Starting phenix.real_space_refine on Sun Oct 25 06:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njs_49489/10_2026/9njs_49489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njs_49489/10_2026/9njs_49489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9njs_49489/10_2026/9njs_49489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njs_49489/10_2026/9njs_49489.map" model { file = "/net/cci-nas-00/data/ceres_data/9njs_49489/10_2026/9njs_49489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njs_49489/10_2026/9njs_49489.cif" } resolution = 3.1 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= -0.012 sd= 0.347 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 80 5.16 5 C 10344 2.51 5 N 2472 2.21 5 O 2740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15636 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3867 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 11, 'TRANS': 467} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "b" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3867 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 11, 'TRANS': 467} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "c" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3867 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 11, 'TRANS': 467} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "d" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3867 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 11, 'TRANS': 467} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "d" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 3.92, per 1000 atoms: 0.25 Number of scatterers: 15636 At special positions: 0 Unit cell: (111.78, 111.78, 103.5, 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 80 16.00 O 2740 8.00 N 2472 7.00 C 10344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS a 331 " - pdb=" SG CYS a 344 " distance=2.03 Simple disulfide: pdb=" SG CYS b 331 " - pdb=" SG CYS b 344 " distance=2.22 Simple disulfide: pdb=" SG CYS c 331 " - pdb=" SG CYS c 344 " distance=2.03 Simple disulfide: pdb=" SG CYS d 331 " - pdb=" SG CYS d 344 " 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 Atom "HETATM15508 O5 NAG a 803 .*. O " rejected from bonding due to valence issues. Atom "HETATM15564 O5 NAG c 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG a 801 " - " ASN a 328 " " NAG a 802 " - " ASN a 362 " " NAG a 803 " - " ASN a 375 " " NAG b 801 " - " ASN b 328 " " NAG b 802 " - " ASN b 362 " " NAG b 803 " - " ASN b 375 " " NAG c 801 " - " ASN c 328 " " NAG c 802 " - " ASN c 362 " " NAG c 803 " - " ASN c 375 " " NAG d 801 " - " ASN d 328 " " NAG d 802 " - " ASN d 362 " " NAG d 803 " - " ASN d 375 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 709.0 milliseconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 63.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'a' and resid 217 through 242 Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.768A pdb=" N THR a 250 " --> pdb=" O VAL a 246 " (cutoff:3.500A) Processing helix chain 'a' and resid 269 through 273 removed outlier: 3.688A pdb=" N LEU a 273 " --> pdb=" O PHE a 270 " (cutoff:3.500A) Processing helix chain 'a' and resid 275 through 292 removed outlier: 3.632A pdb=" N TYR a 292 " --> pdb=" O LEU a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 310 through 312 No H-bonds generated for 'chain 'a' and resid 310 through 312' Processing helix chain 'a' and resid 334 through 338 removed outlier: 3.744A pdb=" N ARG a 338 " --> pdb=" O GLN a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 349 through 353 Processing helix chain 'a' and resid 363 through 367 removed outlier: 3.880A pdb=" N ILE a 367 " --> pdb=" O THR a 364 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 412 Processing helix chain 'a' and resid 467 through 498 removed outlier: 3.622A pdb=" N HIS a 498 " --> pdb=" O GLU a 494 " (cutoff:3.500A) Processing helix chain 'a' and resid 499 through 505 removed outlier: 4.038A pdb=" N SER a 505 " --> pdb=" O HIS a 501 " (cutoff:3.500A) Processing helix chain 'a' and resid 505 through 528 removed outlier: 3.939A pdb=" N CYS a 509 " --> pdb=" O SER a 505 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL a 516 " --> pdb=" O VAL a 512 " (cutoff:3.500A) Processing helix chain 'a' and resid 532 through 542 Processing helix chain 'a' and resid 548 through 572 removed outlier: 3.599A pdb=" N TYR a 553 " --> pdb=" O GLU a 549 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP a 554 " --> pdb=" O HIS a 550 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 577 Processing helix chain 'a' and resid 580 through 619 removed outlier: 3.908A pdb=" N SER a 584 " --> pdb=" O ASN a 580 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN a 585 " --> pdb=" O ARG a 581 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA a 594 " --> pdb=" O MET a 590 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS a 595 " --> pdb=" O SER a 591 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP a 596 " --> pdb=" O ARG a 592 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE a 607 " --> pdb=" O MET a 603 " (cutoff:3.500A) Processing helix chain 'a' and resid 628 through 642 removed outlier: 3.518A pdb=" N LEU a 641 " --> pdb=" O PHE a 637 " (cutoff:3.500A) Processing helix chain 'a' and resid 645 through 653 removed outlier: 3.815A pdb=" N ILE a 649 " --> pdb=" O ASN a 645 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN a 653 " --> pdb=" O ILE a 649 " (cutoff:3.500A) Processing helix chain 'a' and resid 655 through 694 removed outlier: 3.697A pdb=" N ILE a 659 " --> pdb=" O VAL a 655 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR a 683 " --> pdb=" O ILE a 679 " (cutoff:3.500A) Processing helix chain 'b' and resid 218 through 242 Processing helix chain 'b' and resid 246 through 258 removed outlier: 3.759A pdb=" N THR b 250 " --> pdb=" O VAL b 246 " (cutoff:3.500A) Processing helix chain 'b' and resid 269 through 273 removed outlier: 3.703A pdb=" N LEU b 273 " --> pdb=" O PHE b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 275 through 292 removed outlier: 3.586A pdb=" N TYR b 292 " --> pdb=" O LEU b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 310 through 312 No H-bonds generated for 'chain 'b' and resid 310 through 312' Processing helix chain 'b' and resid 334 through 338 removed outlier: 3.583A pdb=" N ARG b 338 " --> pdb=" O GLN b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 349 through 353 Processing helix chain 'b' and resid 363 through 367 removed outlier: 3.607A pdb=" N TRP b 366 " --> pdb=" O GLY b 363 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE b 367 " --> pdb=" O THR b 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 363 through 367' Processing helix chain 'b' and resid 398 through 412 Processing helix chain 'b' and resid 467 through 498 removed outlier: 3.572A pdb=" N HIS b 498 " --> pdb=" O GLU b 494 " (cutoff:3.500A) Processing helix chain 'b' and resid 499 through 505 removed outlier: 4.063A pdb=" N SER b 505 " --> pdb=" O HIS b 501 " (cutoff:3.500A) Processing helix chain 'b' and resid 505 through 528 removed outlier: 3.946A pdb=" N CYS b 509 " --> pdb=" O SER b 505 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL b 516 " --> pdb=" O VAL b 512 " (cutoff:3.500A) Processing helix chain 'b' and resid 532 through 542 removed outlier: 3.574A pdb=" N LEU b 536 " --> pdb=" O VAL b 532 " (cutoff:3.500A) Processing helix chain 'b' and resid 548 through 572 removed outlier: 3.624A pdb=" N TYR b 553 " --> pdb=" O GLU b 549 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP b 554 " --> pdb=" O HIS b 550 " (cutoff:3.500A) Processing helix chain 'b' and resid 573 through 577 Processing helix chain 'b' and resid 580 through 619 removed outlier: 3.895A pdb=" N SER b 584 " --> pdb=" O ASN b 580 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN b 585 " --> pdb=" O ARG b 581 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA b 594 " --> pdb=" O MET b 590 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS b 595 " --> pdb=" O SER b 591 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP b 596 " --> pdb=" O ARG b 592 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE b 607 " --> pdb=" O MET b 603 " (cutoff:3.500A) Processing helix chain 'b' and resid 628 through 642 removed outlier: 3.562A pdb=" N LEU b 641 " --> pdb=" O PHE b 637 " (cutoff:3.500A) Processing helix chain 'b' and resid 645 through 653 removed outlier: 3.800A pdb=" N ILE b 649 " --> pdb=" O ASN b 645 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN b 653 " --> pdb=" O ILE b 649 " (cutoff:3.500A) Processing helix chain 'b' and resid 655 through 694 removed outlier: 3.690A pdb=" N ILE b 659 " --> pdb=" O VAL b 655 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR b 683 " --> pdb=" O ILE b 679 " (cutoff:3.500A) Processing helix chain 'c' and resid 218 through 242 Processing helix chain 'c' and resid 246 through 258 removed outlier: 3.732A pdb=" N THR c 250 " --> pdb=" O VAL c 246 " (cutoff:3.500A) Processing helix chain 'c' and resid 269 through 273 removed outlier: 3.695A pdb=" N LEU c 273 " --> pdb=" O PHE c 270 " (cutoff:3.500A) Processing helix chain 'c' and resid 275 through 292 removed outlier: 3.527A pdb=" N TYR c 292 " --> pdb=" O LEU c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 310 through 312 No H-bonds generated for 'chain 'c' and resid 310 through 312' Processing helix chain 'c' and resid 334 through 338 removed outlier: 3.793A pdb=" N ARG c 338 " --> pdb=" O GLN c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 349 through 353 Processing helix chain 'c' and resid 363 through 367 removed outlier: 3.503A pdb=" N TRP c 366 " --> pdb=" O GLY c 363 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE c 367 " --> pdb=" O THR c 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 363 through 367' Processing helix chain 'c' and resid 398 through 412 Processing helix chain 'c' and resid 467 through 498 removed outlier: 3.590A pdb=" N HIS c 498 " --> pdb=" O GLU c 494 " (cutoff:3.500A) Processing helix chain 'c' and resid 499 through 505 removed outlier: 4.103A pdb=" N SER c 505 " --> pdb=" O HIS c 501 " (cutoff:3.500A) Processing helix chain 'c' and resid 505 through 528 removed outlier: 3.911A pdb=" N CYS c 509 " --> pdb=" O SER c 505 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL c 516 " --> pdb=" O VAL c 512 " (cutoff:3.500A) Processing helix chain 'c' and resid 532 through 542 Processing helix chain 'c' and resid 548 through 572 removed outlier: 3.605A pdb=" N TYR c 553 " --> pdb=" O GLU c 549 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP c 554 " --> pdb=" O HIS c 550 " (cutoff:3.500A) Processing helix chain 'c' and resid 573 through 577 Processing helix chain 'c' and resid 580 through 619 removed outlier: 3.830A pdb=" N SER c 584 " --> pdb=" O ASN c 580 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN c 585 " --> pdb=" O ARG c 581 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA c 594 " --> pdb=" O MET c 590 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS c 595 " --> pdb=" O SER c 591 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASP c 596 " --> pdb=" O ARG c 592 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE c 607 " --> pdb=" O MET c 603 " (cutoff:3.500A) Processing helix chain 'c' and resid 628 through 642 removed outlier: 3.525A pdb=" N LEU c 641 " --> pdb=" O PHE c 637 " (cutoff:3.500A) Processing helix chain 'c' and resid 645 through 653 removed outlier: 3.769A pdb=" N ILE c 649 " --> pdb=" O ASN c 645 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN c 653 " --> pdb=" O ILE c 649 " (cutoff:3.500A) Processing helix chain 'c' and resid 655 through 694 removed outlier: 3.666A pdb=" N ILE c 659 " --> pdb=" O VAL c 655 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR c 683 " --> pdb=" O ILE c 679 " (cutoff:3.500A) Processing helix chain 'd' and resid 218 through 242 Processing helix chain 'd' and resid 246 through 258 removed outlier: 3.777A pdb=" N THR d 250 " --> pdb=" O VAL d 246 " (cutoff:3.500A) Processing helix chain 'd' and resid 269 through 273 removed outlier: 3.748A pdb=" N LEU d 273 " --> pdb=" O PHE d 270 " (cutoff:3.500A) Processing helix chain 'd' and resid 275 through 292 removed outlier: 3.600A pdb=" N TYR d 292 " --> pdb=" O LEU d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 312 No H-bonds generated for 'chain 'd' and resid 310 through 312' Processing helix chain 'd' and resid 334 through 338 removed outlier: 3.591A pdb=" N ARG d 338 " --> pdb=" O GLN d 335 " (cutoff:3.500A) Processing helix chain 'd' and resid 349 through 353 Processing helix chain 'd' and resid 363 through 367 removed outlier: 3.625A pdb=" N TRP d 366 " --> pdb=" O GLY d 363 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE d 367 " --> pdb=" O THR d 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 363 through 367' Processing helix chain 'd' and resid 398 through 412 Processing helix chain 'd' and resid 467 through 498 removed outlier: 3.882A pdb=" N HIS d 498 " --> pdb=" O GLU d 494 " (cutoff:3.500A) Processing helix chain 'd' and resid 499 through 505 removed outlier: 4.182A pdb=" N SER d 505 " --> pdb=" O HIS d 501 " (cutoff:3.500A) Processing helix chain 'd' and resid 506 through 528 removed outlier: 3.680A pdb=" N VAL d 516 " --> pdb=" O VAL d 512 " (cutoff:3.500A) Processing helix chain 'd' and resid 532 through 542 Processing helix chain 'd' and resid 548 through 572 removed outlier: 3.613A pdb=" N TYR d 553 " --> pdb=" O GLU d 549 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP d 554 " --> pdb=" O HIS d 550 " (cutoff:3.500A) Processing helix chain 'd' and resid 573 through 577 Processing helix chain 'd' and resid 580 through 619 removed outlier: 3.773A pdb=" N SER d 584 " --> pdb=" O ASN d 580 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN d 585 " --> pdb=" O ARG d 581 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA d 594 " --> pdb=" O MET d 590 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS d 595 " --> pdb=" O SER d 591 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP d 596 " --> pdb=" O ARG d 592 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE d 607 " --> pdb=" O MET d 603 " (cutoff:3.500A) Processing helix chain 'd' and resid 628 through 642 removed outlier: 3.573A pdb=" N LEU d 641 " --> pdb=" O PHE d 637 " (cutoff:3.500A) Processing helix chain 'd' and resid 645 through 653 removed outlier: 3.756A pdb=" N ILE d 649 " --> pdb=" O ASN d 645 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN d 653 " --> pdb=" O ILE d 649 " (cutoff:3.500A) Processing helix chain 'd' and resid 655 through 694 removed outlier: 3.643A pdb=" N ILE d 659 " --> pdb=" O VAL d 655 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR d 683 " --> pdb=" O ILE d 679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 308 through 309 removed outlier: 3.681A pdb=" N LEU a 435 " --> pdb=" O ASN a 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 391 through 394 removed outlier: 3.927A pdb=" N ALA a 421 " --> pdb=" O LEU a 324 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU a 435 " --> pdb=" O ASN a 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'b' and resid 308 through 309 removed outlier: 7.109A pdb=" N LEU b 316 " --> pdb=" O TYR b 429 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR b 429 " --> pdb=" O LEU b 316 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL b 318 " --> pdb=" O SER b 427 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER b 427 " --> pdb=" O VAL b 318 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA b 421 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU b 435 " --> pdb=" O ASN b 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 391 through 394 removed outlier: 7.109A pdb=" N LEU b 316 " --> pdb=" O TYR b 429 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR b 429 " --> pdb=" O LEU b 316 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL b 318 " --> pdb=" O SER b 427 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER b 427 " --> pdb=" O VAL b 318 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA b 421 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU b 435 " --> pdb=" O ASN b 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'c' and resid 308 through 309 removed outlier: 3.741A pdb=" N LEU c 435 " --> pdb=" O ASN c 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 391 through 394 removed outlier: 3.985A pdb=" N ALA c 421 " --> pdb=" O LEU c 324 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU c 435 " --> pdb=" O ASN c 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'd' and resid 308 through 309 removed outlier: 3.731A pdb=" N LEU d 435 " --> pdb=" O ASN d 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 391 through 394 removed outlier: 3.786A pdb=" N ALA d 421 " --> pdb=" O LEU d 324 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU d 435 " --> pdb=" O ASN d 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 379 through 380 1004 hydrogen bonds defined for protein. 2880 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: 2.69 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3825 1.33 - 1.45: 3666 1.45 - 1.58: 8437 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 16052 Sorted by residual: bond pdb=" C PRO b 334 " pdb=" N GLN b 335 " ideal model delta sigma weight residual 1.335 1.428 -0.093 1.38e-02 5.25e+03 4.53e+01 bond pdb=" C VAL c 220 " pdb=" N LEU c 221 " ideal model delta sigma weight residual 1.334 1.417 -0.083 1.27e-02 6.20e+03 4.27e+01 bond pdb=" C LEU d 217 " pdb=" N LYS d 218 " ideal model delta sigma weight residual 1.334 1.416 -0.082 1.27e-02 6.20e+03 4.14e+01 bond pdb=" C LEU c 224 " pdb=" N VAL c 225 " ideal model delta sigma weight residual 1.334 1.408 -0.074 1.26e-02 6.30e+03 3.44e+01 bond pdb=" C GLU d 494 " pdb=" N ILE d 495 " ideal model delta sigma weight residual 1.335 1.271 0.063 1.15e-02 7.56e+03 3.02e+01 ... (remaining 16047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 21654 3.07 - 6.14: 155 6.14 - 9.20: 14 9.20 - 12.27: 4 12.27 - 15.34: 1 Bond angle restraints: 21828 Sorted by residual: angle pdb=" O SER d 219 " pdb=" C SER d 219 " pdb=" N VAL d 220 " ideal model delta sigma weight residual 122.12 127.13 -5.01 1.06e+00 8.90e-01 2.24e+01 angle pdb=" O ILE d 492 " pdb=" C ILE d 492 " pdb=" N LEU d 493 " ideal model delta sigma weight residual 121.83 117.14 4.69 1.03e+00 9.43e-01 2.07e+01 angle pdb=" O LYS d 218 " pdb=" C LYS d 218 " pdb=" N SER d 219 " ideal model delta sigma weight residual 122.07 126.74 -4.67 1.03e+00 9.43e-01 2.05e+01 angle pdb=" CA ILE d 492 " pdb=" C ILE d 492 " pdb=" N LEU d 493 " ideal model delta sigma weight residual 117.28 122.51 -5.23 1.16e+00 7.43e-01 2.03e+01 angle pdb=" CA LEU c 677 " pdb=" CB LEU c 677 " pdb=" CG LEU c 677 " ideal model delta sigma weight residual 116.30 131.64 -15.34 3.50e+00 8.16e-02 1.92e+01 ... (remaining 21823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.27: 8404 21.27 - 42.53: 811 42.53 - 63.80: 162 63.80 - 85.07: 27 85.07 - 106.33: 12 Dihedral angle restraints: 9416 sinusoidal: 3728 harmonic: 5688 Sorted by residual: dihedral pdb=" CA CYS d 331 " pdb=" C CYS d 331 " pdb=" N SER d 332 " pdb=" CA SER d 332 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS a 331 " pdb=" C CYS a 331 " pdb=" N SER a 332 " pdb=" CA SER a 332 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA CYS d 593 " pdb=" C CYS d 593 " pdb=" N ALA d 594 " pdb=" CA ALA d 594 " ideal model delta harmonic sigma weight residual -180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 9413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 2507 0.228 - 0.456: 7 0.456 - 0.684: 0 0.684 - 0.912: 0 0.912 - 1.140: 2 Chirality restraints: 2516 Sorted by residual: chirality pdb=" C1 NAG d 802 " pdb=" ND2 ASN d 362 " pdb=" C2 NAG d 802 " pdb=" O5 NAG d 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.26 -1.14 2.00e-01 2.50e+01 3.25e+01 chirality pdb=" C1 NAG b 802 " pdb=" ND2 ASN b 362 " pdb=" C2 NAG b 802 " pdb=" O5 NAG b 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.43 -0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" C1 NAG c 801 " pdb=" ND2 ASN c 328 " pdb=" C2 NAG c 801 " pdb=" O5 NAG c 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 2513 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN b 362 " 0.293 2.00e-02 2.50e+03 2.64e-01 8.74e+02 pdb=" CG ASN b 362 " -0.107 2.00e-02 2.50e+03 pdb=" OD1 ASN b 362 " -0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN b 362 " -0.294 2.00e-02 2.50e+03 pdb=" C1 NAG b 802 " 0.337 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN a 375 " -0.159 2.00e-02 2.50e+03 1.66e-01 3.44e+02 pdb=" CG ASN a 375 " 0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN a 375 " 0.183 2.00e-02 2.50e+03 pdb=" ND2 ASN a 375 " 0.131 2.00e-02 2.50e+03 pdb=" C1 NAG a 803 " -0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN d 362 " 0.139 2.00e-02 2.50e+03 1.46e-01 2.67e+02 pdb=" CG ASN d 362 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN d 362 " -0.146 2.00e-02 2.50e+03 pdb=" ND2 ASN d 362 " 0.175 2.00e-02 2.50e+03 pdb=" C1 NAG d 802 " -0.188 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 9 2.17 - 2.85: 5626 2.85 - 3.53: 21013 3.53 - 4.22: 33669 4.22 - 4.90: 63310 Nonbonded interactions: 123627 Sorted by model distance: nonbonded pdb=" ND2 ASN d 362 " pdb=" N2 NAG d 802 " model vdw 1.487 2.560 nonbonded pdb=" OD1 ASN a 375 " pdb=" C1 NAG a 803 " model vdw 1.559 2.776 nonbonded pdb=" ND2 ASN d 362 " pdb=" C7 NAG d 802 " model vdw 1.737 3.350 nonbonded pdb=" CB ASN d 362 " pdb=" C1 NAG d 802 " model vdw 1.981 3.096 nonbonded pdb=" OD1 ASN c 328 " pdb=" C1 NAG c 801 " model vdw 2.058 2.776 ... (remaining 123622 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: 0.02 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.008 0.496 16068 Z= 0.471 Angle : 1.180 55.060 21872 Z= 0.538 Chirality : 0.055 1.140 2516 Planarity : 0.004 0.032 2688 Dihedral : 17.396 106.332 5724 Min Nonbonded Distance : 1.487 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.65 % Allowed : 20.78 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1908 helix: 1.25 (0.16), residues: 1012 sheet: -1.29 (0.34), residues: 232 loop : -1.49 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 306 TYR 0.013 0.001 TYR d 348 PHE 0.028 0.002 PHE b 670 TRP 0.025 0.002 TRP a 570 HIS 0.004 0.001 HIS a 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.34 (16052) covalent geometry : angle 0.72238 / 0.43 (21828) SS BOND : bond 0.09512 / 4.53 ( 4) SS BOND : angle 10.11557 / 4.05 ( 8) hydrogen bonds : bond 0.16472 / 10.84 ( 963) hydrogen bonds : angle 5.80091 / 4.05 ( 2880) link_NAG-ASN : bond 0.22863 / 14.93 ( 12) link_NAG-ASN : angle 22.49675 / 15.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: a 341 ILE cc_start: 0.8214 (mt) cc_final: 0.7922 (mt) REVERT: c 677 LEU cc_start: 0.8220 (mp) cc_final: 0.7878 (tp) outliers start: 27 outliers final: 22 residues processed: 236 average time/residue: 0.1139 time to fit residues: 41.1551 Evaluate side-chains 217 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 274 SER Chi-restraints excluded: chain a residue 307 SER Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 416 ASP Chi-restraints excluded: chain b residue 267 LYS Chi-restraints excluded: chain b residue 274 SER Chi-restraints excluded: chain b residue 307 SER Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain b residue 416 ASP Chi-restraints excluded: chain c residue 307 SER Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 350 VAL Chi-restraints excluded: chain c residue 510 LEU Chi-restraints excluded: chain c residue 512 VAL Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 349 SER Chi-restraints excluded: chain d residue 512 VAL Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 584 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 498 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.149569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.108325 restraints weight = 17357.019| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.73 r_work: 0.2942 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16068 Z= 0.135 Angle : 0.567 9.055 21872 Z= 0.300 Chirality : 0.040 0.206 2516 Planarity : 0.004 0.032 2688 Dihedral : 7.130 62.967 2376 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.06 % Allowed : 18.83 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1908 helix: 1.45 (0.16), residues: 1044 sheet: -0.74 (0.38), residues: 200 loop : -1.50 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 361 TYR 0.010 0.001 TYR c 348 PHE 0.018 0.001 PHE a 600 TRP 0.010 0.001 TRP a 570 HIS 0.004 0.001 HIS b 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (16052) covalent geometry : angle 0.54930 / 0.30 (21828) SS BOND : bond 0.00082 / 0.04 ( 4) SS BOND : angle 3.43194 / 1.52 ( 8) hydrogen bonds : bond 0.05731 / 3.78 ( 963) hydrogen bonds : angle 4.53752 / 3.17 ( 2880) link_NAG-ASN : bond 0.00324 / 0.18 ( 12) link_NAG-ASN : angle 3.08633 / 2.11 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 0.553 Fit side-chains REVERT: a 241 MET cc_start: 0.7254 (mmm) cc_final: 0.6946 (mtt) REVERT: a 341 ILE cc_start: 0.8291 (mt) cc_final: 0.7922 (mt) REVERT: b 266 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6803 (mm-30) REVERT: b 344 CYS cc_start: 0.6370 (OUTLIER) cc_final: 0.5669 (t) REVERT: b 349 SER cc_start: 0.9170 (t) cc_final: 0.8748 (p) REVERT: b 371 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: b 397 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7644 (mtm180) REVERT: b 650 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: c 306 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7720 (mtm-85) REVERT: c 462 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8727 (mp) REVERT: c 578 ASN cc_start: 0.8944 (m-40) cc_final: 0.8740 (m110) REVERT: d 316 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8716 (mt) REVERT: d 338 ARG cc_start: 0.8685 (tpp-160) cc_final: 0.8385 (tpp80) REVERT: d 371 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: d 619 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7170 (p90) REVERT: d 650 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8100 (tt0) outliers start: 50 outliers final: 28 residues processed: 254 average time/residue: 0.1109 time to fit residues: 42.6289 Evaluate side-chains 233 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 566 VAL Chi-restraints excluded: chain a residue 571 ILE Chi-restraints excluded: chain a residue 687 VAL Chi-restraints excluded: chain b residue 236 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 344 CYS Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 397 ARG Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 511 VAL Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 566 VAL Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 462 LEU Chi-restraints excluded: chain c residue 511 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 566 VAL Chi-restraints excluded: chain c residue 571 ILE Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 316 LEU Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 331 CYS Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 566 VAL Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [105, 116, 74, 120, 187, 53, 1, 144, 70, 103, 137] chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 585 GLN c 585 GLN d 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.146954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.105423 restraints weight = 17356.578| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.73 r_work: 0.2879 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16068 Z= 0.183 Angle : 0.603 8.844 21872 Z= 0.322 Chirality : 0.042 0.209 2516 Planarity : 0.005 0.039 2688 Dihedral : 5.957 59.397 2350 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.97 % Allowed : 18.77 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1908 helix: 1.45 (0.16), residues: 1036 sheet: -0.86 (0.36), residues: 200 loop : -1.64 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 322 TYR 0.012 0.002 TYR b 248 PHE 0.020 0.002 PHE b 600 TRP 0.007 0.001 TRP c 414 HIS 0.004 0.001 HIS b 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (16052) covalent geometry : angle 0.58115 / 0.32 (21828) SS BOND : bond 0.00204 / 0.10 ( 4) SS BOND : angle 4.26301 / 1.85 ( 8) hydrogen bonds : bond 0.06462 / 4.27 ( 963) hydrogen bonds : angle 4.58842 / 3.21 ( 2880) link_NAG-ASN : bond 0.00551 / 0.35 ( 12) link_NAG-ASN : angle 3.50247 / 2.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 212 time to evaluate : 0.536 Fit side-chains REVERT: a 341 ILE cc_start: 0.8459 (mt) cc_final: 0.8030 (mt) REVERT: a 654 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8356 (ttm170) REVERT: b 266 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6840 (mm-30) REVERT: b 349 SER cc_start: 0.9140 (t) cc_final: 0.8760 (p) REVERT: b 371 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: b 397 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7704 (mtm180) REVERT: b 650 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: c 306 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7763 (mtm-85) REVERT: c 343 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6530 (mt-10) REVERT: c 462 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8731 (mp) REVERT: c 578 ASN cc_start: 0.8897 (m-40) cc_final: 0.8695 (m110) REVERT: c 650 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: d 338 ARG cc_start: 0.8797 (tpp-160) cc_final: 0.8458 (tpp80) REVERT: d 361 ARG cc_start: 0.8655 (mtt90) cc_final: 0.8205 (mtt-85) REVERT: d 371 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: d 619 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.7269 (p90) REVERT: d 650 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: d 654 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8364 (ttm170) outliers start: 65 outliers final: 35 residues processed: 256 average time/residue: 0.1217 time to fit residues: 46.5365 Evaluate side-chains 245 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 416 ASP Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 566 VAL Chi-restraints excluded: chain a residue 654 ARG Chi-restraints excluded: chain a residue 668 MET Chi-restraints excluded: chain a residue 687 VAL Chi-restraints excluded: chain b residue 236 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 397 ARG Chi-restraints excluded: chain b residue 443 VAL Chi-restraints excluded: chain b residue 479 ILE Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 566 VAL Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 416 ASP Chi-restraints excluded: chain c residue 443 VAL Chi-restraints excluded: chain c residue 462 LEU Chi-restraints excluded: chain c residue 510 LEU Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 549 GLU Chi-restraints excluded: chain c residue 566 VAL Chi-restraints excluded: chain c residue 650 GLU Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 349 SER Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 443 VAL Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 566 VAL Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Chi-restraints excluded: chain d residue 654 ARG Chi-restraints excluded: chain d residue 668 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [31, 123, 160, 63, 93, 183, 33, 82, 54, 155, 118] chunk 31 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.0170 chunk 155 optimal weight: 0.0470 chunk 118 optimal weight: 1.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 585 GLN ** c 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 578 ASN d 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.149243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107367 restraints weight = 17336.097| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.75 r_work: 0.2938 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16068 Z= 0.123 Angle : 0.536 8.775 21872 Z= 0.284 Chirality : 0.039 0.172 2516 Planarity : 0.004 0.036 2688 Dihedral : 5.329 59.086 2350 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.36 % Allowed : 19.01 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1908 helix: 1.51 (0.16), residues: 1048 sheet: -0.71 (0.37), residues: 200 loop : -1.49 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 325 TYR 0.009 0.001 TYR d 239 PHE 0.016 0.001 PHE a 600 TRP 0.007 0.001 TRP c 570 HIS 0.003 0.001 HIS b 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16052) covalent geometry : angle 0.51484 / 0.28 (21828) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 3.91765 / 1.74 ( 8) hydrogen bonds : bond 0.05237 / 3.47 ( 963) hydrogen bonds : angle 4.40026 / 3.08 ( 2880) link_NAG-ASN : bond 0.00610 / 0.33 ( 12) link_NAG-ASN : angle 3.19412 / 2.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.764 Fit side-chains REVERT: a 361 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8345 (mtt-85) REVERT: a 654 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8424 (mtm180) REVERT: b 266 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6837 (mm-30) REVERT: b 267 LYS cc_start: 0.7933 (tmmt) cc_final: 0.7507 (tttp) REVERT: b 371 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: b 397 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7715 (mtm180) REVERT: b 650 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: c 306 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7657 (mtm-85) REVERT: c 343 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6687 (mt-10) REVERT: c 536 LEU cc_start: 0.7972 (mp) cc_final: 0.7581 (mt) REVERT: c 578 ASN cc_start: 0.8867 (m-40) cc_final: 0.8665 (m110) REVERT: c 650 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: c 674 ASN cc_start: 0.8705 (m110) cc_final: 0.8315 (m110) REVERT: d 371 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: d 619 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7111 (p90) REVERT: d 650 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: d 654 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8426 (ttm170) outliers start: 55 outliers final: 33 residues processed: 241 average time/residue: 0.1131 time to fit residues: 41.9002 Evaluate side-chains 233 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 331 CYS Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 361 ARG Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 534 VAL Chi-restraints excluded: chain a residue 654 ARG Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 397 ARG Chi-restraints excluded: chain b residue 443 VAL Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 274 SER Chi-restraints excluded: chain c residue 294 LYS Chi-restraints excluded: chain c residue 331 CYS Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 443 VAL Chi-restraints excluded: chain c residue 512 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 650 GLU Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 331 CYS Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 443 VAL Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 VAL Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Chi-restraints excluded: chain d residue 654 ARG Chi-restraints excluded: chain d residue 668 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [76, 186, 28, 67, 63, 133, 128, 130, 9, 39, 148] chunk 76 optimal weight: 4.9990 chunk 186 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 674 ASN ** 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 = 0.3546 r_free = 0.3546 target = 0.146267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104413 restraints weight = 17442.811| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.76 r_work: 0.2890 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16068 Z= 0.166 Angle : 0.589 8.972 21872 Z= 0.312 Chirality : 0.042 0.275 2516 Planarity : 0.004 0.039 2688 Dihedral : 5.233 59.959 2350 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.85 % Allowed : 18.89 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1908 helix: 1.55 (0.16), residues: 1036 sheet: -0.82 (0.36), residues: 200 loop : -1.56 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 322 TYR 0.011 0.001 TYR b 248 PHE 0.021 0.002 PHE a 600 TRP 0.012 0.001 TRP c 570 HIS 0.003 0.001 HIS b 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16052) covalent geometry : angle 0.56542 / 0.31 (21828) SS BOND : bond 0.00252 / 0.13 ( 4) SS BOND : angle 4.63637 / 2.08 ( 8) hydrogen bonds : bond 0.06033 / 3.99 ( 963) hydrogen bonds : angle 4.47740 / 3.13 ( 2880) link_NAG-ASN : bond 0.00590 / 0.30 ( 12) link_NAG-ASN : angle 3.45969 / 2.40 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 0.456 Fit side-chains REVERT: a 361 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8371 (mtt-85) REVERT: a 654 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8444 (ttm170) REVERT: a 674 ASN cc_start: 0.8021 (m-40) cc_final: 0.7743 (m-40) REVERT: b 266 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6881 (mm-30) REVERT: b 267 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7467 (tttp) REVERT: b 361 ARG cc_start: 0.8684 (mtt90) cc_final: 0.8312 (mtt-85) REVERT: b 371 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: b 397 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7795 (mtm180) REVERT: b 619 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.6994 (p90) REVERT: b 650 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: c 306 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7741 (mtm-85) REVERT: c 343 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7048 (mt-10) REVERT: c 650 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: d 371 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: d 529 THR cc_start: 0.7697 (m) cc_final: 0.7392 (m) REVERT: d 619 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.7296 (p90) REVERT: d 650 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: d 654 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8428 (ttm170) outliers start: 63 outliers final: 46 residues processed: 243 average time/residue: 0.1141 time to fit residues: 42.7594 Evaluate side-chains 247 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 361 ARG Chi-restraints excluded: chain a residue 416 ASP Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 534 VAL Chi-restraints excluded: chain a residue 566 VAL Chi-restraints excluded: chain a residue 643 ASP Chi-restraints excluded: chain a residue 654 ARG Chi-restraints excluded: chain a residue 668 MET Chi-restraints excluded: chain a residue 687 VAL Chi-restraints excluded: chain b residue 236 ILE Chi-restraints excluded: chain b residue 267 LYS Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 397 ARG Chi-restraints excluded: chain b residue 416 ASP Chi-restraints excluded: chain b residue 443 VAL Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 566 VAL Chi-restraints excluded: chain b residue 619 PHE Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 274 SER Chi-restraints excluded: chain c residue 294 LYS Chi-restraints excluded: chain c residue 331 CYS Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 416 ASP Chi-restraints excluded: chain c residue 443 VAL Chi-restraints excluded: chain c residue 510 LEU Chi-restraints excluded: chain c residue 512 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 566 VAL Chi-restraints excluded: chain c residue 650 GLU Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 331 CYS Chi-restraints excluded: chain d residue 349 SER Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 443 VAL Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 VAL Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 566 VAL Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Chi-restraints excluded: chain d residue 654 ARG Chi-restraints excluded: chain d residue 668 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [137, 0, 36, 178, 119, 58, 116, 76, 166, 17, 93] chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 578 ASN ** c 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.147655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.106135 restraints weight = 17116.376| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.75 r_work: 0.2877 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16068 Z= 0.167 Angle : 0.596 10.285 21872 Z= 0.313 Chirality : 0.041 0.226 2516 Planarity : 0.004 0.038 2688 Dihedral : 5.190 59.157 2350 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.03 % Allowed : 19.25 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1908 helix: 1.51 (0.16), residues: 1040 sheet: -0.87 (0.36), residues: 200 loop : -1.50 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 306 TYR 0.011 0.001 TYR d 248 PHE 0.020 0.002 PHE a 600 TRP 0.017 0.001 TRP c 570 HIS 0.003 0.001 HIS a 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (16052) covalent geometry : angle 0.57174 / 0.31 (21828) SS BOND : bond 0.00135 / 0.07 ( 4) SS BOND : angle 4.70832 / 2.15 ( 8) hydrogen bonds : bond 0.06049 / 4.01 ( 963) hydrogen bonds : angle 4.46846 / 3.12 ( 2880) link_NAG-ASN : bond 0.00559 / 0.29 ( 12) link_NAG-ASN : angle 3.57165 / 2.50 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 193 time to evaluate : 0.561 Fit side-chains REVERT: a 361 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8381 (mtt-85) REVERT: a 619 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7044 (p90) REVERT: a 654 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8371 (ttm170) REVERT: b 267 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7407 (tttp) REVERT: b 361 ARG cc_start: 0.8712 (mtt90) cc_final: 0.8359 (mtt-85) REVERT: b 371 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: b 619 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.6917 (p90) REVERT: b 650 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: b 674 ASN cc_start: 0.8798 (m-40) cc_final: 0.8397 (m-40) REVERT: c 306 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7720 (mtm-85) REVERT: c 343 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7224 (mt-10) REVERT: c 529 THR cc_start: 0.7656 (m) cc_final: 0.7393 (m) REVERT: c 536 LEU cc_start: 0.7948 (mp) cc_final: 0.7486 (mt) REVERT: c 619 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.6939 (p90) REVERT: c 650 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8435 (tm-30) REVERT: c 677 LEU cc_start: 0.8325 (mm) cc_final: 0.7768 (tp) REVERT: d 371 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: d 619 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7229 (p90) REVERT: d 650 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: d 654 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8414 (ttm170) outliers start: 66 outliers final: 47 residues processed: 239 average time/residue: 0.1089 time to fit residues: 40.7576 Evaluate side-chains 251 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 361 ARG Chi-restraints excluded: chain a residue 416 ASP Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 534 VAL Chi-restraints excluded: chain a residue 566 VAL Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 643 ASP Chi-restraints excluded: chain a residue 654 ARG Chi-restraints excluded: chain a residue 668 MET Chi-restraints excluded: chain a residue 687 VAL Chi-restraints excluded: chain b residue 236 ILE Chi-restraints excluded: chain b residue 267 LYS Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 416 ASP Chi-restraints excluded: chain b residue 443 VAL Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 566 VAL Chi-restraints excluded: chain b residue 619 PHE Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 274 SER Chi-restraints excluded: chain c residue 294 LYS Chi-restraints excluded: chain c residue 331 CYS Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 416 ASP Chi-restraints excluded: chain c residue 443 VAL Chi-restraints excluded: chain c residue 510 LEU Chi-restraints excluded: chain c residue 512 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 566 VAL Chi-restraints excluded: chain c residue 619 PHE Chi-restraints excluded: chain c residue 643 ASP Chi-restraints excluded: chain c residue 650 GLU Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 331 CYS Chi-restraints excluded: chain d residue 349 SER Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 443 VAL Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 VAL Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 566 VAL Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Chi-restraints excluded: chain d residue 654 ARG Chi-restraints excluded: chain d residue 668 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [106, 89, 83, 140, 147, 187, 96, 18, 22, 151, 11] chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 187 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 674 ASN ** c 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.147285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.106330 restraints weight = 17134.904| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.70 r_work: 0.2917 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16068 Z= 0.143 Angle : 0.565 10.900 21872 Z= 0.297 Chirality : 0.041 0.226 2516 Planarity : 0.004 0.038 2688 Dihedral : 5.053 59.156 2350 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.91 % Allowed : 19.38 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1908 helix: 1.52 (0.16), residues: 1048 sheet: -0.85 (0.36), residues: 200 loop : -1.42 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 325 TYR 0.011 0.001 TYR d 239 PHE 0.018 0.001 PHE a 600 TRP 0.020 0.001 TRP c 570 HIS 0.002 0.001 HIS c 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16052) covalent geometry : angle 0.54287 / 0.29 (21828) SS BOND : bond 0.00091 / 0.05 ( 4) SS BOND : angle 4.41236 / 2.06 ( 8) hydrogen bonds : bond 0.05598 / 3.71 ( 963) hydrogen bonds : angle 4.40422 / 3.08 ( 2880) link_NAG-ASN : bond 0.00645 / 0.33 ( 12) link_NAG-ASN : angle 3.28449 / 2.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 0.523 Fit side-chains REVERT: a 361 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8348 (mtt-85) REVERT: a 619 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.6961 (p90) REVERT: a 654 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8352 (ttm170) REVERT: b 267 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7382 (tttp) REVERT: b 361 ARG cc_start: 0.8671 (mtt90) cc_final: 0.8195 (mtt-85) REVERT: b 371 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: b 619 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.6917 (p90) REVERT: b 650 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: b 674 ASN cc_start: 0.8654 (m-40) cc_final: 0.8191 (m-40) REVERT: c 306 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7708 (mtm-85) REVERT: c 343 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7305 (mt-10) REVERT: c 536 LEU cc_start: 0.7930 (mp) cc_final: 0.7558 (mt) REVERT: c 619 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.6925 (p90) REVERT: c 650 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: c 677 LEU cc_start: 0.8303 (mm) cc_final: 0.7684 (tp) REVERT: d 371 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: d 619 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7180 (p90) REVERT: d 650 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: d 654 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8400 (ttm170) outliers start: 64 outliers final: 48 residues processed: 229 average time/residue: 0.1052 time to fit residues: 37.5925 Evaluate side-chains 247 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 331 CYS Chi-restraints excluded: chain a residue 341 ILE Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 361 ARG Chi-restraints excluded: chain a residue 416 ASP Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 534 VAL Chi-restraints excluded: chain a residue 566 VAL Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 643 ASP Chi-restraints excluded: chain a residue 654 ARG Chi-restraints excluded: chain a residue 668 MET Chi-restraints excluded: chain a residue 687 VAL Chi-restraints excluded: chain b residue 236 ILE Chi-restraints excluded: chain b residue 267 LYS Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 331 CYS Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 416 ASP Chi-restraints excluded: chain b residue 443 VAL Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 566 VAL Chi-restraints excluded: chain b residue 619 PHE Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 274 SER Chi-restraints excluded: chain c residue 331 CYS Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 416 ASP Chi-restraints excluded: chain c residue 443 VAL Chi-restraints excluded: chain c residue 512 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 566 VAL Chi-restraints excluded: chain c residue 619 PHE Chi-restraints excluded: chain c residue 643 ASP Chi-restraints excluded: chain c residue 650 GLU Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 331 CYS Chi-restraints excluded: chain d residue 349 SER Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 443 VAL Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 VAL Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 566 VAL Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Chi-restraints excluded: chain d residue 654 ARG Chi-restraints excluded: chain d residue 668 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [58, 66, 103, 187, 83, 11, 64, 114, 51, 15, 129] chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 674 ASN ** 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 = 0.3541 r_free = 0.3541 target = 0.145728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104325 restraints weight = 17245.681| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.72 r_work: 0.2875 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16068 Z= 0.192 Angle : 0.634 12.935 21872 Z= 0.331 Chirality : 0.042 0.230 2516 Planarity : 0.005 0.039 2688 Dihedral : 5.278 58.005 2350 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.10 % Allowed : 19.25 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1908 helix: 1.50 (0.16), residues: 1040 sheet: -1.02 (0.35), residues: 200 loop : -1.46 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 338 TYR 0.013 0.002 TYR b 248 PHE 0.022 0.002 PHE a 600 TRP 0.021 0.002 TRP c 570 HIS 0.004 0.001 HIS a 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (16052) covalent geometry : angle 0.61049 / 0.32 (21828) SS BOND : bond 0.00182 / 0.09 ( 4) SS BOND : angle 5.25674 / 2.46 ( 8) hydrogen bonds : bond 0.06460 / 4.28 ( 963) hydrogen bonds : angle 4.51870 / 3.15 ( 2880) link_NAG-ASN : bond 0.00639 / 0.33 ( 12) link_NAG-ASN : angle 3.49909 / 2.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 0.560 Fit side-chains REVERT: a 361 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8346 (mtt-85) REVERT: a 619 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7010 (p90) REVERT: a 654 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8303 (ttm170) REVERT: b 267 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7427 (tttp) REVERT: b 361 ARG cc_start: 0.8686 (mtt90) cc_final: 0.8331 (mtt-85) REVERT: b 371 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: b 619 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7027 (p90) REVERT: b 650 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: b 674 ASN cc_start: 0.8753 (m-40) cc_final: 0.8350 (m-40) REVERT: c 306 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: c 343 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7423 (mt-10) REVERT: c 529 THR cc_start: 0.7642 (m) cc_final: 0.7321 (m) REVERT: c 536 LEU cc_start: 0.7962 (mp) cc_final: 0.7608 (mt) REVERT: c 619 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7017 (p90) REVERT: c 650 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: c 677 LEU cc_start: 0.8372 (mm) cc_final: 0.7784 (tp) REVERT: d 371 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: d 619 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7219 (p90) REVERT: d 650 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: d 654 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8330 (ttm170) outliers start: 67 outliers final: 49 residues processed: 237 average time/residue: 0.1071 time to fit residues: 39.8410 Evaluate side-chains 251 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 331 CYS Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 361 ARG Chi-restraints excluded: chain a residue 416 ASP Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 534 VAL Chi-restraints excluded: chain a residue 566 VAL Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 643 ASP Chi-restraints excluded: chain a residue 654 ARG Chi-restraints excluded: chain a residue 668 MET Chi-restraints excluded: chain a residue 677 LEU Chi-restraints excluded: chain a residue 687 VAL Chi-restraints excluded: chain b residue 236 ILE Chi-restraints excluded: chain b residue 267 LYS Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 331 CYS Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 416 ASP Chi-restraints excluded: chain b residue 443 VAL Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 566 VAL Chi-restraints excluded: chain b residue 619 PHE Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 274 SER Chi-restraints excluded: chain c residue 331 CYS Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 416 ASP Chi-restraints excluded: chain c residue 443 VAL Chi-restraints excluded: chain c residue 510 LEU Chi-restraints excluded: chain c residue 512 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 566 VAL Chi-restraints excluded: chain c residue 619 PHE Chi-restraints excluded: chain c residue 650 GLU Chi-restraints excluded: chain c residue 687 VAL Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 331 CYS Chi-restraints excluded: chain d residue 349 SER Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 443 VAL Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 VAL Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 566 VAL Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Chi-restraints excluded: chain d residue 654 ARG Chi-restraints excluded: chain d residue 668 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [180, 129, 147, 4, 104, 144, 8, 52, 183, 88, 116] chunk 180 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 580 ASN ** c 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.147572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.106397 restraints weight = 17245.459| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.71 r_work: 0.2908 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16068 Z= 0.150 Angle : 0.583 12.440 21872 Z= 0.305 Chirality : 0.041 0.232 2516 Planarity : 0.004 0.039 2688 Dihedral : 5.131 59.764 2350 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.85 % Allowed : 19.25 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1908 helix: 1.50 (0.16), residues: 1048 sheet: -0.91 (0.36), residues: 200 loop : -1.36 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 338 TYR 0.011 0.001 TYR d 239 PHE 0.018 0.002 PHE a 600 TRP 0.027 0.002 TRP c 570 HIS 0.002 0.001 HIS a 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (16052) covalent geometry : angle 0.56085 / 0.30 (21828) SS BOND : bond 0.00118 / 0.06 ( 4) SS BOND : angle 4.56476 / 2.13 ( 8) hydrogen bonds : bond 0.05734 / 3.79 ( 963) hydrogen bonds : angle 4.42449 / 3.09 ( 2880) link_NAG-ASN : bond 0.00549 / 0.28 ( 12) link_NAG-ASN : angle 3.36844 / 2.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 0.449 Fit side-chains REVERT: a 361 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8334 (mtt-85) REVERT: a 619 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.6986 (p90) REVERT: a 654 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8352 (ttm170) REVERT: b 267 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7385 (tttp) REVERT: b 361 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8292 (mtt-85) REVERT: b 371 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: b 619 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.6948 (p90) REVERT: b 650 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: b 674 ASN cc_start: 0.8517 (m-40) cc_final: 0.8032 (m-40) REVERT: c 306 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: c 343 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7459 (mt-10) REVERT: c 529 THR cc_start: 0.7478 (m) cc_final: 0.7166 (m) REVERT: c 536 LEU cc_start: 0.7923 (mp) cc_final: 0.7597 (mt) REVERT: c 619 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.6953 (p90) REVERT: c 650 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: c 677 LEU cc_start: 0.8104 (mm) cc_final: 0.7864 (mm) REVERT: d 338 ARG cc_start: 0.8864 (tpp-160) cc_final: 0.8645 (mmt90) REVERT: d 371 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: d 619 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7198 (p90) REVERT: d 650 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: d 654 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8395 (ttm170) outliers start: 63 outliers final: 48 residues processed: 233 average time/residue: 0.1047 time to fit residues: 38.5373 Evaluate side-chains 250 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 331 CYS Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 361 ARG Chi-restraints excluded: chain a residue 416 ASP Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 534 VAL Chi-restraints excluded: chain a residue 566 VAL Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 643 ASP Chi-restraints excluded: chain a residue 654 ARG Chi-restraints excluded: chain a residue 668 MET Chi-restraints excluded: chain a residue 677 LEU Chi-restraints excluded: chain a residue 687 VAL Chi-restraints excluded: chain b residue 236 ILE Chi-restraints excluded: chain b residue 267 LYS Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 331 CYS Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 416 ASP Chi-restraints excluded: chain b residue 443 VAL Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 566 VAL Chi-restraints excluded: chain b residue 619 PHE Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 274 SER Chi-restraints excluded: chain c residue 331 CYS Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 416 ASP Chi-restraints excluded: chain c residue 443 VAL Chi-restraints excluded: chain c residue 510 LEU Chi-restraints excluded: chain c residue 512 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 566 VAL Chi-restraints excluded: chain c residue 619 PHE Chi-restraints excluded: chain c residue 650 GLU Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 331 CYS Chi-restraints excluded: chain d residue 349 SER Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 443 VAL Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 VAL Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 566 VAL Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Chi-restraints excluded: chain d residue 654 ARG Chi-restraints excluded: chain d residue 668 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [88, 17, 150, 131, 24, 112, 49, 164, 38, 34, 69] chunk 88 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 674 ASN ** 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 = 0.3561 r_free = 0.3561 target = 0.147658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.106813 restraints weight = 17085.675| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.69 r_work: 0.2918 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16068 Z= 0.145 Angle : 0.589 12.345 21872 Z= 0.305 Chirality : 0.041 0.261 2516 Planarity : 0.004 0.039 2688 Dihedral : 5.091 59.044 2350 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.79 % Allowed : 19.62 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1908 helix: 1.53 (0.16), residues: 1044 sheet: -0.86 (0.36), residues: 200 loop : -1.39 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 338 TYR 0.012 0.001 TYR b 239 PHE 0.018 0.001 PHE a 600 TRP 0.031 0.002 TRP c 570 HIS 0.002 0.001 HIS a 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (16052) covalent geometry : angle 0.56781 / 0.30 (21828) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 4.51988 / 2.14 ( 8) hydrogen bonds : bond 0.05621 / 3.72 ( 963) hydrogen bonds : angle 4.40976 / 3.08 ( 2880) link_NAG-ASN : bond 0.00566 / 0.29 ( 12) link_NAG-ASN : angle 3.32818 / 2.33 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.510 Fit side-chains REVERT: a 361 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8360 (mtt-85) REVERT: a 619 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.6951 (p90) REVERT: a 654 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8348 (ttm170) REVERT: b 267 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7393 (tttp) REVERT: b 361 ARG cc_start: 0.8643 (mtt90) cc_final: 0.8177 (mtt-85) REVERT: b 371 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: b 503 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: b 619 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.6913 (p90) REVERT: b 650 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: b 674 ASN cc_start: 0.8400 (m-40) cc_final: 0.7999 (m-40) REVERT: c 306 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: c 343 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7468 (mt-10) REVERT: c 529 THR cc_start: 0.7513 (m) cc_final: 0.7222 (m) REVERT: c 536 LEU cc_start: 0.7938 (mp) cc_final: 0.7618 (mt) REVERT: c 619 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.6912 (p90) REVERT: c 650 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8403 (tm-30) REVERT: c 677 LEU cc_start: 0.8333 (mm) cc_final: 0.7750 (tp) REVERT: d 371 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: d 619 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7165 (p90) REVERT: d 650 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: d 654 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8352 (ttm170) outliers start: 62 outliers final: 48 residues processed: 231 average time/residue: 0.1033 time to fit residues: 38.0318 Evaluate side-chains 249 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 326 VAL Chi-restraints excluded: chain a residue 331 CYS Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 361 ARG Chi-restraints excluded: chain a residue 416 ASP Chi-restraints excluded: chain a residue 443 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 519 VAL Chi-restraints excluded: chain a residue 533 GLU Chi-restraints excluded: chain a residue 534 VAL Chi-restraints excluded: chain a residue 566 VAL Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 643 ASP Chi-restraints excluded: chain a residue 654 ARG Chi-restraints excluded: chain a residue 668 MET Chi-restraints excluded: chain a residue 677 LEU Chi-restraints excluded: chain a residue 687 VAL Chi-restraints excluded: chain b residue 236 ILE Chi-restraints excluded: chain b residue 267 LYS Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 331 CYS Chi-restraints excluded: chain b residue 371 GLU Chi-restraints excluded: chain b residue 416 ASP Chi-restraints excluded: chain b residue 443 VAL Chi-restraints excluded: chain b residue 503 PHE Chi-restraints excluded: chain b residue 510 LEU Chi-restraints excluded: chain b residue 512 VAL Chi-restraints excluded: chain b residue 519 VAL Chi-restraints excluded: chain b residue 566 VAL Chi-restraints excluded: chain b residue 619 PHE Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 687 VAL Chi-restraints excluded: chain c residue 274 SER Chi-restraints excluded: chain c residue 331 CYS Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 416 ASP Chi-restraints excluded: chain c residue 443 VAL Chi-restraints excluded: chain c residue 510 LEU Chi-restraints excluded: chain c residue 512 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 566 VAL Chi-restraints excluded: chain c residue 619 PHE Chi-restraints excluded: chain c residue 650 GLU Chi-restraints excluded: chain d residue 236 ILE Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 331 CYS Chi-restraints excluded: chain d residue 349 SER Chi-restraints excluded: chain d residue 371 GLU Chi-restraints excluded: chain d residue 416 ASP Chi-restraints excluded: chain d residue 443 VAL Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 VAL Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 533 GLU Chi-restraints excluded: chain d residue 566 VAL Chi-restraints excluded: chain d residue 619 PHE Chi-restraints excluded: chain d residue 650 GLU Chi-restraints excluded: chain d residue 654 ARG Chi-restraints excluded: chain d residue 668 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [72, 181, 73, 94, 160, 58, 116, 185, 142, 69, 84] chunk 72 optimal weight: 8.9990 chunk 181 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 674 ASN ** c 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.148416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107380 restraints weight = 17164.007| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.71 r_work: 0.2904 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16068 Z= 0.156 Angle : 0.609 12.544 21872 Z= 0.314 Chirality : 0.041 0.247 2516 Planarity : 0.004 0.039 2688 Dihedral : 5.125 59.520 2350 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.79 % Allowed : 19.87 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1908 helix: 1.51 (0.16), residues: 1048 sheet: -0.90 (0.36), residues: 200 loop : -1.35 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 306 TYR 0.013 0.001 TYR c 553 PHE 0.020 0.002 PHE c 600 TRP 0.027 0.002 TRP c 570 HIS 0.003 0.001 HIS a 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (16052) covalent geometry : angle 0.58670 / 0.31 (21828) SS BOND : bond 0.00084 / 0.04 ( 4) SS BOND : angle 4.76609 / 2.25 ( 8) hydrogen bonds : bond 0.05811 / 3.85 ( 963) hydrogen bonds : angle 4.43691 / 3.10 ( 2880) link_NAG-ASN : bond 0.00523 / 0.27 ( 12) link_NAG-ASN : angle 3.41220 / 2.39 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3633.13 seconds wall clock time: 62 minutes 50.30 seconds (3770.30 seconds total)