Starting phenix.real_space_refine on Thu Feb 5 00:37:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2p_64736/02_2026/9v2p_64736.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2p_64736/02_2026/9v2p_64736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v2p_64736/02_2026/9v2p_64736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2p_64736/02_2026/9v2p_64736.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v2p_64736/02_2026/9v2p_64736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2p_64736/02_2026/9v2p_64736.map" } resolution = 2.4 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= 0.010 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 65 5.16 5 C 8892 2.51 5 N 2248 2.21 5 O 2686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13891 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5957 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 27, 'TRANS': 699} Chain: "B" Number of atoms: 5957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5957 Classifications: {'peptide': 727} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 697} Chain: "G" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1616 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "C" 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: "D" 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: "E" 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: "F" 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: "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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.47, per 1000 atoms: 0.25 Number of scatterers: 13891 At special positions: 0 Unit cell: (92.3812, 136.423, 140.72, 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 65 16.00 O 2686 8.00 N 2248 7.00 C 8892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.04 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 472 " distance=2.01 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 762 " distance=2.02 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 444 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 762 " distance=2.04 Simple disulfide: pdb=" SG CYS G 388 " - pdb=" SG CYS G 412 " distance=2.03 Simple disulfide: pdb=" SG CYS G 430 " - pdb=" SG CYS G 483 " distance=2.04 Simple disulfide: pdb=" SG CYS G 442 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 507 " - pdb=" SG CYS G 531 " distance=2.02 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 801 " - " ASN A 92 " " NAG C 1 " - " ASN A 85 " " NAG D 1 " - " ASN A 150 " " NAG E 1 " - " ASN A 229 " " NAG F 1 " - " ASN A 281 " " NAG H 1 " - " ASN A 219 " " NAG I 1 " - " ASN A 321 " " NAG J 1 " - " ASN B 85 " " NAG K 1 " - " ASN B 92 " " NAG L 1 " - " ASN B 229 " " NAG M 1 " - " ASN B 321 " " NAG N 1 " - " ASN B 150 " " NAG O 1 " - " ASN B 281 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 554.2 milliseconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 28 sheets defined 20.9% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 93 through 97 removed outlier: 4.285A pdb=" N ASP A 96 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 497 through 505 Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 590 through 595 removed outlier: 4.246A pdb=" N ILE A 594 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 615 removed outlier: 4.007A pdb=" N LYS A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.892A pdb=" N TYR A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 Processing helix chain 'A' and resid 688 through 698 removed outlier: 5.065A pdb=" N GLU A 693 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 697 " --> pdb=" O ASN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 4.368A pdb=" N SER A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 764 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 93 through 97 removed outlier: 4.339A pdb=" N GLU B 97 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.661A pdb=" N ARG B 343 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 497 through 505 Processing helix chain 'B' and resid 562 through 572 removed outlier: 3.630A pdb=" N ASN B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 600 through 615 removed outlier: 3.618A pdb=" N LYS B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.696A pdb=" N THR B 667 " --> pdb=" O ASP B 663 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 Processing helix chain 'B' and resid 686 through 687 No H-bonds generated for 'chain 'B' and resid 686 through 687' Processing helix chain 'B' and resid 688 through 698 removed outlier: 5.192A pdb=" N GLU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 697 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 726 removed outlier: 4.336A pdb=" N SER B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 764 Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.533A pdb=" N LYS G 395 " --> pdb=" O PRO G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 423 removed outlier: 3.543A pdb=" N LEU G 419 " --> pdb=" O ASN G 415 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER G 421 " --> pdb=" O THR G 417 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE G 423 " --> pdb=" O LEU G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 439 removed outlier: 3.671A pdb=" N ILE G 438 " --> pdb=" O SER G 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 473 removed outlier: 3.550A pdb=" N LEU G 471 " --> pdb=" O GLY G 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 7.704A pdb=" N LYS A 41 " --> pdb=" O GLN A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.615A pdb=" N ILE A 76 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 4.293A pdb=" N TYR A 120 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 129 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 134 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.707A pdb=" N TRP A 154 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA7, first strand: chain 'A' and resid 235 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 305 removed outlier: 6.587A pdb=" N GLN A 314 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER A 312 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP A 305 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ARG A 310 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 329 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 305 removed outlier: 6.587A pdb=" N GLN A 314 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER A 312 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP A 305 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ARG A 310 " --> pdb=" O TRP A 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.519A pdb=" N THR A 395 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 410 removed outlier: 7.061A pdb=" N TYR A 416 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU A 410 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 457 through 461 removed outlier: 6.676A pdb=" N LEU A 482 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL A 493 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N SER A 484 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 491 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 511 through 519 removed outlier: 5.054A pdb=" N PHE A 578 " --> pdb=" O ASP A 545 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N TYR A 540 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG A 623 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 542 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP A 629 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS A 649 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR A 700 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N MET A 733 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 702 " --> pdb=" O MET A 733 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N TYR A 735 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS A 704 " --> pdb=" O TYR A 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 42 removed outlier: 7.896A pdb=" N LYS B 41 " --> pdb=" O GLN B 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.515A pdb=" N ARG B 61 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 76 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 104 through 107 removed outlier: 4.476A pdb=" N TYR B 120 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B 129 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 152 through 157 removed outlier: 6.556A pdb=" N VAL B 167 " --> pdb=" O GLN B 153 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 155 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA B 165 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'B' and resid 235 through 240 Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 305 removed outlier: 6.557A pdb=" N GLN B 314 " --> pdb=" O CYS B 301 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL B 303 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER B 312 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP B 305 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ARG B 310 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 317 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 410 removed outlier: 6.830A pdb=" N TYR B 416 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU B 410 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 454 through 461 removed outlier: 7.404A pdb=" N CYS B 454 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR B 456 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 482 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B 493 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N SER B 484 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU B 491 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 511 through 519 removed outlier: 3.950A pdb=" N TRP B 525 " --> pdb=" O ASP B 579 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE B 578 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N TYR B 540 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N ALA B 625 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 542 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TRP B 627 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU B 544 " --> pdb=" O TRP B 627 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TRP B 629 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL B 546 " --> pdb=" O TRP B 629 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N CYS B 649 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 624 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ILE B 651 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 626 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL B 653 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY B 628 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR B 700 " --> pdb=" O GLN B 731 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N MET B 733 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 702 " --> pdb=" O MET B 733 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N TYR B 735 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS B 704 " --> pdb=" O TYR B 735 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 405 through 409 removed outlier: 4.060A pdb=" N ILE G 578 " --> pdb=" O CYS G 483 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR G 482 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER G 488 " --> pdb=" O VAL G 425 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL G 425 " --> pdb=" O SER G 488 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 412 through 414 removed outlier: 6.364A pdb=" N CYS G 412 " --> pdb=" O CYS G 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 501 through 509 removed outlier: 6.344A pdb=" N VAL G 562 " --> pdb=" O SER G 505 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N CYS G 507 " --> pdb=" O ILE G 560 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 560 " --> pdb=" O CYS G 507 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ARG G 509 " --> pdb=" O LEU G 558 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU G 558 " --> pdb=" O ARG G 509 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1230 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: 2.78 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2216 1.32 - 1.44: 4348 1.44 - 1.57: 7616 1.57 - 1.69: 0 1.69 - 1.82: 98 Bond restraints: 14278 Sorted by residual: bond pdb=" CA SER A 217 " pdb=" CB SER A 217 " ideal model delta sigma weight residual 1.525 1.447 0.078 1.52e-02 4.33e+03 2.64e+01 bond pdb=" CA SER A 583 " pdb=" CB SER A 583 " ideal model delta sigma weight residual 1.529 1.455 0.073 1.66e-02 3.63e+03 1.95e+01 bond pdb=" N ASN A 75 " pdb=" CA ASN A 75 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.22e-02 6.72e+03 1.14e+01 bond pdb=" N ARG B 147 " pdb=" CA ARG B 147 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.23e-02 6.61e+03 1.06e+01 bond pdb=" N GLU B 146 " pdb=" CA GLU B 146 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 ... (remaining 14273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 18615 2.53 - 5.05: 704 5.05 - 7.58: 71 7.58 - 10.11: 25 10.11 - 12.63: 3 Bond angle restraints: 19418 Sorted by residual: angle pdb=" N TYR A 547 " pdb=" CA TYR A 547 " pdb=" C TYR A 547 " ideal model delta sigma weight residual 112.72 101.60 11.12 1.28e+00 6.10e-01 7.55e+01 angle pdb=" N ASP A 588 " pdb=" CA ASP A 588 " pdb=" C ASP A 588 " ideal model delta sigma weight residual 114.04 105.45 8.59 1.24e+00 6.50e-01 4.79e+01 angle pdb=" C ASN A 150 " pdb=" CA ASN A 150 " pdb=" CB ASN A 150 " ideal model delta sigma weight residual 111.50 103.40 8.10 1.29e+00 6.01e-01 3.94e+01 angle pdb=" C PHE G 428 " pdb=" CA PHE G 428 " pdb=" CB PHE G 428 " ideal model delta sigma weight residual 110.74 100.89 9.85 1.61e+00 3.86e-01 3.74e+01 angle pdb=" C ASN A 75 " pdb=" N ILE A 76 " pdb=" CA ILE A 76 " ideal model delta sigma weight residual 123.10 114.87 8.23 1.36e+00 5.41e-01 3.66e+01 ... (remaining 19413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 7918 21.10 - 42.19: 649 42.19 - 63.29: 115 63.29 - 84.38: 21 84.38 - 105.48: 8 Dihedral angle restraints: 8711 sinusoidal: 3795 harmonic: 4916 Sorted by residual: dihedral pdb=" CB CYS B 328 " pdb=" SG CYS B 328 " pdb=" SG CYS B 339 " pdb=" CB CYS B 339 " ideal model delta sinusoidal sigma weight residual -86.00 -5.64 -80.36 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " pdb=" SG CYS B 762 " pdb=" CB CYS B 762 " ideal model delta sinusoidal sigma weight residual -86.00 -156.11 70.11 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual 93.00 38.76 54.24 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 8708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1878 0.099 - 0.197: 216 0.197 - 0.296: 33 0.296 - 0.395: 4 0.395 - 0.493: 2 Chirality restraints: 2133 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.82e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.74e+01 ... (remaining 2130 not shown) Planarity restraints: 2453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG H 2 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.070 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.520 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.325 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG M 2 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.102 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.507 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.324 2.00e-02 2.50e+03 2.82e-01 9.95e+02 pdb=" C7 NAG H 1 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.505 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.154 2.00e-02 2.50e+03 ... (remaining 2450 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 317 2.67 - 3.23: 13157 3.23 - 3.79: 22128 3.79 - 4.34: 30590 4.34 - 4.90: 48787 Nonbonded interactions: 114979 Sorted by model distance: nonbonded pdb=" O VAL B 639 " pdb=" OG SER B 642 " model vdw 2.113 3.040 nonbonded pdb=" O GLY B 580 " pdb=" OG SER B 583 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP B 104 " pdb=" N TYR B 105 " model vdw 2.174 3.120 nonbonded pdb=" OD1 ASP A 104 " pdb=" N TYR A 105 " model vdw 2.185 3.120 nonbonded pdb=" O GLU A 244 " pdb=" OH TYR B 661 " model vdw 2.188 3.040 ... (remaining 114974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 766) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.200 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 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 : 0.007 0.078 14318 Z= 0.418 Angle : 1.081 21.086 19524 Z= 0.658 Chirality : 0.067 0.493 2133 Planarity : 0.017 0.294 2440 Dihedral : 15.496 105.478 5539 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.77 % Favored : 94.87 % Rotamer: Outliers : 2.23 % Allowed : 22.52 % Favored : 75.25 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1657 helix: 0.66 (0.36), residues: 224 sheet: 0.02 (0.22), residues: 518 loop : -1.06 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 623 TYR 0.022 0.002 TYR A 322 PHE 0.021 0.002 PHE G 428 TRP 0.017 0.002 TRP A 659 HIS 0.005 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00667 (14278) covalent geometry : angle 1.06020 (19418) SS BOND : bond 0.00809 ( 14) SS BOND : angle 1.98958 ( 28) hydrogen bonds : bond 0.15262 ( 461) hydrogen bonds : angle 6.79439 ( 1230) link_BETA1-4 : bond 0.00255 ( 13) link_BETA1-4 : angle 1.77382 ( 39) link_NAG-ASN : bond 0.00936 ( 13) link_NAG-ASN : angle 4.45257 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 320 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 689 MET cc_start: 0.6698 (mpp) cc_final: 0.6445 (mpp) outliers start: 33 outliers final: 8 residues processed: 344 average time/residue: 0.5685 time to fit residues: 215.3042 Evaluate side-chains 151 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 436 ASP Chi-restraints excluded: chain G residue 468 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0020 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 2.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 75 ASN A 338 ASN A 435 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 595 ASN A 612 GLN A 754 HIS A 761 GLN B 153 GLN B 595 ASN B 715 GLN B 749 GLN B 761 GLN G 516 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.142707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.117233 restraints weight = 26685.217| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.08 r_work: 0.3876 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14318 Z= 0.141 Angle : 0.762 14.723 19524 Z= 0.373 Chirality : 0.048 0.316 2133 Planarity : 0.004 0.067 2440 Dihedral : 7.356 66.296 2409 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 3.51 % Allowed : 22.18 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % 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: -0.54 (0.20), residues: 1657 helix: 0.65 (0.35), residues: 216 sheet: 0.27 (0.22), residues: 509 loop : -0.96 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 147 TYR 0.020 0.001 TYR A 53 PHE 0.028 0.002 PHE G 394 TRP 0.015 0.001 TRP A 168 HIS 0.007 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00311 (14278) covalent geometry : angle 0.74155 (19418) SS BOND : bond 0.00544 ( 14) SS BOND : angle 1.69291 ( 28) hydrogen bonds : bond 0.04134 ( 461) hydrogen bonds : angle 5.65060 ( 1230) link_BETA1-4 : bond 0.00763 ( 13) link_BETA1-4 : angle 2.02325 ( 39) link_NAG-ASN : bond 0.00408 ( 13) link_NAG-ASN : angle 3.31979 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.7890 (t0) cc_final: 0.7626 (t0) REVERT: A 243 ASP cc_start: 0.8345 (t0) cc_final: 0.8127 (t70) REVERT: A 326 ASP cc_start: 0.8014 (t0) cc_final: 0.7693 (t0) REVERT: A 378 GLU cc_start: 0.8535 (pm20) cc_final: 0.8051 (pm20) REVERT: A 379 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8312 (mp0) REVERT: A 689 MET cc_start: 0.8496 (mpp) cc_final: 0.8207 (mpp) REVERT: B 146 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: B 379 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6618 (tm-30) REVERT: B 573 ILE cc_start: 0.7589 (tp) cc_final: 0.7321 (mt) REVERT: B 622 LYS cc_start: 0.8780 (mtpm) cc_final: 0.8573 (ttpp) REVERT: B 646 VAL cc_start: 0.6207 (m) cc_final: 0.5837 (p) REVERT: B 742 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.7026 (mt) REVERT: G 503 TYR cc_start: 0.8145 (p90) cc_final: 0.7693 (p90) REVERT: G 574 MET cc_start: 0.6981 (mmm) cc_final: 0.6482 (mmm) outliers start: 52 outliers final: 11 residues processed: 210 average time/residue: 0.5295 time to fit residues: 123.5768 Evaluate side-chains 141 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain G residue 469 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN B 363 HIS B 740 HIS G 516 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.138375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.112174 restraints weight = 26889.023| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.09 r_work: 0.3786 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14318 Z= 0.132 Angle : 0.677 10.490 19524 Z= 0.333 Chirality : 0.046 0.284 2133 Planarity : 0.004 0.081 2440 Dihedral : 6.366 58.253 2402 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 4.11 % Allowed : 22.18 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % 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: -0.50 (0.20), residues: 1657 helix: 0.53 (0.35), residues: 210 sheet: 0.32 (0.23), residues: 502 loop : -0.90 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 532 TYR 0.020 0.002 TYR B 48 PHE 0.023 0.002 PHE B 387 TRP 0.012 0.001 TRP A 659 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00294 (14278) covalent geometry : angle 0.65940 (19418) SS BOND : bond 0.00444 ( 14) SS BOND : angle 1.76624 ( 28) hydrogen bonds : bond 0.03724 ( 461) hydrogen bonds : angle 5.33984 ( 1230) link_BETA1-4 : bond 0.00581 ( 13) link_BETA1-4 : angle 1.77817 ( 39) link_NAG-ASN : bond 0.00308 ( 13) link_NAG-ASN : angle 2.79995 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 141 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7482 (m-80) cc_final: 0.7269 (m-80) REVERT: A 98 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: A 104 ASP cc_start: 0.8044 (t0) cc_final: 0.7688 (t0) REVERT: A 140 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.5594 (tmm160) REVERT: A 141 GLN cc_start: 0.7213 (pm20) cc_final: 0.7012 (pm20) REVERT: A 243 ASP cc_start: 0.8399 (t0) cc_final: 0.8060 (t70) REVERT: A 326 ASP cc_start: 0.8238 (t0) cc_final: 0.7801 (t0) REVERT: A 466 LYS cc_start: 0.8319 (mmpt) cc_final: 0.8118 (mmmt) REVERT: B 71 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8209 (tmmm) REVERT: B 146 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6589 (pm20) REVERT: B 287 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7494 (mp) REVERT: B 376 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8375 (t) REVERT: B 379 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: B 517 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8063 (pp) REVERT: B 646 VAL cc_start: 0.6621 (m) cc_final: 0.6216 (p) REVERT: G 509 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7534 (ttm-80) REVERT: G 574 MET cc_start: 0.6705 (mmm) cc_final: 0.6128 (mmm) outliers start: 61 outliers final: 23 residues processed: 194 average time/residue: 0.5047 time to fit residues: 109.6113 Evaluate side-chains 153 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain G residue 469 ILE Chi-restraints excluded: chain G residue 510 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 141 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.130636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.103641 restraints weight = 26833.529| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.07 r_work: 0.3638 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14318 Z= 0.201 Angle : 0.726 10.602 19524 Z= 0.357 Chirality : 0.049 0.348 2133 Planarity : 0.004 0.049 2440 Dihedral : 6.221 57.480 2402 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 4.45 % Allowed : 21.24 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % 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: -0.70 (0.20), residues: 1657 helix: 0.12 (0.34), residues: 217 sheet: 0.13 (0.22), residues: 498 loop : -0.92 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 253 TYR 0.031 0.002 TYR B 48 PHE 0.025 0.002 PHE B 387 TRP 0.017 0.002 TRP A 659 HIS 0.008 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00478 (14278) covalent geometry : angle 0.71081 (19418) SS BOND : bond 0.00624 ( 14) SS BOND : angle 1.48341 ( 28) hydrogen bonds : bond 0.04110 ( 461) hydrogen bonds : angle 5.57664 ( 1230) link_BETA1-4 : bond 0.00433 ( 13) link_BETA1-4 : angle 1.82081 ( 39) link_NAG-ASN : bond 0.00336 ( 13) link_NAG-ASN : angle 2.75773 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7859 (m-80) cc_final: 0.7590 (m-80) REVERT: A 98 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: A 104 ASP cc_start: 0.8231 (t0) cc_final: 0.7727 (t0) REVERT: A 243 ASP cc_start: 0.8559 (t0) cc_final: 0.8286 (t70) REVERT: A 317 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7854 (mtt180) REVERT: A 326 ASP cc_start: 0.8531 (t0) cc_final: 0.8124 (t0) REVERT: A 527 GLN cc_start: 0.8150 (pt0) cc_final: 0.7838 (pt0) REVERT: A 638 MET cc_start: 0.8652 (mmm) cc_final: 0.7764 (mmt) REVERT: B 136 ASP cc_start: 0.8120 (t0) cc_final: 0.7177 (t0) REVERT: B 141 GLN cc_start: 0.6431 (pm20) cc_final: 0.6157 (pm20) REVERT: B 146 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6383 (pm20) REVERT: B 195 TYR cc_start: 0.6261 (OUTLIER) cc_final: 0.5664 (m-10) REVERT: B 376 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8707 (t) REVERT: B 379 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: B 517 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8037 (pp) REVERT: G 390 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7587 (t80) REVERT: G 393 MET cc_start: 0.7434 (tmt) cc_final: 0.6382 (mtt) REVERT: G 407 LEU cc_start: 0.8013 (pt) cc_final: 0.7268 (pt) REVERT: G 509 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: G 532 ARG cc_start: 0.7595 (ptm160) cc_final: 0.6836 (ttm170) REVERT: G 574 MET cc_start: 0.7373 (mmm) cc_final: 0.6821 (mmm) outliers start: 66 outliers final: 32 residues processed: 185 average time/residue: 0.5490 time to fit residues: 112.6998 Evaluate side-chains 146 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain G residue 390 PHE Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 469 ILE Chi-restraints excluded: chain G residue 516 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 0.0470 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 147 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS B 123 GLN G 516 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.131065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.104032 restraints weight = 26761.561| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.99 r_work: 0.3643 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14318 Z= 0.143 Angle : 0.668 10.270 19524 Z= 0.327 Chirality : 0.047 0.255 2133 Planarity : 0.004 0.045 2440 Dihedral : 6.170 59.871 2402 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 3.24 % Allowed : 23.20 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1657 helix: 0.24 (0.34), residues: 217 sheet: 0.17 (0.23), residues: 496 loop : -0.88 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 147 TYR 0.020 0.002 TYR B 48 PHE 0.017 0.001 PHE B 371 TRP 0.014 0.001 TRP A 659 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00330 (14278) covalent geometry : angle 0.65344 (19418) SS BOND : bond 0.00638 ( 14) SS BOND : angle 1.53852 ( 28) hydrogen bonds : bond 0.03642 ( 461) hydrogen bonds : angle 5.40389 ( 1230) link_BETA1-4 : bond 0.00442 ( 13) link_BETA1-4 : angle 1.68441 ( 39) link_NAG-ASN : bond 0.00266 ( 13) link_NAG-ASN : angle 2.50648 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8089 (m-80) cc_final: 0.7821 (m-80) REVERT: A 98 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: A 104 ASP cc_start: 0.8213 (t0) cc_final: 0.7732 (t0) REVERT: A 243 ASP cc_start: 0.8571 (t0) cc_final: 0.8260 (t70) REVERT: A 326 ASP cc_start: 0.8425 (t0) cc_final: 0.8041 (t0) REVERT: A 466 LYS cc_start: 0.8502 (mmpt) cc_final: 0.8111 (mmmt) REVERT: A 527 GLN cc_start: 0.8196 (pt0) cc_final: 0.7848 (pt0) REVERT: B 136 ASP cc_start: 0.8186 (t0) cc_final: 0.7339 (t0) REVERT: B 146 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6423 (pm20) REVERT: B 376 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8762 (t) REVERT: B 379 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: B 517 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8007 (pp) REVERT: G 393 MET cc_start: 0.7385 (tmt) cc_final: 0.6334 (mpm) REVERT: G 509 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7080 (ttm-80) REVERT: G 518 GLU cc_start: 0.8279 (tt0) cc_final: 0.7655 (tm-30) REVERT: G 532 ARG cc_start: 0.7662 (ptm160) cc_final: 0.7276 (ptm160) REVERT: G 574 MET cc_start: 0.7431 (mmm) cc_final: 0.6838 (mmm) outliers start: 48 outliers final: 23 residues processed: 153 average time/residue: 0.4973 time to fit residues: 84.9577 Evaluate side-chains 132 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 405 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS B 123 GLN B 141 GLN B 247 GLN G 544 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.127954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.100801 restraints weight = 26558.905| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.96 r_work: 0.3588 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14318 Z= 0.202 Angle : 0.714 10.452 19524 Z= 0.354 Chirality : 0.048 0.258 2133 Planarity : 0.004 0.042 2440 Dihedral : 6.371 58.387 2402 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 4.38 % Allowed : 22.12 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % 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: -0.73 (0.20), residues: 1657 helix: 0.11 (0.34), residues: 219 sheet: 0.17 (0.23), residues: 484 loop : -0.97 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 147 TYR 0.026 0.002 TYR B 48 PHE 0.017 0.002 PHE B 461 TRP 0.015 0.002 TRP A 659 HIS 0.008 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00474 (14278) covalent geometry : angle 0.69736 (19418) SS BOND : bond 0.00777 ( 14) SS BOND : angle 2.20859 ( 28) hydrogen bonds : bond 0.04145 ( 461) hydrogen bonds : angle 5.56321 ( 1230) link_BETA1-4 : bond 0.00327 ( 13) link_BETA1-4 : angle 1.74017 ( 39) link_NAG-ASN : bond 0.00296 ( 13) link_NAG-ASN : angle 2.61029 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 107 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8583 (m-80) cc_final: 0.8244 (m-80) REVERT: A 98 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: A 104 ASP cc_start: 0.8326 (t0) cc_final: 0.7720 (t0) REVERT: A 243 ASP cc_start: 0.8673 (t0) cc_final: 0.8194 (t0) REVERT: A 326 ASP cc_start: 0.8631 (t0) cc_final: 0.8230 (t0) REVERT: A 466 LYS cc_start: 0.8570 (mmpt) cc_final: 0.7878 (mmmm) REVERT: A 527 GLN cc_start: 0.8230 (pt0) cc_final: 0.7827 (pt0) REVERT: A 638 MET cc_start: 0.8654 (mmm) cc_final: 0.8296 (mmt) REVERT: B 83 TYR cc_start: 0.8455 (m-80) cc_final: 0.8140 (m-80) REVERT: B 136 ASP cc_start: 0.8486 (t0) cc_final: 0.7679 (t0) REVERT: B 146 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: B 152 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8338 (p) REVERT: B 376 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8748 (t) REVERT: B 379 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: B 517 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8016 (pp) REVERT: B 591 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.6850 (tpt) REVERT: B 608 GLU cc_start: 0.8849 (tp30) cc_final: 0.8482 (tm-30) REVERT: G 468 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7152 (p0) REVERT: G 509 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7111 (ttm-80) REVERT: G 574 MET cc_start: 0.7561 (mmm) cc_final: 0.6769 (mpp) outliers start: 65 outliers final: 28 residues processed: 163 average time/residue: 0.5813 time to fit residues: 104.9594 Evaluate side-chains 134 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 612 GLN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 405 LYS Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 524 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 74 optimal weight: 0.0060 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 0.0270 chunk 125 optimal weight: 0.6980 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN B 75 ASN B 123 GLN B 141 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.131257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.104340 restraints weight = 26551.422| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.98 r_work: 0.3648 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14318 Z= 0.110 Angle : 0.658 11.327 19524 Z= 0.321 Chirality : 0.046 0.251 2133 Planarity : 0.004 0.042 2440 Dihedral : 6.182 59.933 2402 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 2.70 % Allowed : 23.74 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1657 helix: 0.37 (0.35), residues: 219 sheet: 0.24 (0.23), residues: 496 loop : -0.90 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 147 TYR 0.014 0.001 TYR B 752 PHE 0.018 0.001 PHE B 371 TRP 0.014 0.001 TRP A 659 HIS 0.004 0.001 HIS B 748 Details of bonding type rmsd covalent geometry : bond 0.00244 (14278) covalent geometry : angle 0.64597 (19418) SS BOND : bond 0.00419 ( 14) SS BOND : angle 1.58334 ( 28) hydrogen bonds : bond 0.03414 ( 461) hydrogen bonds : angle 5.29142 ( 1230) link_BETA1-4 : bond 0.00457 ( 13) link_BETA1-4 : angle 1.51196 ( 39) link_NAG-ASN : bond 0.00269 ( 13) link_NAG-ASN : angle 2.24960 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8568 (m-80) cc_final: 0.8215 (m-80) REVERT: A 98 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: A 104 ASP cc_start: 0.8207 (t0) cc_final: 0.7650 (t0) REVERT: A 243 ASP cc_start: 0.8633 (t0) cc_final: 0.8099 (t0) REVERT: A 326 ASP cc_start: 0.8485 (t0) cc_final: 0.8045 (t0) REVERT: A 425 MET cc_start: 0.6694 (ttm) cc_final: 0.6396 (mtp) REVERT: A 466 LYS cc_start: 0.8580 (mmpt) cc_final: 0.7894 (mmmm) REVERT: A 527 GLN cc_start: 0.8159 (pt0) cc_final: 0.7775 (pt0) REVERT: A 638 MET cc_start: 0.8603 (mmm) cc_final: 0.8218 (mmt) REVERT: B 83 TYR cc_start: 0.8443 (m-80) cc_final: 0.8146 (m-80) REVERT: B 136 ASP cc_start: 0.8385 (t0) cc_final: 0.7602 (t0) REVERT: B 145 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: B 146 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6166 (pm20) REVERT: B 147 ARG cc_start: 0.7005 (ptt-90) cc_final: 0.6751 (ptt90) REVERT: B 348 MET cc_start: 0.8079 (ttt) cc_final: 0.7870 (tpp) REVERT: B 376 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8767 (t) REVERT: B 379 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: B 384 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7074 (mt) REVERT: B 517 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.7981 (pp) REVERT: B 608 GLU cc_start: 0.8836 (tp30) cc_final: 0.8433 (tm-30) REVERT: G 468 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7328 (p0) REVERT: G 509 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7394 (ttm-80) REVERT: G 518 GLU cc_start: 0.8281 (tt0) cc_final: 0.7716 (tm-30) REVERT: G 574 MET cc_start: 0.7415 (mmm) cc_final: 0.6857 (mmm) outliers start: 40 outliers final: 18 residues processed: 154 average time/residue: 0.5788 time to fit residues: 98.8646 Evaluate side-chains 128 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain G residue 405 LYS Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 524 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 70 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.128854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.101797 restraints weight = 26574.028| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.99 r_work: 0.3605 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14318 Z= 0.160 Angle : 0.691 12.532 19524 Z= 0.339 Chirality : 0.047 0.253 2133 Planarity : 0.004 0.044 2440 Dihedral : 6.135 55.158 2402 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer: Outliers : 2.83 % Allowed : 23.87 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1657 helix: 0.36 (0.35), residues: 219 sheet: 0.18 (0.23), residues: 497 loop : -0.92 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 358 TYR 0.019 0.002 TYR B 48 PHE 0.050 0.002 PHE B 387 TRP 0.014 0.002 TRP B 305 HIS 0.006 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00373 (14278) covalent geometry : angle 0.67518 (19418) SS BOND : bond 0.00584 ( 14) SS BOND : angle 2.45944 ( 28) hydrogen bonds : bond 0.03775 ( 461) hydrogen bonds : angle 5.35188 ( 1230) link_BETA1-4 : bond 0.00396 ( 13) link_BETA1-4 : angle 1.58150 ( 39) link_NAG-ASN : bond 0.00226 ( 13) link_NAG-ASN : angle 2.34177 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8645 (m-80) cc_final: 0.8326 (m-80) REVERT: A 98 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: A 104 ASP cc_start: 0.8316 (t0) cc_final: 0.7772 (t0) REVERT: A 243 ASP cc_start: 0.8642 (t0) cc_final: 0.8152 (t0) REVERT: A 326 ASP cc_start: 0.8591 (t0) cc_final: 0.8135 (t0) REVERT: A 466 LYS cc_start: 0.8559 (mmpt) cc_final: 0.7875 (mmmm) REVERT: A 577 SER cc_start: 0.8062 (m) cc_final: 0.7770 (t) REVERT: A 638 MET cc_start: 0.8637 (mmm) cc_final: 0.8230 (mmt) REVERT: B 83 TYR cc_start: 0.8507 (m-80) cc_final: 0.8166 (m-80) REVERT: B 145 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: B 146 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6280 (pm20) REVERT: B 147 ARG cc_start: 0.7060 (ptt-90) cc_final: 0.6787 (ptt90) REVERT: B 348 MET cc_start: 0.8091 (ttt) cc_final: 0.7815 (tpp) REVERT: B 376 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8723 (t) REVERT: B 379 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: B 517 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8014 (pp) REVERT: B 591 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.6555 (tpt) REVERT: B 608 GLU cc_start: 0.8857 (tp30) cc_final: 0.8429 (tm-30) REVERT: G 393 MET cc_start: 0.7055 (ppp) cc_final: 0.6241 (ppp) REVERT: G 468 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7325 (p0) REVERT: G 471 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7893 (pt) REVERT: G 509 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7342 (ttm-80) REVERT: G 574 MET cc_start: 0.7481 (mmm) cc_final: 0.6885 (mmm) outliers start: 42 outliers final: 21 residues processed: 141 average time/residue: 0.5846 time to fit residues: 91.4785 Evaluate side-chains 130 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 405 LYS Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 469 ILE Chi-restraints excluded: chain G residue 471 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 147 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 141 GLN G 544 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.130704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.103817 restraints weight = 26724.284| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.00 r_work: 0.3640 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14318 Z= 0.115 Angle : 0.680 13.759 19524 Z= 0.332 Chirality : 0.046 0.250 2133 Planarity : 0.004 0.041 2440 Dihedral : 5.956 56.020 2401 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 2.43 % Allowed : 24.61 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % 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: -0.53 (0.20), residues: 1657 helix: 0.51 (0.35), residues: 219 sheet: 0.22 (0.23), residues: 497 loop : -0.87 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 147 TYR 0.015 0.001 TYR B 752 PHE 0.045 0.001 PHE B 387 TRP 0.014 0.001 TRP A 659 HIS 0.007 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00263 (14278) covalent geometry : angle 0.65799 (19418) SS BOND : bond 0.00482 ( 14) SS BOND : angle 3.61318 ( 28) hydrogen bonds : bond 0.03386 ( 461) hydrogen bonds : angle 5.21592 ( 1230) link_BETA1-4 : bond 0.00417 ( 13) link_BETA1-4 : angle 1.45612 ( 39) link_NAG-ASN : bond 0.00239 ( 13) link_NAG-ASN : angle 2.13210 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8648 (m-80) cc_final: 0.8370 (m-80) REVERT: A 98 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: A 104 ASP cc_start: 0.8262 (t0) cc_final: 0.7717 (t0) REVERT: A 140 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6148 (tpt90) REVERT: A 243 ASP cc_start: 0.8633 (t0) cc_final: 0.8120 (t0) REVERT: A 326 ASP cc_start: 0.8487 (t0) cc_final: 0.8039 (t0) REVERT: A 527 GLN cc_start: 0.7902 (pt0) cc_final: 0.7546 (pt0) REVERT: A 577 SER cc_start: 0.7915 (m) cc_final: 0.7637 (t) REVERT: A 638 MET cc_start: 0.8626 (mmm) cc_final: 0.8232 (mmt) REVERT: B 83 TYR cc_start: 0.8356 (m-80) cc_final: 0.8005 (m-80) REVERT: B 136 ASP cc_start: 0.8492 (t0) cc_final: 0.7689 (t0) REVERT: B 145 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: B 146 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: B 347 GLU cc_start: 0.7082 (tp30) cc_final: 0.6663 (tm-30) REVERT: B 379 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: B 517 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8019 (pp) REVERT: B 608 GLU cc_start: 0.8852 (tp30) cc_final: 0.8401 (tm-30) REVERT: B 693 GLU cc_start: 0.8316 (pp20) cc_final: 0.8095 (pp20) REVERT: G 509 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7450 (ttm-80) REVERT: G 574 MET cc_start: 0.7540 (mmm) cc_final: 0.6960 (mmm) outliers start: 36 outliers final: 19 residues processed: 135 average time/residue: 0.6200 time to fit residues: 92.2917 Evaluate side-chains 125 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain G residue 405 LYS Chi-restraints excluded: chain G residue 469 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 54 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 141 GLN ** B 682 HIS ** 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 = 0.4110 r_free = 0.4110 target = 0.127225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.100242 restraints weight = 26675.436| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.99 r_work: 0.3578 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14318 Z= 0.195 Angle : 0.727 12.307 19524 Z= 0.356 Chirality : 0.048 0.257 2133 Planarity : 0.004 0.044 2440 Dihedral : 6.062 55.141 2401 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer: Outliers : 2.09 % Allowed : 25.02 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % 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: -0.68 (0.20), residues: 1657 helix: 0.28 (0.33), residues: 231 sheet: 0.12 (0.23), residues: 494 loop : -0.95 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 147 TYR 0.020 0.002 TYR A 752 PHE 0.044 0.002 PHE B 387 TRP 0.022 0.002 TRP A 627 HIS 0.007 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00461 (14278) covalent geometry : angle 0.71178 (19418) SS BOND : bond 0.00612 ( 14) SS BOND : angle 2.28419 ( 28) hydrogen bonds : bond 0.04005 ( 461) hydrogen bonds : angle 5.43013 ( 1230) link_BETA1-4 : bond 0.00306 ( 13) link_BETA1-4 : angle 1.59597 ( 39) link_NAG-ASN : bond 0.00247 ( 13) link_NAG-ASN : angle 2.40586 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 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: A 83 TYR cc_start: 0.8756 (m-80) cc_final: 0.8385 (m-80) REVERT: A 98 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: A 104 ASP cc_start: 0.8420 (t0) cc_final: 0.7843 (t0) REVERT: A 243 ASP cc_start: 0.8645 (t0) cc_final: 0.8178 (t0) REVERT: A 326 ASP cc_start: 0.8612 (t0) cc_final: 0.8180 (t0) REVERT: A 425 MET cc_start: 0.6648 (mtm) cc_final: 0.5904 (mtm) REVERT: A 638 MET cc_start: 0.8675 (mmm) cc_final: 0.8219 (mmt) REVERT: B 74 ASN cc_start: 0.7623 (t0) cc_final: 0.7399 (t0) REVERT: B 145 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: B 146 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6299 (pm20) REVERT: B 147 ARG cc_start: 0.7352 (ptt90) cc_final: 0.7141 (ptt-90) REVERT: B 379 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: B 382 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6260 (mtt-85) REVERT: B 517 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8049 (pp) REVERT: B 591 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.6587 (tpt) REVERT: B 608 GLU cc_start: 0.8841 (tp30) cc_final: 0.8492 (tm-30) REVERT: G 393 MET cc_start: 0.6992 (ppp) cc_final: 0.6284 (ppp) REVERT: G 509 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7544 (ttm-80) REVERT: G 574 MET cc_start: 0.7466 (mmm) cc_final: 0.6859 (mmm) outliers start: 31 outliers final: 20 residues processed: 126 average time/residue: 0.6078 time to fit residues: 84.4116 Evaluate side-chains 123 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 382 ARG Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain G residue 405 LYS Chi-restraints excluded: chain G residue 469 ILE Chi-restraints excluded: chain G residue 524 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 31 optimal weight: 0.0470 chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 0.0870 chunk 137 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN B 123 GLN B 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.130830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.103918 restraints weight = 26564.059| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.97 r_work: 0.3642 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14318 Z= 0.109 Angle : 0.677 12.287 19524 Z= 0.330 Chirality : 0.046 0.251 2133 Planarity : 0.004 0.040 2440 Dihedral : 5.875 56.295 2401 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 1.75 % Allowed : 25.35 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.13 % 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: -0.54 (0.20), residues: 1657 helix: 0.49 (0.34), residues: 230 sheet: 0.20 (0.23), residues: 496 loop : -0.87 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 54 TYR 0.015 0.001 TYR B 752 PHE 0.037 0.001 PHE B 387 TRP 0.018 0.001 TRP A 124 HIS 0.004 0.001 HIS B 748 Details of bonding type rmsd covalent geometry : bond 0.00243 (14278) covalent geometry : angle 0.66384 (19418) SS BOND : bond 0.00417 ( 14) SS BOND : angle 2.32677 ( 28) hydrogen bonds : bond 0.03315 ( 461) hydrogen bonds : angle 5.25738 ( 1230) link_BETA1-4 : bond 0.00445 ( 13) link_BETA1-4 : angle 1.41409 ( 39) link_NAG-ASN : bond 0.00272 ( 13) link_NAG-ASN : angle 2.01547 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7218.29 seconds wall clock time: 123 minutes 33.71 seconds (7413.71 seconds total)