 0.7822 (t0) REVERT: G 104 MET cc_start: 0.8976 (tpp) cc_final: 0.8533 (tpt) REVERT: G 107 ASP cc_start: 0.8516 (m-30) cc_final: 0.8094 (t70) REVERT: G 161 MET cc_start: 0.8768 (tpp) cc_final: 0.8216 (tpt) REVERT: G 279 ASN cc_start: 0.8787 (t0) cc_final: 0.8549 (t0) REVERT: G 356 ASN cc_start: 0.7560 (p0) cc_final: 0.7091 (p0) REVERT: B 584 GLU cc_start: 0.8359 (tp30) cc_final: 0.8072 (tp30) REVERT: B 606 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8100 (p) REVERT: B 617 ARG cc_start: 0.6824 (mtt180) cc_final: 0.6536 (mtt-85) REVERT: B 639 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7639 (m) REVERT: F 107 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: F 114 GLN cc_start: 0.8243 (mt0) cc_final: 0.7684 (mm-40) REVERT: F 180 ASP cc_start: 0.8980 (m-30) cc_final: 0.8689 (t0) REVERT: F 356 ASN cc_start: 0.7213 (p0) cc_final: 0.6827 (p0) REVERT: F 422 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7396 (mm-40) REVERT: A 584 GLU cc_start: 0.8317 (tp30) cc_final: 0.7974 (tp30) REVERT: E 161 MET cc_start: 0.8879 (tpp) cc_final: 0.8485 (tpt) REVERT: E 356 ASN cc_start: 0.7440 (p0) cc_final: 0.7213 (p0) outliers start: 57 outliers final: 50 residues processed: 258 average time/residue: 0.1038 time to fit residues: 40.7016 Evaluate side-chains 270 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 138 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113560 restraints weight = 20589.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116586 restraints weight = 13639.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118781 restraints weight = 10121.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120372 restraints weight = 8072.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121390 restraints weight = 6757.531| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14283 Z= 0.128 Angle : 0.547 11.233 19506 Z= 0.274 Chirality : 0.045 0.283 2337 Planarity : 0.003 0.042 2391 Dihedral : 5.431 55.388 2952 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.91 % Allowed : 22.40 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1620 helix: 1.83 (0.28), residues: 396 sheet: 0.08 (0.25), residues: 393 loop : -0.93 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 166 TYR 0.027 0.001 TYR A 638 PHE 0.013 0.001 PHE G 53 TRP 0.011 0.001 TRP C 631 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14190) covalent geometry : angle 0.52385 / 0.27 (19263) SS BOND : bond 0.00191 / 0.11 ( 36) SS BOND : angle 1.08418 / 0.61 ( 72) hydrogen bonds : bond 0.03090 / 2.07 ( 489) hydrogen bonds : angle 3.99672 / 2.85 ( 1359) link_BETA1-4 : bond 0.00297 / 0.18 ( 9) link_BETA1-4 : angle 1.43025 / 0.80 ( 27) link_NAG-ASN : bond 0.00308 / 0.18 ( 48) link_NAG-ASN : angle 1.70048 / 1.24 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8248 (t0) cc_final: 0.7805 (t0) REVERT: G 104 MET cc_start: 0.8969 (tpp) cc_final: 0.8619 (tpt) REVERT: G 161 MET cc_start: 0.8772 (tpp) cc_final: 0.8227 (tpt) REVERT: G 279 ASN cc_start: 0.8779 (t0) cc_final: 0.8522 (t0) REVERT: G 356 ASN cc_start: 0.7565 (p0) cc_final: 0.7243 (p0) REVERT: B 584 GLU cc_start: 0.8359 (tp30) cc_final: 0.8065 (tp30) REVERT: B 606 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8104 (p) REVERT: B 617 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6580 (mtt-85) REVERT: B 639 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7665 (m) REVERT: F 107 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: F 114 GLN cc_start: 0.8255 (mt0) cc_final: 0.7698 (mm-40) REVERT: F 180 ASP cc_start: 0.8965 (m-30) cc_final: 0.8674 (t0) REVERT: F 356 ASN cc_start: 0.7365 (p0) cc_final: 0.7107 (p0) REVERT: F 422 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7431 (mm-40) REVERT: A 584 GLU cc_start: 0.8322 (tp30) cc_final: 0.7968 (tp30) REVERT: A 623 TRP cc_start: 0.8870 (m100) cc_final: 0.8546 (m100) REVERT: E 95 MET cc_start: 0.8594 (ppp) cc_final: 0.8003 (ptt) REVERT: E 161 MET cc_start: 0.8893 (tpp) cc_final: 0.8490 (tpt) outliers start: 58 outliers final: 50 residues processed: 260 average time/residue: 0.1077 time to fit residues: 42.7131 Evaluate side-chains 270 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 0.0010 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 630 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113809 restraints weight = 20607.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116880 restraints weight = 13605.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119105 restraints weight = 10060.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120685 restraints weight = 7989.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121757 restraints weight = 6683.681| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14283 Z= 0.120 Angle : 0.544 11.064 19506 Z= 0.273 Chirality : 0.045 0.283 2337 Planarity : 0.003 0.042 2391 Dihedral : 5.378 55.196 2952 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.78 % Allowed : 22.54 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1620 helix: 1.91 (0.28), residues: 393 sheet: 0.11 (0.25), residues: 393 loop : -0.94 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 166 TYR 0.025 0.001 TYR A 638 PHE 0.013 0.001 PHE G 53 TRP 0.011 0.001 TRP C 631 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14190) covalent geometry : angle 0.52113 / 0.27 (19263) SS BOND : bond 0.00200 / 0.12 ( 36) SS BOND : angle 1.03541 / 0.59 ( 72) hydrogen bonds : bond 0.03024 / 2.04 ( 489) hydrogen bonds : angle 3.98505 / 2.84 ( 1359) link_BETA1-4 : bond 0.00313 / 0.19 ( 9) link_BETA1-4 : angle 1.40616 / 0.78 ( 27) link_NAG-ASN : bond 0.00307 / 0.18 ( 48) link_NAG-ASN : angle 1.67565 / 1.22 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.79 seconds wall clock time: 36 minutes 11.43 seconds (2171.43 seconds total)