Starting phenix.real_space_refine on Sun Feb 8 08:54:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8v_62181/02_2026/9k8v_62181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8v_62181/02_2026/9k8v_62181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8v_62181/02_2026/9k8v_62181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8v_62181/02_2026/9k8v_62181.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8v_62181/02_2026/9k8v_62181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8v_62181/02_2026/9k8v_62181.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 165 5.16 5 C 26895 2.51 5 N 7365 2.21 5 O 8565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42990 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2866 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 11, 'TRANS': 366} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 4.40, per 1000 atoms: 0.10 Number of scatterers: 42990 At special positions: 0 Unit cell: (177.02, 176.352, 143.62, 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 165 16.00 O 8565 8.00 N 7365 7.00 C 26895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.8 seconds 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10410 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 47 sheets defined 25.7% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 382 through 393 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN A 587 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'B' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 421 through 428 Processing helix chain 'B' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 582' Processing helix chain 'B' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN B 587 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA B 616 " --> pdb=" O ASP B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 670 Processing helix chain 'C' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 282 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 338 Processing helix chain 'C' and resid 382 through 393 Processing helix chain 'C' and resid 421 through 428 Processing helix chain 'C' and resid 578 through 582 removed outlier: 3.656A pdb=" N ASP C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 578 through 582' Processing helix chain 'C' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN C 587 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA C 616 " --> pdb=" O ASP C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 670 Processing helix chain 'D' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 282 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 382 through 393 Processing helix chain 'D' and resid 421 through 428 Processing helix chain 'D' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 578 through 582' Processing helix chain 'D' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN D 587 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA D 616 " --> pdb=" O ASP D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 670 Processing helix chain 'E' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL E 282 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 338 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 421 through 428 Processing helix chain 'E' and resid 578 through 582 removed outlier: 3.656A pdb=" N ASP E 581 " --> pdb=" O LEU E 578 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 578 through 582' Processing helix chain 'E' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN E 587 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA E 616 " --> pdb=" O ASP E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 670 Processing helix chain 'F' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 282 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 338 Processing helix chain 'F' and resid 382 through 393 Processing helix chain 'F' and resid 421 through 428 Processing helix chain 'F' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 578 through 582' Processing helix chain 'F' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN F 587 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA F 616 " --> pdb=" O ASP F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 670 Processing helix chain 'G' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU G 281 " --> pdb=" O GLU G 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL G 282 " --> pdb=" O ASP G 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL G 286 " --> pdb=" O VAL G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 338 Processing helix chain 'G' and resid 382 through 393 Processing helix chain 'G' and resid 421 through 428 Processing helix chain 'G' and resid 578 through 582 removed outlier: 3.656A pdb=" N ASP G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE G 582 " --> pdb=" O LEU G 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 578 through 582' Processing helix chain 'G' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN G 587 " --> pdb=" O LEU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA G 616 " --> pdb=" O ASP G 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 660 through 670 Processing helix chain 'H' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU H 281 " --> pdb=" O GLU H 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL H 282 " --> pdb=" O ASP H 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY H 285 " --> pdb=" O GLU H 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL H 286 " --> pdb=" O VAL H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 338 Processing helix chain 'H' and resid 382 through 393 Processing helix chain 'H' and resid 421 through 428 Processing helix chain 'H' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP H 581 " --> pdb=" O LEU H 578 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE H 582 " --> pdb=" O LEU H 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 578 through 582' Processing helix chain 'H' and resid 584 through 588 removed outlier: 4.096A pdb=" N GLN H 587 " --> pdb=" O LEU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA H 616 " --> pdb=" O ASP H 612 " (cutoff:3.500A) Processing helix chain 'H' and resid 660 through 670 Processing helix chain 'I' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 282 " --> pdb=" O ASP I 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY I 285 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL I 286 " --> pdb=" O VAL I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 338 Processing helix chain 'I' and resid 382 through 393 Processing helix chain 'I' and resid 421 through 428 Processing helix chain 'I' and resid 578 through 582 removed outlier: 3.656A pdb=" N ASP I 581 " --> pdb=" O LEU I 578 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE I 582 " --> pdb=" O LEU I 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 578 through 582' Processing helix chain 'I' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN I 587 " --> pdb=" O LEU I 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA I 616 " --> pdb=" O ASP I 612 " (cutoff:3.500A) Processing helix chain 'I' and resid 660 through 670 Processing helix chain 'J' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU J 281 " --> pdb=" O GLU J 277 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL J 282 " --> pdb=" O ASP J 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY J 285 " --> pdb=" O GLU J 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL J 286 " --> pdb=" O VAL J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 338 Processing helix chain 'J' and resid 382 through 393 Processing helix chain 'J' and resid 421 through 428 Processing helix chain 'J' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP J 581 " --> pdb=" O LEU J 578 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE J 582 " --> pdb=" O LEU J 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 578 through 582' Processing helix chain 'J' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN J 587 " --> pdb=" O LEU J 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA J 616 " --> pdb=" O ASP J 612 " (cutoff:3.500A) Processing helix chain 'J' and resid 660 through 670 Processing helix chain 'K' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU K 281 " --> pdb=" O GLU K 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL K 282 " --> pdb=" O ASP K 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL K 286 " --> pdb=" O VAL K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 323 through 338 Processing helix chain 'K' and resid 382 through 393 Processing helix chain 'K' and resid 421 through 428 Processing helix chain 'K' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP K 581 " --> pdb=" O LEU K 578 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE K 582 " --> pdb=" O LEU K 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 578 through 582' Processing helix chain 'K' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN K 587 " --> pdb=" O LEU K 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA K 616 " --> pdb=" O ASP K 612 " (cutoff:3.500A) Processing helix chain 'K' and resid 660 through 670 Processing helix chain 'L' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU L 281 " --> pdb=" O GLU L 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL L 282 " --> pdb=" O ASP L 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY L 285 " --> pdb=" O GLU L 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL L 286 " --> pdb=" O VAL L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 338 Processing helix chain 'L' and resid 382 through 393 Processing helix chain 'L' and resid 421 through 428 Processing helix chain 'L' and resid 578 through 582 removed outlier: 3.656A pdb=" N ASP L 581 " --> pdb=" O LEU L 578 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE L 582 " --> pdb=" O LEU L 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 578 through 582' Processing helix chain 'L' and resid 584 through 588 removed outlier: 4.096A pdb=" N GLN L 587 " --> pdb=" O LEU L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA L 616 " --> pdb=" O ASP L 612 " (cutoff:3.500A) Processing helix chain 'L' and resid 660 through 670 Processing helix chain 'M' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU M 281 " --> pdb=" O GLU M 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL M 282 " --> pdb=" O ASP M 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY M 285 " --> pdb=" O GLU M 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL M 286 " --> pdb=" O VAL M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 323 through 338 Processing helix chain 'M' and resid 382 through 393 Processing helix chain 'M' and resid 421 through 428 Processing helix chain 'M' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP M 581 " --> pdb=" O LEU M 578 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 582 " --> pdb=" O LEU M 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 578 through 582' Processing helix chain 'M' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN M 587 " --> pdb=" O LEU M 584 " (cutoff:3.500A) Processing helix chain 'M' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA M 616 " --> pdb=" O ASP M 612 " (cutoff:3.500A) Processing helix chain 'M' and resid 660 through 670 Processing helix chain 'N' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU N 281 " --> pdb=" O GLU N 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL N 282 " --> pdb=" O ASP N 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY N 285 " --> pdb=" O GLU N 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL N 286 " --> pdb=" O VAL N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 338 Processing helix chain 'N' and resid 382 through 393 Processing helix chain 'N' and resid 421 through 428 Processing helix chain 'N' and resid 578 through 582 removed outlier: 3.655A pdb=" N ASP N 581 " --> pdb=" O LEU N 578 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE N 582 " --> pdb=" O LEU N 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 578 through 582' Processing helix chain 'N' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN N 587 " --> pdb=" O LEU N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA N 616 " --> pdb=" O ASP N 612 " (cutoff:3.500A) Processing helix chain 'N' and resid 660 through 670 Processing helix chain 'O' and resid 275 through 288 removed outlier: 4.140A pdb=" N GLU O 281 " --> pdb=" O GLU O 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL O 282 " --> pdb=" O ASP O 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY O 285 " --> pdb=" O GLU O 281 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL O 286 " --> pdb=" O VAL O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 323 through 338 Processing helix chain 'O' and resid 382 through 393 Processing helix chain 'O' and resid 421 through 428 Processing helix chain 'O' and resid 578 through 582 removed outlier: 3.656A pdb=" N ASP O 581 " --> pdb=" O LEU O 578 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE O 582 " --> pdb=" O LEU O 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 578 through 582' Processing helix chain 'O' and resid 584 through 588 removed outlier: 4.095A pdb=" N GLN O 587 " --> pdb=" O LEU O 584 " (cutoff:3.500A) Processing helix chain 'O' and resid 612 through 637 removed outlier: 3.658A pdb=" N ALA O 616 " --> pdb=" O ASP O 612 " (cutoff:3.500A) Processing helix chain 'O' and resid 660 through 670 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 270 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 366 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 373 through 375 current: chain 'A' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 444 through 467 current: chain 'A' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 590 through 610 current: chain 'B' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 373 through 375 current: chain 'B' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 444 through 467 current: chain 'B' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 590 through 610 current: chain 'C' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 373 through 375 current: chain 'C' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 444 through 467 current: chain 'C' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 590 through 610 current: chain 'D' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 373 through 375 current: chain 'D' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 444 through 467 current: chain 'D' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 590 through 610 current: chain 'E' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 373 through 375 current: chain 'E' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 444 through 467 current: chain 'E' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 590 through 610 current: chain 'F' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 373 through 375 current: chain 'F' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 444 through 467 current: chain 'F' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 590 through 610 current: chain 'G' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 373 through 375 current: chain 'G' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 444 through 467 current: chain 'G' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 590 through 610 current: chain 'H' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 373 through 375 current: chain 'H' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 444 through 467 current: chain 'H' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 590 through 610 current: chain 'I' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 373 through 375 current: chain 'I' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 444 through 467 current: chain 'I' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 590 through 610 current: chain 'J' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 373 through 375 current: chain 'J' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 444 through 467 current: chain 'J' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 590 through 610 current: chain 'K' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 373 through 375 current: chain 'K' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 444 through 467 current: chain 'K' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 590 through 610 current: chain 'L' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 373 through 375 current: chain 'L' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 444 through 467 current: chain 'L' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 590 through 610 current: chain 'M' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 373 through 375 current: chain 'M' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 444 through 467 current: chain 'M' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 590 through 610 current: chain 'N' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 373 through 375 current: chain 'N' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 444 through 467 current: chain 'N' and resid 590 through 610 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 590 through 610 current: chain 'O' and resid 373 through 375 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 373 through 375 current: chain 'O' and resid 444 through 467 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 444 through 467 current: chain 'O' and resid 590 through 610 Processing sheet with id=AA3, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA4, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA5, first strand: chain 'A' and resid 412 through 413 Processing sheet with id=AA6, first strand: chain 'A' and resid 472 through 483 removed outlier: 12.691A pdb=" N GLU A 503 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL A 531 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU B 503 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL B 531 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU C 503 " --> pdb=" O VAL C 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL C 531 " --> pdb=" O GLU C 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU D 503 " --> pdb=" O VAL D 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL D 531 " --> pdb=" O GLU D 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU E 503 " --> pdb=" O VAL E 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL E 531 " --> pdb=" O GLU E 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU F 503 " --> pdb=" O VAL F 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL F 531 " --> pdb=" O GLU F 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU G 503 " --> pdb=" O VAL G 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL G 531 " --> pdb=" O GLU G 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU H 503 " --> pdb=" O VAL H 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL H 531 " --> pdb=" O GLU H 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU I 503 " --> pdb=" O VAL I 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL I 531 " --> pdb=" O GLU I 503 " (cutoff:3.500A) removed outlier: 12.690A pdb=" N GLU J 503 " --> pdb=" O VAL J 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL J 531 " --> pdb=" O GLU J 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU K 503 " --> pdb=" O VAL K 531 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL K 531 " --> pdb=" O GLU K 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU L 503 " --> pdb=" O VAL L 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL L 531 " --> pdb=" O GLU L 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU M 503 " --> pdb=" O VAL M 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL M 531 " --> pdb=" O GLU M 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU N 503 " --> pdb=" O VAL N 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL N 531 " --> pdb=" O GLU N 503 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N GLU O 503 " --> pdb=" O VAL O 531 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL O 531 " --> pdb=" O GLU O 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 266 through 270 Processing sheet with id=AA8, first strand: chain 'B' and resid 396 through 397 Processing sheet with id=AA9, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AB1, first strand: chain 'C' and resid 266 through 270 Processing sheet with id=AB2, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AB3, first strand: chain 'C' and resid 402 through 403 Processing sheet with id=AB4, first strand: chain 'D' and resid 266 through 270 Processing sheet with id=AB5, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AB6, first strand: chain 'D' and resid 402 through 403 removed outlier: 3.507A pdb=" N ASN E 412 " --> pdb=" O TYR D 403 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 266 through 270 Processing sheet with id=AB8, first strand: chain 'E' and resid 396 through 397 Processing sheet with id=AB9, first strand: chain 'E' and resid 402 through 403 Processing sheet with id=AC1, first strand: chain 'F' and resid 266 through 270 Processing sheet with id=AC2, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AC3, first strand: chain 'F' and resid 402 through 403 Processing sheet with id=AC4, first strand: chain 'G' and resid 266 through 270 Processing sheet with id=AC5, first strand: chain 'G' and resid 396 through 397 Processing sheet with id=AC6, first strand: chain 'G' and resid 402 through 403 removed outlier: 3.502A pdb=" N ASN H 412 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 266 through 270 Processing sheet with id=AC8, first strand: chain 'H' and resid 396 through 397 Processing sheet with id=AC9, first strand: chain 'H' and resid 402 through 403 Processing sheet with id=AD1, first strand: chain 'I' and resid 266 through 270 Processing sheet with id=AD2, first strand: chain 'I' and resid 396 through 397 Processing sheet with id=AD3, first strand: chain 'I' and resid 402 through 403 Processing sheet with id=AD4, first strand: chain 'J' and resid 266 through 270 Processing sheet with id=AD5, first strand: chain 'J' and resid 396 through 397 Processing sheet with id=AD6, first strand: chain 'J' and resid 402 through 403 Processing sheet with id=AD7, first strand: chain 'K' and resid 266 through 270 Processing sheet with id=AD8, first strand: chain 'K' and resid 396 through 397 Processing sheet with id=AD9, first strand: chain 'K' and resid 402 through 403 Processing sheet with id=AE1, first strand: chain 'L' and resid 266 through 270 Processing sheet with id=AE2, first strand: chain 'L' and resid 396 through 397 Processing sheet with id=AE3, first strand: chain 'L' and resid 402 through 403 removed outlier: 3.503A pdb=" N ASN M 412 " --> pdb=" O TYR L 403 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 266 through 270 Processing sheet with id=AE5, first strand: chain 'M' and resid 396 through 397 Processing sheet with id=AE6, first strand: chain 'M' and resid 402 through 403 Processing sheet with id=AE7, first strand: chain 'N' and resid 266 through 270 Processing sheet with id=AE8, first strand: chain 'N' and resid 396 through 397 Processing sheet with id=AE9, first strand: chain 'N' and resid 402 through 403 Processing sheet with id=AF1, first strand: chain 'O' and resid 266 through 270 Processing sheet with id=AF2, first strand: chain 'O' and resid 396 through 397 1754 hydrogen bonds defined for protein. 4956 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: 9.54 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7836 1.32 - 1.44: 9564 1.44 - 1.56: 25695 1.56 - 1.69: 0 1.69 - 1.81: 330 Bond restraints: 43425 Sorted by residual: bond pdb=" C LYS E 400 " pdb=" O LYS E 400 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.17e-02 7.31e+03 1.05e+01 bond pdb=" C LYS G 400 " pdb=" O LYS G 400 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.17e-02 7.31e+03 1.05e+01 bond pdb=" C LYS L 400 " pdb=" O LYS L 400 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" C LYS H 400 " pdb=" O LYS H 400 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" C LYS N 400 " pdb=" O LYS N 400 " ideal model delta sigma weight residual 1.237 1.199 0.037 1.17e-02 7.31e+03 1.03e+01 ... (remaining 43420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 56147 1.42 - 2.83: 2129 2.83 - 4.25: 359 4.25 - 5.66: 75 5.66 - 7.08: 15 Bond angle restraints: 58725 Sorted by residual: angle pdb=" N ALA D 401 " pdb=" CA ALA D 401 " pdb=" C ALA D 401 " ideal model delta sigma weight residual 111.54 106.24 5.30 1.36e+00 5.41e-01 1.52e+01 angle pdb=" N ALA E 401 " pdb=" CA ALA E 401 " pdb=" C ALA E 401 " ideal model delta sigma weight residual 111.54 106.25 5.29 1.36e+00 5.41e-01 1.52e+01 angle pdb=" N ALA C 401 " pdb=" CA ALA C 401 " pdb=" C ALA C 401 " ideal model delta sigma weight residual 111.54 106.25 5.29 1.36e+00 5.41e-01 1.51e+01 angle pdb=" N ALA L 401 " pdb=" CA ALA L 401 " pdb=" C ALA L 401 " ideal model delta sigma weight residual 111.54 106.26 5.28 1.36e+00 5.41e-01 1.51e+01 angle pdb=" N ALA I 401 " pdb=" CA ALA I 401 " pdb=" C ALA I 401 " ideal model delta sigma weight residual 111.54 106.26 5.28 1.36e+00 5.41e-01 1.51e+01 ... (remaining 58720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 21896 17.05 - 34.10: 3274 34.10 - 51.15: 959 51.15 - 68.20: 331 68.20 - 85.26: 150 Dihedral angle restraints: 26610 sinusoidal: 10485 harmonic: 16125 Sorted by residual: dihedral pdb=" CA LEU G 410 " pdb=" C LEU G 410 " pdb=" N ARG G 411 " pdb=" CA ARG G 411 " ideal model delta harmonic sigma weight residual -180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LEU D 410 " pdb=" C LEU D 410 " pdb=" N ARG D 411 " pdb=" CA ARG D 411 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LEU J 410 " pdb=" C LEU J 410 " pdb=" N ARG J 411 " pdb=" CA ARG J 411 " ideal model delta harmonic sigma weight residual -180.00 -161.26 -18.74 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 26607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5103 0.048 - 0.097: 1434 0.097 - 0.145: 453 0.145 - 0.194: 45 0.194 - 0.242: 15 Chirality restraints: 7050 Sorted by residual: chirality pdb=" CA TYR E 403 " pdb=" N TYR E 403 " pdb=" C TYR E 403 " pdb=" CB TYR E 403 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA TYR H 403 " pdb=" N TYR H 403 " pdb=" C TYR H 403 " pdb=" CB TYR H 403 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA TYR J 403 " pdb=" N TYR J 403 " pdb=" C TYR J 403 " pdb=" CB TYR J 403 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 7047 not shown) Planarity restraints: 7650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 511 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO L 512 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO L 512 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 512 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 511 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 512 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 512 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 512 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL N 511 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO N 512 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO N 512 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 512 " 0.024 5.00e-02 4.00e+02 ... (remaining 7647 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 10932 2.81 - 3.33: 36759 3.33 - 3.86: 69297 3.86 - 4.38: 79958 4.38 - 4.90: 145008 Nonbonded interactions: 341954 Sorted by model distance: nonbonded pdb=" O SER E 486 " pdb=" OG SER E 486 " model vdw 2.291 3.040 nonbonded pdb=" O SER M 486 " pdb=" OG SER M 486 " model vdw 2.291 3.040 nonbonded pdb=" O SER K 486 " pdb=" OG SER K 486 " model vdw 2.291 3.040 nonbonded pdb=" O SER F 486 " pdb=" OG SER F 486 " model vdw 2.291 3.040 nonbonded pdb=" O SER C 486 " pdb=" OG SER C 486 " model vdw 2.291 3.040 ... (remaining 341949 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 9.980 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: 0.040 Extract box with map and model: 0.860 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 32.460 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 43425 Z= 0.209 Angle : 0.643 7.078 58725 Z= 0.358 Chirality : 0.050 0.242 7050 Planarity : 0.005 0.044 7650 Dihedral : 19.377 85.256 16200 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.87 % Allowed : 29.25 % Favored : 66.88 % 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: -0.28 (0.11), residues: 5550 helix: 1.46 (0.14), residues: 1320 sheet: 0.18 (0.09), residues: 2820 loop : -2.51 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 411 TYR 0.025 0.002 TYR N 403 PHE 0.012 0.002 PHE O 474 TRP 0.005 0.001 TRP C 365 HIS 0.003 0.001 HIS L 659 Details of bonding type rmsd covalent geometry : bond 0.00419 (43425) covalent geometry : angle 0.64265 (58725) hydrogen bonds : bond 0.14564 ( 1754) hydrogen bonds : angle 6.04413 ( 4956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 666 time to evaluate : 1.090 Fit side-chains REVERT: A 493 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5195 (p0) REVERT: A 498 THR cc_start: 0.6350 (OUTLIER) cc_final: 0.6126 (p) REVERT: A 602 MET cc_start: 0.8944 (tpp) cc_final: 0.8732 (ttm) REVERT: B 493 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5516 (p0) REVERT: B 498 THR cc_start: 0.6390 (OUTLIER) cc_final: 0.6176 (p) REVERT: B 602 MET cc_start: 0.8921 (tpp) cc_final: 0.8651 (mtt) REVERT: C 493 ASP cc_start: 0.5948 (OUTLIER) cc_final: 0.5148 (p0) REVERT: C 497 GLN cc_start: 0.4795 (OUTLIER) cc_final: 0.4545 (mm110) REVERT: C 498 THR cc_start: 0.6437 (OUTLIER) cc_final: 0.6119 (p) REVERT: D 493 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5208 (p0) REVERT: D 498 THR cc_start: 0.6438 (OUTLIER) cc_final: 0.6215 (p) REVERT: D 602 MET cc_start: 0.8962 (tpp) cc_final: 0.8727 (ttm) REVERT: E 493 ASP cc_start: 0.5980 (OUTLIER) cc_final: 0.5260 (p0) REVERT: E 498 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.6067 (p) REVERT: F 493 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5435 (p0) REVERT: F 602 MET cc_start: 0.8911 (tpp) cc_final: 0.8699 (ttm) REVERT: G 493 ASP cc_start: 0.6093 (OUTLIER) cc_final: 0.5320 (p0) REVERT: G 498 THR cc_start: 0.6520 (OUTLIER) cc_final: 0.6232 (p) REVERT: G 602 MET cc_start: 0.8912 (tpp) cc_final: 0.8633 (mtt) REVERT: H 493 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5299 (p0) REVERT: H 498 THR cc_start: 0.6376 (OUTLIER) cc_final: 0.6116 (p) REVERT: I 493 ASP cc_start: 0.6032 (OUTLIER) cc_final: 0.5460 (p0) REVERT: I 498 THR cc_start: 0.6354 (OUTLIER) cc_final: 0.6064 (p) REVERT: J 493 ASP cc_start: 0.6081 (OUTLIER) cc_final: 0.5488 (p0) REVERT: J 498 THR cc_start: 0.6437 (OUTLIER) cc_final: 0.6223 (p) REVERT: J 602 MET cc_start: 0.8928 (tpp) cc_final: 0.8667 (mtt) REVERT: K 493 ASP cc_start: 0.6004 (OUTLIER) cc_final: 0.5194 (p0) REVERT: K 498 THR cc_start: 0.6377 (OUTLIER) cc_final: 0.6144 (p) REVERT: K 602 MET cc_start: 0.8935 (tpp) cc_final: 0.8638 (mtt) REVERT: L 493 ASP cc_start: 0.5970 (OUTLIER) cc_final: 0.5185 (p0) REVERT: L 494 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.5757 (t0) REVERT: L 498 THR cc_start: 0.6385 (OUTLIER) cc_final: 0.6130 (p) REVERT: L 602 MET cc_start: 0.8911 (tpp) cc_final: 0.8655 (mtt) REVERT: M 493 ASP cc_start: 0.6050 (OUTLIER) cc_final: 0.5141 (p0) REVERT: M 498 THR cc_start: 0.6469 (OUTLIER) cc_final: 0.6187 (p) REVERT: M 602 MET cc_start: 0.8940 (tpp) cc_final: 0.8620 (mtt) REVERT: N 440 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6737 (mtp) REVERT: N 493 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5146 (p0) REVERT: N 498 THR cc_start: 0.6387 (OUTLIER) cc_final: 0.6131 (p) REVERT: O 493 ASP cc_start: 0.6037 (OUTLIER) cc_final: 0.5307 (p0) REVERT: O 602 MET cc_start: 0.8936 (tpp) cc_final: 0.8686 (mtt) outliers start: 184 outliers final: 17 residues processed: 820 average time/residue: 0.7674 time to fit residues: 758.9757 Evaluate side-chains 384 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 336 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 646 SER Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 646 SER Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 646 SER Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 646 SER Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain K residue 646 SER Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 494 ASN Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 646 SER Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain M residue 646 SER Chi-restraints excluded: chain N residue 440 MET Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain N residue 646 SER Chi-restraints excluded: chain O residue 493 ASP Chi-restraints excluded: chain O residue 646 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 595 GLN B 432 GLN B 595 GLN C 432 GLN D 432 GLN D 595 GLN E 432 GLN E 595 GLN F 432 GLN G 432 GLN G 595 GLN H 432 GLN H 595 GLN I 432 GLN I 595 GLN J 432 GLN J 595 GLN K 432 GLN K 595 GLN L 432 GLN M 432 GLN N 432 GLN O 432 GLN O 595 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110698 restraints weight = 57794.165| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.75 r_work: 0.3202 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 43425 Z= 0.272 Angle : 0.764 7.629 58725 Z= 0.413 Chirality : 0.052 0.192 7050 Planarity : 0.006 0.050 7650 Dihedral : 6.596 74.869 6025 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.58 % Allowed : 24.67 % Favored : 70.75 % 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: -0.59 (0.11), residues: 5550 helix: 1.31 (0.14), residues: 1320 sheet: 0.16 (0.10), residues: 2580 loop : -2.72 (0.12), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 501 TYR 0.012 0.002 TYR H 626 PHE 0.023 0.003 PHE L 474 TRP 0.007 0.002 TRP F 365 HIS 0.005 0.002 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00642 (43425) covalent geometry : angle 0.76390 (58725) hydrogen bonds : bond 0.07261 ( 1754) hydrogen bonds : angle 5.59597 ( 4956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 372 time to evaluate : 1.797 Fit side-chains REVERT: A 309 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8636 (mm) REVERT: A 493 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5189 (p0) REVERT: B 309 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8574 (mm) REVERT: B 493 ASP cc_start: 0.6157 (OUTLIER) cc_final: 0.4990 (p0) REVERT: C 324 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7741 (tp40) REVERT: C 493 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5134 (p0) REVERT: D 493 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.4838 (p0) REVERT: D 598 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8677 (mttt) REVERT: E 484 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7155 (p) REVERT: E 493 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5201 (p0) REVERT: F 309 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8676 (mm) REVERT: F 324 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7717 (tp40) REVERT: F 493 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5213 (p0) REVERT: G 324 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7788 (tp40) REVERT: G 493 ASP cc_start: 0.6077 (OUTLIER) cc_final: 0.4878 (p0) REVERT: H 308 MET cc_start: 0.7642 (tpp) cc_final: 0.7438 (tpp) REVERT: H 493 ASP cc_start: 0.6276 (OUTLIER) cc_final: 0.5324 (p0) REVERT: I 309 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8574 (mm) REVERT: I 324 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7658 (tp40) REVERT: I 493 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.5001 (p0) REVERT: J 309 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (mm) REVERT: J 493 ASP cc_start: 0.6182 (OUTLIER) cc_final: 0.5133 (p0) REVERT: K 493 ASP cc_start: 0.6137 (OUTLIER) cc_final: 0.4925 (p0) REVERT: K 670 MET cc_start: 0.5085 (tmm) cc_final: 0.4669 (pp-130) REVERT: L 484 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7177 (p) REVERT: L 493 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.4944 (p0) REVERT: M 324 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7828 (tp40) REVERT: M 493 ASP cc_start: 0.6174 (OUTLIER) cc_final: 0.5216 (p0) REVERT: N 493 ASP cc_start: 0.6057 (OUTLIER) cc_final: 0.4865 (p0) REVERT: O 309 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8405 (mm) REVERT: O 493 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.4981 (p0) REVERT: O 598 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8123 (mppt) outliers start: 218 outliers final: 66 residues processed: 546 average time/residue: 0.7807 time to fit residues: 514.8234 Evaluate side-chains 402 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 306 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 646 SER Chi-restraints excluded: chain C residue 324 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 637 LYS Chi-restraints excluded: chain E residue 646 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 324 GLN Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 494 ASN Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 637 LYS Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain G residue 324 GLN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 585 LEU Chi-restraints excluded: chain H residue 646 SER Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 324 GLN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 646 SER Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain K residue 646 SER Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 484 THR Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 646 SER Chi-restraints excluded: chain M residue 324 GLN Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 646 SER Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 646 SER Chi-restraints excluded: chain O residue 309 ILE Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 493 ASP Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 646 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 411 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 542 optimal weight: 4.9990 chunk 484 optimal weight: 0.3980 chunk 229 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 525 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 595 GLN B 432 GLN B 595 GLN C 432 GLN C 595 GLN D 324 GLN D 432 GLN D 595 GLN E 432 GLN E 595 GLN G 432 GLN G 595 GLN H 595 GLN I 595 GLN J 595 GLN K 432 GLN K 595 GLN L 432 GLN L 595 GLN M 432 GLN M 595 GLN O 432 GLN O 595 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098523 restraints weight = 57469.941| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.86 r_work: 0.3230 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43425 Z= 0.147 Angle : 0.580 5.362 58725 Z= 0.319 Chirality : 0.047 0.159 7050 Planarity : 0.005 0.045 7650 Dihedral : 5.577 27.097 6000 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.11 % Allowed : 25.74 % Favored : 71.15 % 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 (0.11), residues: 5550 helix: 1.52 (0.14), residues: 1320 sheet: 0.38 (0.10), residues: 2460 loop : -2.67 (0.12), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 411 TYR 0.009 0.001 TYR L 403 PHE 0.018 0.002 PHE M 474 TRP 0.003 0.001 TRP M 365 HIS 0.003 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00325 (43425) covalent geometry : angle 0.57993 (58725) hydrogen bonds : bond 0.05571 ( 1754) hydrogen bonds : angle 5.33161 ( 4956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 321 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 493 ASP cc_start: 0.5859 (OUTLIER) cc_final: 0.4690 (p0) REVERT: A 532 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 309 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8491 (mm) REVERT: B 493 ASP cc_start: 0.5799 (m-30) cc_final: 0.4653 (p0) REVERT: B 532 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 437 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8052 (m) REVERT: C 493 ASP cc_start: 0.5857 (m-30) cc_final: 0.4613 (p0) REVERT: C 497 GLN cc_start: 0.4850 (OUTLIER) cc_final: 0.4587 (mm110) REVERT: C 532 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8592 (mt) REVERT: D 493 ASP cc_start: 0.5762 (m-30) cc_final: 0.4520 (p0) REVERT: D 532 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8564 (mt) REVERT: D 541 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.7592 (mtp180) REVERT: D 598 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8670 (mttt) REVERT: E 327 MET cc_start: 0.8466 (mmt) cc_final: 0.8180 (tpp) REVERT: E 493 ASP cc_start: 0.5774 (m-30) cc_final: 0.4526 (p0) REVERT: E 532 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8621 (mt) REVERT: F 493 ASP cc_start: 0.5848 (m-30) cc_final: 0.4663 (p0) REVERT: F 532 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8492 (mt) REVERT: G 493 ASP cc_start: 0.5752 (m-30) cc_final: 0.4586 (p0) REVERT: G 532 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8568 (mt) REVERT: H 493 ASP cc_start: 0.5807 (m-30) cc_final: 0.4677 (p0) REVERT: H 532 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8556 (mt) REVERT: H 541 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7625 (mtp180) REVERT: H 670 MET cc_start: 0.4637 (tmm) cc_final: 0.4428 (pp-130) REVERT: I 493 ASP cc_start: 0.5795 (m-30) cc_final: 0.4721 (p0) REVERT: I 532 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8526 (mt) REVERT: J 309 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8565 (mm) REVERT: J 493 ASP cc_start: 0.5730 (m-30) cc_final: 0.4531 (p0) REVERT: J 532 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8589 (mt) REVERT: K 493 ASP cc_start: 0.5728 (m-30) cc_final: 0.4742 (p0) REVERT: K 532 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8530 (mt) REVERT: K 670 MET cc_start: 0.5106 (tmm) cc_final: 0.4717 (pp-130) REVERT: L 437 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.7947 (m) REVERT: L 493 ASP cc_start: 0.5860 (m-30) cc_final: 0.4777 (p0) REVERT: L 532 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8559 (mt) REVERT: M 493 ASP cc_start: 0.5936 (m-30) cc_final: 0.4742 (p0) REVERT: M 532 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8611 (mt) REVERT: N 493 ASP cc_start: 0.5744 (m-30) cc_final: 0.4521 (p0) REVERT: N 532 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8546 (mt) REVERT: N 670 MET cc_start: 0.4741 (tmm) cc_final: 0.4388 (pp-130) REVERT: O 493 ASP cc_start: 0.5834 (m-30) cc_final: 0.4753 (p0) REVERT: O 532 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8532 (mt) REVERT: O 541 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.7606 (mtp180) outliers start: 148 outliers final: 58 residues processed: 448 average time/residue: 0.7747 time to fit residues: 424.1193 Evaluate side-chains 402 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 318 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 646 SER Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 532 LEU Chi-restraints excluded: chain H residue 541 ARG Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 369 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 494 ASN Chi-restraints excluded: chain J residue 532 LEU Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain K residue 369 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 532 LEU Chi-restraints excluded: chain N residue 369 GLU Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 532 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 541 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 286 optimal weight: 5.9990 chunk 455 optimal weight: 9.9990 chunk 250 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 296 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 367 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN B 595 GLN C 432 GLN C 595 GLN D 595 GLN E 595 GLN G 595 GLN H 595 GLN I 595 GLN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 GLN J 595 GLN K 595 GLN L 595 GLN M 595 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.131517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098038 restraints weight = 57236.335| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.84 r_work: 0.3221 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 43425 Z= 0.158 Angle : 0.583 5.362 58725 Z= 0.322 Chirality : 0.047 0.160 7050 Planarity : 0.005 0.042 7650 Dihedral : 5.472 19.104 5958 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.30 % Allowed : 25.83 % Favored : 70.87 % 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 (0.11), residues: 5550 helix: 1.64 (0.14), residues: 1320 sheet: 0.06 (0.10), residues: 2670 loop : -2.48 (0.13), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 501 TYR 0.009 0.002 TYR L 403 PHE 0.018 0.002 PHE M 474 TRP 0.004 0.001 TRP M 365 HIS 0.003 0.001 HIS G 659 Details of bonding type rmsd covalent geometry : bond 0.00350 (43425) covalent geometry : angle 0.58340 (58725) hydrogen bonds : bond 0.05792 ( 1754) hydrogen bonds : angle 5.32565 ( 4956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 325 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8544 (mm) REVERT: A 493 ASP cc_start: 0.5686 (m-30) cc_final: 0.4468 (p0) REVERT: A 532 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8578 (mt) REVERT: B 309 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8505 (mm) REVERT: B 493 ASP cc_start: 0.5830 (m-30) cc_final: 0.4628 (p0) REVERT: B 532 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8576 (mt) REVERT: C 437 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8034 (m) REVERT: C 440 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (mtp) REVERT: C 493 ASP cc_start: 0.5721 (m-30) cc_final: 0.4445 (p0) REVERT: C 497 GLN cc_start: 0.4870 (OUTLIER) cc_final: 0.4651 (tp-100) REVERT: C 532 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8595 (mt) REVERT: D 437 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.7956 (m) REVERT: D 440 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7367 (ptp) REVERT: D 493 ASP cc_start: 0.5794 (m-30) cc_final: 0.4479 (p0) REVERT: D 532 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8539 (mt) REVERT: D 541 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.7618 (mtp180) REVERT: D 598 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8651 (mttt) REVERT: E 484 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7220 (p) REVERT: E 493 ASP cc_start: 0.5741 (m-30) cc_final: 0.4490 (p0) REVERT: E 532 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8634 (mt) REVERT: F 437 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8031 (m) REVERT: F 493 ASP cc_start: 0.5820 (OUTLIER) cc_final: 0.4654 (p0) REVERT: F 498 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.6084 (t) REVERT: F 532 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8503 (mt) REVERT: F 541 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8081 (mtp180) REVERT: G 493 ASP cc_start: 0.5793 (m-30) cc_final: 0.4538 (p0) REVERT: G 541 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8064 (mtp180) REVERT: H 493 ASP cc_start: 0.5851 (m-30) cc_final: 0.4743 (p0) REVERT: H 532 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8538 (mt) REVERT: H 541 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.7671 (mtp180) REVERT: H 670 MET cc_start: 0.4660 (tmm) cc_final: 0.4366 (pp-130) REVERT: I 308 MET cc_start: 0.7540 (tpp) cc_final: 0.7276 (tmm) REVERT: I 493 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.4713 (p0) REVERT: I 532 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8517 (mt) REVERT: J 309 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8563 (mm) REVERT: J 493 ASP cc_start: 0.5846 (m-30) cc_final: 0.4595 (p0) REVERT: J 532 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8591 (mt) REVERT: K 493 ASP cc_start: 0.5806 (OUTLIER) cc_final: 0.4774 (p0) REVERT: K 532 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8513 (mt) REVERT: K 670 MET cc_start: 0.5249 (OUTLIER) cc_final: 0.4861 (pp-130) REVERT: L 437 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7944 (m) REVERT: L 484 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7152 (p) REVERT: L 493 ASP cc_start: 0.5889 (m-30) cc_final: 0.4755 (p0) REVERT: L 532 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8562 (mt) REVERT: M 493 ASP cc_start: 0.5849 (m-30) cc_final: 0.4594 (p0) REVERT: M 532 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8599 (mt) REVERT: N 493 ASP cc_start: 0.5782 (m-30) cc_final: 0.4512 (p0) REVERT: N 532 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8529 (mt) REVERT: N 670 MET cc_start: 0.4962 (tmm) cc_final: 0.4677 (tmm) REVERT: O 493 ASP cc_start: 0.5695 (m-30) cc_final: 0.4598 (p0) REVERT: O 532 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8523 (mt) REVERT: O 541 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.7601 (mtp180) outliers start: 157 outliers final: 67 residues processed: 460 average time/residue: 0.7159 time to fit residues: 405.3936 Evaluate side-chains 412 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 308 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 541 ARG Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 541 ARG Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 532 LEU Chi-restraints excluded: chain H residue 541 ARG Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 369 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 532 LEU Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain J residue 646 SER Chi-restraints excluded: chain K residue 369 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain K residue 670 MET Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 484 THR Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 605 ILE Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 532 LEU Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 437 SER Chi-restraints excluded: chain N residue 532 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 541 ARG Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 605 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 189 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 395 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 411 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 242 optimal weight: 0.6980 chunk 512 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN B 595 GLN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 595 GLN D 595 GLN D 664 GLN E 595 GLN ** G 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 GLN ** H 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 595 GLN I 595 GLN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN K 595 GLN K 664 GLN L 595 GLN ** M 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.131747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098253 restraints weight = 57257.520| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.85 r_work: 0.3226 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 43425 Z= 0.148 Angle : 0.565 5.027 58725 Z= 0.313 Chirality : 0.047 0.163 7050 Planarity : 0.005 0.042 7650 Dihedral : 5.372 18.867 5955 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.13 % Allowed : 26.12 % Favored : 70.75 % 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: -0.33 (0.11), residues: 5550 helix: 1.74 (0.14), residues: 1320 sheet: 0.13 (0.10), residues: 2610 loop : -2.46 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 501 TYR 0.010 0.001 TYR D 403 PHE 0.017 0.002 PHE M 474 TRP 0.003 0.001 TRP M 365 HIS 0.003 0.001 HIS G 659 Details of bonding type rmsd covalent geometry : bond 0.00326 (43425) covalent geometry : angle 0.56499 (58725) hydrogen bonds : bond 0.05561 ( 1754) hydrogen bonds : angle 5.27958 ( 4956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 321 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: A 309 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8530 (mm) REVERT: A 493 ASP cc_start: 0.5588 (m-30) cc_final: 0.4527 (p0) REVERT: A 532 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8553 (mt) REVERT: B 309 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8501 (mm) REVERT: B 493 ASP cc_start: 0.5776 (OUTLIER) cc_final: 0.4632 (p0) REVERT: B 532 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8581 (mt) REVERT: C 437 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8048 (m) REVERT: C 440 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7430 (mtp) REVERT: C 493 ASP cc_start: 0.5703 (m-30) cc_final: 0.4482 (p0) REVERT: C 497 GLN cc_start: 0.4837 (OUTLIER) cc_final: 0.4608 (tp-100) REVERT: C 532 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8597 (mt) REVERT: D 437 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.7967 (m) REVERT: D 493 ASP cc_start: 0.5690 (m-30) cc_final: 0.4553 (p0) REVERT: D 532 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8550 (mt) REVERT: D 541 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7595 (mtp180) REVERT: D 598 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8647 (mttt) REVERT: E 327 MET cc_start: 0.8491 (mmt) cc_final: 0.8216 (tpp) REVERT: E 484 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7110 (p) REVERT: E 493 ASP cc_start: 0.5743 (m-30) cc_final: 0.4541 (p0) REVERT: E 532 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8632 (mt) REVERT: F 437 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8020 (m) REVERT: F 493 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.4688 (p0) REVERT: F 532 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8494 (mt) REVERT: G 493 ASP cc_start: 0.5773 (m-30) cc_final: 0.4571 (p0) REVERT: G 532 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8578 (mt) REVERT: G 541 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8045 (mtp180) REVERT: H 493 ASP cc_start: 0.5836 (m-30) cc_final: 0.4815 (p0) REVERT: H 532 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8541 (mt) REVERT: H 541 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7643 (mtp180) REVERT: H 670 MET cc_start: 0.4983 (tmm) cc_final: 0.4581 (pp-130) REVERT: I 308 MET cc_start: 0.7485 (tpp) cc_final: 0.7250 (tmm) REVERT: I 324 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7526 (tp40) REVERT: I 437 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7965 (m) REVERT: I 493 ASP cc_start: 0.5773 (m-30) cc_final: 0.4712 (p0) REVERT: I 532 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8514 (mt) REVERT: J 309 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8493 (mm) REVERT: J 493 ASP cc_start: 0.5777 (m-30) cc_final: 0.4605 (p0) REVERT: J 532 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8587 (mt) REVERT: K 493 ASP cc_start: 0.5731 (m-30) cc_final: 0.4750 (p0) REVERT: K 532 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8514 (mt) REVERT: K 598 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8677 (mptt) REVERT: K 670 MET cc_start: 0.5301 (OUTLIER) cc_final: 0.4902 (pp-130) REVERT: L 437 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.7939 (m) REVERT: L 440 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7340 (mtp) REVERT: L 484 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.7111 (p) REVERT: L 493 ASP cc_start: 0.5782 (m-30) cc_final: 0.4771 (p0) REVERT: L 532 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8570 (mt) REVERT: M 493 ASP cc_start: 0.5807 (m-30) cc_final: 0.4633 (p0) REVERT: M 532 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8603 (mt) REVERT: N 493 ASP cc_start: 0.5642 (m-30) cc_final: 0.4492 (p0) REVERT: N 532 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8534 (mt) REVERT: N 670 MET cc_start: 0.5065 (tmm) cc_final: 0.4743 (tmm) REVERT: O 493 ASP cc_start: 0.5644 (m-30) cc_final: 0.4621 (p0) REVERT: O 532 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8526 (mt) REVERT: O 541 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7589 (mtp180) outliers start: 149 outliers final: 74 residues processed: 446 average time/residue: 0.7114 time to fit residues: 391.1134 Evaluate side-chains 418 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 306 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 266 ASN Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 541 ARG Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 437 SER Chi-restraints excluded: chain H residue 532 LEU Chi-restraints excluded: chain H residue 541 ARG Chi-restraints excluded: chain H residue 585 LEU Chi-restraints excluded: chain I residue 266 ASN Chi-restraints excluded: chain I residue 324 GLN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 437 SER Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 369 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 532 LEU Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain J residue 646 SER Chi-restraints excluded: chain K residue 369 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain K residue 598 LYS Chi-restraints excluded: chain K residue 670 MET Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 440 MET Chi-restraints excluded: chain L residue 484 THR Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 605 ILE Chi-restraints excluded: chain L residue 655 ASP Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 532 LEU Chi-restraints excluded: chain M residue 605 ILE Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 437 SER Chi-restraints excluded: chain N residue 532 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 266 ASN Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 541 ARG Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 605 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 232 optimal weight: 9.9990 chunk 126 optimal weight: 0.3980 chunk 217 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 308 optimal weight: 0.8980 chunk 547 optimal weight: 9.9990 chunk 470 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 481 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN B 595 GLN C 266 ASN C 432 GLN C 595 GLN G 266 ASN G 595 GLN ** H 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 664 GLN J 266 ASN J 595 GLN J 664 GLN K 595 GLN L 595 GLN ** M 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.132407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098897 restraints weight = 57396.977| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.85 r_work: 0.3229 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 43425 Z= 0.127 Angle : 0.529 5.361 58725 Z= 0.294 Chirality : 0.046 0.163 7050 Planarity : 0.004 0.040 7650 Dihedral : 5.183 18.265 5955 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.20 % Allowed : 26.48 % Favored : 70.33 % 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: -0.23 (0.11), residues: 5550 helix: 1.87 (0.14), residues: 1320 sheet: 0.17 (0.10), residues: 2610 loop : -2.41 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 411 TYR 0.009 0.001 TYR L 403 PHE 0.016 0.002 PHE M 474 TRP 0.002 0.001 TRP A 365 HIS 0.002 0.001 HIS G 659 Details of bonding type rmsd covalent geometry : bond 0.00272 (43425) covalent geometry : angle 0.52869 (58725) hydrogen bonds : bond 0.05143 ( 1754) hydrogen bonds : angle 5.18340 ( 4956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 312 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8518 (mm) REVERT: A 493 ASP cc_start: 0.5638 (m-30) cc_final: 0.4558 (p0) REVERT: A 532 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 309 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8476 (mm) REVERT: B 493 ASP cc_start: 0.5707 (m-30) cc_final: 0.4598 (p0) REVERT: B 532 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 493 ASP cc_start: 0.5604 (m-30) cc_final: 0.4379 (p0) REVERT: C 532 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8598 (mt) REVERT: D 383 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8597 (tt) REVERT: D 437 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.7961 (m) REVERT: D 493 ASP cc_start: 0.5604 (m-30) cc_final: 0.4490 (p0) REVERT: D 532 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8571 (mt) REVERT: D 541 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7608 (mtp180) REVERT: D 598 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8641 (mttt) REVERT: E 327 MET cc_start: 0.8420 (mmt) cc_final: 0.8205 (tpp) REVERT: E 484 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7118 (p) REVERT: E 493 ASP cc_start: 0.5685 (m-30) cc_final: 0.4591 (p0) REVERT: E 532 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8634 (mt) REVERT: F 493 ASP cc_start: 0.5649 (m-30) cc_final: 0.4631 (p0) REVERT: F 498 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.5974 (t) REVERT: F 532 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8506 (mt) REVERT: G 493 ASP cc_start: 0.5789 (m-30) cc_final: 0.4562 (p0) REVERT: G 532 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8584 (mt) REVERT: G 541 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8050 (mtp180) REVERT: H 493 ASP cc_start: 0.5700 (m-30) cc_final: 0.4596 (p0) REVERT: H 532 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8546 (mt) REVERT: H 541 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7665 (mtp180) REVERT: H 670 MET cc_start: 0.5052 (tmm) cc_final: 0.4530 (pp-130) REVERT: I 324 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7447 (tp40) REVERT: I 383 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8636 (tt) REVERT: I 437 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.7971 (m) REVERT: I 493 ASP cc_start: 0.5728 (m-30) cc_final: 0.4626 (p0) REVERT: I 532 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8521 (mt) REVERT: J 309 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8402 (mm) REVERT: J 493 ASP cc_start: 0.5800 (m-30) cc_final: 0.4574 (p0) REVERT: J 532 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8588 (mt) REVERT: K 493 ASP cc_start: 0.5659 (m-30) cc_final: 0.4669 (p0) REVERT: K 532 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8531 (mt) REVERT: K 598 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8687 (mptt) REVERT: K 670 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.4880 (pp-130) REVERT: L 437 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.7937 (m) REVERT: L 484 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7150 (p) REVERT: L 493 ASP cc_start: 0.5761 (m-30) cc_final: 0.4667 (p0) REVERT: L 532 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8579 (mt) REVERT: M 493 ASP cc_start: 0.5678 (m-30) cc_final: 0.4531 (p0) REVERT: M 532 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8591 (mt) REVERT: N 493 ASP cc_start: 0.5598 (m-30) cc_final: 0.4395 (p0) REVERT: N 532 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8551 (mt) REVERT: N 670 MET cc_start: 0.5045 (tmm) cc_final: 0.4737 (tmm) REVERT: O 493 ASP cc_start: 0.5602 (m-30) cc_final: 0.4503 (p0) REVERT: O 532 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8527 (mt) REVERT: O 541 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7610 (mtp180) outliers start: 152 outliers final: 72 residues processed: 444 average time/residue: 0.7247 time to fit residues: 396.5906 Evaluate side-chains 396 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 290 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 266 ASN Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 541 ARG Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 437 SER Chi-restraints excluded: chain H residue 532 LEU Chi-restraints excluded: chain H residue 541 ARG Chi-restraints excluded: chain I residue 266 ASN Chi-restraints excluded: chain I residue 324 GLN Chi-restraints excluded: chain I residue 383 ILE Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 437 SER Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 369 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 532 LEU Chi-restraints excluded: chain K residue 369 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain K residue 598 LYS Chi-restraints excluded: chain K residue 670 MET Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 484 THR Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 655 ASP Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 532 LEU Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 437 SER Chi-restraints excluded: chain N residue 532 LEU Chi-restraints excluded: chain O residue 266 ASN Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 541 ARG Chi-restraints excluded: chain O residue 585 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 25 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 535 optimal weight: 9.9990 chunk 400 optimal weight: 4.9990 chunk 41 optimal weight: 0.0870 chunk 517 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 428 optimal weight: 5.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN A 664 GLN B 664 GLN C 432 GLN C 664 GLN E 664 GLN F 266 ASN F 664 GLN G 595 GLN G 664 GLN ** H 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 ASN L 595 GLN ** M 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 664 GLN ** N 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 664 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096820 restraints weight = 56867.970| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.84 r_work: 0.3199 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 43425 Z= 0.214 Angle : 0.658 6.631 58725 Z= 0.360 Chirality : 0.048 0.178 7050 Planarity : 0.005 0.043 7650 Dihedral : 5.718 19.935 5955 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.49 % Allowed : 26.94 % Favored : 69.57 % 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: -0.48 (0.11), residues: 5550 helix: 1.67 (0.14), residues: 1305 sheet: -0.06 (0.10), residues: 2685 loop : -2.47 (0.13), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 501 TYR 0.011 0.002 TYR D 403 PHE 0.020 0.003 PHE L 474 TRP 0.005 0.001 TRP A 365 HIS 0.003 0.002 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00495 (43425) covalent geometry : angle 0.65764 (58725) hydrogen bonds : bond 0.06514 ( 1754) hydrogen bonds : angle 5.44960 ( 4956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 305 time to evaluate : 1.872 Fit side-chains revert: symmetry clash REVERT: A 493 ASP cc_start: 0.5806 (m-30) cc_final: 0.4770 (p0) REVERT: B 309 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8592 (mm) REVERT: B 493 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.4756 (p0) REVERT: B 532 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8583 (mt) REVERT: C 437 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8071 (m) REVERT: C 493 ASP cc_start: 0.5698 (m-30) cc_final: 0.4481 (p0) REVERT: C 667 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6794 (pt) REVERT: D 437 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.7995 (m) REVERT: D 493 ASP cc_start: 0.5972 (m-30) cc_final: 0.4809 (p0) REVERT: D 541 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: D 598 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8660 (mttt) REVERT: E 327 MET cc_start: 0.8513 (mmt) cc_final: 0.8180 (tpp) REVERT: E 484 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7138 (p) REVERT: E 493 ASP cc_start: 0.5913 (OUTLIER) cc_final: 0.4746 (p0) REVERT: F 437 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8071 (m) REVERT: F 493 ASP cc_start: 0.5852 (OUTLIER) cc_final: 0.4902 (p0) REVERT: G 309 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8572 (mm) REVERT: G 493 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.4680 (p0) REVERT: G 541 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8089 (mtp180) REVERT: H 320 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8902 (mt) REVERT: H 493 ASP cc_start: 0.5863 (m-30) cc_final: 0.4831 (p0) REVERT: H 541 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.7670 (mtp180) REVERT: H 670 MET cc_start: 0.5058 (tmm) cc_final: 0.4489 (pp-130) REVERT: I 308 MET cc_start: 0.7664 (tpp) cc_final: 0.7193 (tmm) REVERT: I 324 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7594 (tp40) REVERT: I 383 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8729 (tt) REVERT: I 437 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.7997 (m) REVERT: I 493 ASP cc_start: 0.5942 (OUTLIER) cc_final: 0.4858 (p0) REVERT: J 309 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8647 (mm) REVERT: J 493 ASP cc_start: 0.5840 (OUTLIER) cc_final: 0.4793 (p0) REVERT: K 493 ASP cc_start: 0.5873 (OUTLIER) cc_final: 0.4834 (p0) REVERT: K 598 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8689 (mptt) REVERT: K 670 MET cc_start: 0.5268 (OUTLIER) cc_final: 0.4851 (pp-130) REVERT: L 320 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8794 (mt) REVERT: L 437 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.7944 (m) REVERT: L 493 ASP cc_start: 0.5847 (m-30) cc_final: 0.4784 (p0) REVERT: L 532 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8587 (mt) REVERT: M 493 ASP cc_start: 0.5894 (OUTLIER) cc_final: 0.4778 (p0) REVERT: N 493 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.4584 (p0) REVERT: N 670 MET cc_start: 0.5174 (tmm) cc_final: 0.4839 (tmm) REVERT: O 493 ASP cc_start: 0.5778 (m-30) cc_final: 0.4704 (p0) REVERT: O 541 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7845 (mtp180) REVERT: O 598 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8705 (mptt) outliers start: 166 outliers final: 83 residues processed: 445 average time/residue: 0.7165 time to fit residues: 396.8049 Evaluate side-chains 414 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 298 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 266 ASN Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 541 ARG Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 437 SER Chi-restraints excluded: chain H residue 541 ARG Chi-restraints excluded: chain I residue 324 GLN Chi-restraints excluded: chain I residue 383 ILE Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 437 SER Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 321 THR Chi-restraints excluded: chain J residue 369 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain J residue 605 ILE Chi-restraints excluded: chain J residue 646 SER Chi-restraints excluded: chain K residue 369 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain K residue 598 LYS Chi-restraints excluded: chain K residue 670 MET Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 655 ASP Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 605 ILE Chi-restraints excluded: chain M residue 646 SER Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 437 SER Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 637 LYS Chi-restraints excluded: chain N residue 646 SER Chi-restraints excluded: chain O residue 321 THR Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 541 ARG Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 605 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 184 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 480 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 522 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 420 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN C 432 GLN F 266 ASN G 595 GLN H 266 ASN I 266 ASN L 595 GLN M 266 ASN N 266 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100917 restraints weight = 57952.083| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.77 r_work: 0.3229 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43425 Z= 0.144 Angle : 0.563 6.408 58725 Z= 0.312 Chirality : 0.047 0.167 7050 Planarity : 0.005 0.042 7650 Dihedral : 5.382 18.555 5955 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.13 % Allowed : 27.57 % Favored : 69.30 % 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 (0.11), residues: 5550 helix: 1.71 (0.14), residues: 1320 sheet: 0.08 (0.10), residues: 2625 loop : -2.40 (0.13), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 267 TYR 0.010 0.001 TYR L 403 PHE 0.017 0.002 PHE E 474 TRP 0.003 0.001 TRP A 365 HIS 0.003 0.001 HIS G 659 Details of bonding type rmsd covalent geometry : bond 0.00316 (43425) covalent geometry : angle 0.56325 (58725) hydrogen bonds : bond 0.05488 ( 1754) hydrogen bonds : angle 5.27873 ( 4956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 306 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.5731 (m-30) cc_final: 0.4627 (p0) REVERT: A 532 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8542 (mt) REVERT: A 598 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8643 (mptt) REVERT: B 309 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8531 (mm) REVERT: B 493 ASP cc_start: 0.5760 (m-30) cc_final: 0.4625 (p0) REVERT: B 532 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8594 (mt) REVERT: C 437 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8059 (m) REVERT: C 493 ASP cc_start: 0.5564 (m-30) cc_final: 0.4388 (p0) REVERT: C 532 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 667 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6794 (pt) REVERT: D 437 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.7988 (m) REVERT: D 493 ASP cc_start: 0.5863 (m-30) cc_final: 0.4685 (p0) REVERT: D 532 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8541 (mt) REVERT: D 541 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.7579 (mtp180) REVERT: D 598 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8642 (mttt) REVERT: E 327 MET cc_start: 0.8426 (mmt) cc_final: 0.8184 (tpp) REVERT: E 484 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7138 (p) REVERT: E 493 ASP cc_start: 0.5759 (m-30) cc_final: 0.4642 (p0) REVERT: E 532 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8627 (mt) REVERT: F 437 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.8049 (m) REVERT: F 493 ASP cc_start: 0.5645 (OUTLIER) cc_final: 0.4682 (p0) REVERT: F 498 THR cc_start: 0.6487 (OUTLIER) cc_final: 0.5982 (t) REVERT: F 532 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8520 (mt) REVERT: G 493 ASP cc_start: 0.5843 (m-30) cc_final: 0.4552 (p0) REVERT: G 541 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8040 (mtp180) REVERT: H 369 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7681 (pp20) REVERT: H 493 ASP cc_start: 0.5709 (m-30) cc_final: 0.4659 (p0) REVERT: H 541 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7647 (mtp180) REVERT: H 670 MET cc_start: 0.5014 (tmm) cc_final: 0.4438 (pp-130) REVERT: I 308 MET cc_start: 0.7547 (tpp) cc_final: 0.7034 (tmt) REVERT: I 383 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8659 (tt) REVERT: I 437 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.7964 (m) REVERT: I 493 ASP cc_start: 0.5740 (m-30) cc_final: 0.4655 (p0) REVERT: I 532 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8538 (mt) REVERT: J 309 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8431 (mm) REVERT: J 493 ASP cc_start: 0.5695 (m-30) cc_final: 0.4679 (p0) REVERT: K 493 ASP cc_start: 0.5724 (m-30) cc_final: 0.4645 (p0) REVERT: K 532 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8515 (mt) REVERT: K 598 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8668 (mptt) REVERT: K 670 MET cc_start: 0.5197 (OUTLIER) cc_final: 0.4787 (pp-130) REVERT: L 320 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8653 (mt) REVERT: L 437 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7932 (m) REVERT: L 493 ASP cc_start: 0.5595 (m-30) cc_final: 0.4506 (p0) REVERT: L 532 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8577 (mt) REVERT: M 493 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.4518 (p0) REVERT: N 493 ASP cc_start: 0.5663 (m-30) cc_final: 0.4464 (p0) REVERT: N 532 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8549 (mt) REVERT: N 670 MET cc_start: 0.5173 (tmm) cc_final: 0.4839 (tmm) REVERT: O 493 ASP cc_start: 0.5712 (m-30) cc_final: 0.4560 (p0) REVERT: O 541 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: O 598 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8699 (mptt) outliers start: 149 outliers final: 82 residues processed: 436 average time/residue: 0.6235 time to fit residues: 337.4783 Evaluate side-chains 411 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 295 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 541 ARG Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain H residue 369 GLU Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 437 SER Chi-restraints excluded: chain H residue 541 ARG Chi-restraints excluded: chain H residue 585 LEU Chi-restraints excluded: chain I residue 383 ILE Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 437 SER Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 321 THR Chi-restraints excluded: chain J residue 369 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain J residue 605 ILE Chi-restraints excluded: chain J residue 646 SER Chi-restraints excluded: chain K residue 369 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain K residue 598 LYS Chi-restraints excluded: chain K residue 670 MET Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 655 ASP Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 605 ILE Chi-restraints excluded: chain M residue 646 SER Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 437 SER Chi-restraints excluded: chain N residue 532 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 321 THR Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 541 ARG Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 605 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 244 optimal weight: 7.9990 chunk 428 optimal weight: 0.6980 chunk 544 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 402 optimal weight: 8.9990 chunk 411 optimal weight: 3.9990 chunk 474 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 chunk 316 optimal weight: 0.0470 chunk 512 optimal weight: 8.9990 overall best weight: 3.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN F 266 ASN G 595 GLN H 664 GLN I 266 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100567 restraints weight = 57559.745| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.77 r_work: 0.3219 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 43425 Z= 0.204 Angle : 0.648 7.050 58725 Z= 0.356 Chirality : 0.048 0.174 7050 Planarity : 0.005 0.043 7650 Dihedral : 5.702 19.415 5955 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.94 % Allowed : 27.74 % Favored : 69.32 % 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: -0.56 (0.11), residues: 5550 helix: 1.64 (0.14), residues: 1305 sheet: -0.15 (0.10), residues: 2715 loop : -2.49 (0.13), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 501 TYR 0.012 0.002 TYR D 403 PHE 0.019 0.003 PHE L 474 TRP 0.005 0.001 TRP A 365 HIS 0.003 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00471 (43425) covalent geometry : angle 0.64845 (58725) hydrogen bonds : bond 0.06395 ( 1754) hydrogen bonds : angle 5.44190 ( 4956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 308 time to evaluate : 1.768 Fit side-chains revert: symmetry clash REVERT: A 493 ASP cc_start: 0.5704 (m-30) cc_final: 0.4702 (p0) REVERT: A 598 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8745 (mptt) REVERT: B 309 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8595 (mm) REVERT: B 493 ASP cc_start: 0.5714 (m-30) cc_final: 0.4673 (p0) REVERT: B 532 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8588 (mt) REVERT: C 437 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.8039 (m) REVERT: C 493 ASP cc_start: 0.5519 (m-30) cc_final: 0.4399 (p0) REVERT: C 667 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6994 (pt) REVERT: D 437 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.7972 (m) REVERT: D 493 ASP cc_start: 0.5774 (m-30) cc_final: 0.4677 (p0) REVERT: D 541 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.7627 (mtp180) REVERT: D 598 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8692 (mttt) REVERT: E 327 MET cc_start: 0.8457 (mmt) cc_final: 0.8113 (tpp) REVERT: E 484 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7023 (p) REVERT: E 493 ASP cc_start: 0.5791 (m-30) cc_final: 0.4782 (p0) REVERT: F 437 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8064 (m) REVERT: F 493 ASP cc_start: 0.5708 (OUTLIER) cc_final: 0.4820 (p0) REVERT: G 493 ASP cc_start: 0.5796 (m-30) cc_final: 0.4572 (p0) REVERT: G 541 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8079 (mtp180) REVERT: H 369 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7719 (pp20) REVERT: H 493 ASP cc_start: 0.5589 (m-30) cc_final: 0.4634 (p0) REVERT: H 541 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7667 (mtp180) REVERT: H 670 MET cc_start: 0.5167 (tmm) cc_final: 0.4557 (pp-130) REVERT: I 308 MET cc_start: 0.7576 (tpp) cc_final: 0.7125 (tmm) REVERT: I 324 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7615 (tp40) REVERT: I 383 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8721 (tt) REVERT: I 437 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.7989 (m) REVERT: I 493 ASP cc_start: 0.5692 (m-30) cc_final: 0.4606 (p0) REVERT: J 309 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8619 (mm) REVERT: J 493 ASP cc_start: 0.5655 (m-30) cc_final: 0.4727 (p0) REVERT: K 493 ASP cc_start: 0.5716 (m-30) cc_final: 0.4705 (p0) REVERT: K 598 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8732 (mptt) REVERT: K 670 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.4794 (pp-130) REVERT: L 320 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8738 (mt) REVERT: L 437 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.7912 (m) REVERT: L 493 ASP cc_start: 0.5592 (m-30) cc_final: 0.4543 (p0) REVERT: L 532 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8571 (mt) REVERT: M 493 ASP cc_start: 0.5532 (OUTLIER) cc_final: 0.4475 (p0) REVERT: N 493 ASP cc_start: 0.5645 (m-30) cc_final: 0.4514 (p0) REVERT: N 670 MET cc_start: 0.5394 (tmm) cc_final: 0.5004 (tmm) REVERT: O 493 ASP cc_start: 0.5759 (m-30) cc_final: 0.4642 (p0) REVERT: O 541 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7830 (mtp180) REVERT: O 598 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8745 (mptt) outliers start: 140 outliers final: 80 residues processed: 434 average time/residue: 0.7057 time to fit residues: 377.2720 Evaluate side-chains 404 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 298 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 266 ASN Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain F residue 637 LYS Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 541 ARG Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain H residue 369 GLU Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 437 SER Chi-restraints excluded: chain H residue 541 ARG Chi-restraints excluded: chain I residue 324 GLN Chi-restraints excluded: chain I residue 383 ILE Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 437 SER Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 321 THR Chi-restraints excluded: chain J residue 369 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain J residue 605 ILE Chi-restraints excluded: chain J residue 646 SER Chi-restraints excluded: chain K residue 369 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain K residue 598 LYS Chi-restraints excluded: chain K residue 670 MET Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 655 ASP Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 605 ILE Chi-restraints excluded: chain M residue 646 SER Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 437 SER Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 646 SER Chi-restraints excluded: chain O residue 321 THR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 541 ARG Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 605 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 387 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 411 optimal weight: 6.9990 chunk 473 optimal weight: 4.9990 chunk 372 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 409 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN D 595 GLN F 266 ASN G 595 GLN I 266 ASN L 266 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.132095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.099427 restraints weight = 57663.274| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.74 r_work: 0.3204 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 43425 Z= 0.214 Angle : 0.667 6.939 58725 Z= 0.366 Chirality : 0.049 0.179 7050 Planarity : 0.005 0.044 7650 Dihedral : 5.780 20.159 5955 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.84 % Allowed : 27.76 % Favored : 69.40 % 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: -0.62 (0.11), residues: 5550 helix: 1.55 (0.15), residues: 1305 sheet: -0.17 (0.10), residues: 2715 loop : -2.50 (0.13), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 267 TYR 0.013 0.002 TYR O 626 PHE 0.020 0.003 PHE L 474 TRP 0.005 0.001 TRP A 365 HIS 0.003 0.001 HIS L 659 Details of bonding type rmsd covalent geometry : bond 0.00492 (43425) covalent geometry : angle 0.66670 (58725) hydrogen bonds : bond 0.06508 ( 1754) hydrogen bonds : angle 5.49188 ( 4956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11100 Ramachandran restraints generated. 5550 Oldfield, 0 Emsley, 5550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 308 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 437 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8157 (m) REVERT: A 493 ASP cc_start: 0.5901 (m-30) cc_final: 0.4871 (p0) REVERT: A 598 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8644 (mptt) REVERT: B 309 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8613 (mm) REVERT: B 493 ASP cc_start: 0.5917 (m-30) cc_final: 0.4882 (p0) REVERT: B 532 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8590 (mt) REVERT: C 437 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8053 (m) REVERT: C 493 ASP cc_start: 0.5689 (m-30) cc_final: 0.4590 (p0) REVERT: C 667 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6867 (pt) REVERT: D 437 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7987 (m) REVERT: D 493 ASP cc_start: 0.5964 (m-30) cc_final: 0.4862 (p0) REVERT: D 541 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7610 (mtp180) REVERT: D 598 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8658 (mttt) REVERT: E 327 MET cc_start: 0.8511 (mmt) cc_final: 0.8180 (tpp) REVERT: E 484 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7156 (p) REVERT: E 493 ASP cc_start: 0.5996 (m-30) cc_final: 0.5009 (p0) REVERT: F 437 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8055 (m) REVERT: F 493 ASP cc_start: 0.5837 (OUTLIER) cc_final: 0.5019 (p0) REVERT: F 498 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6280 (t) REVERT: G 493 ASP cc_start: 0.5963 (m-30) cc_final: 0.4717 (p0) REVERT: G 541 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8067 (mtp180) REVERT: H 369 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: H 493 ASP cc_start: 0.5802 (m-30) cc_final: 0.4785 (p0) REVERT: H 541 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7652 (mtp180) REVERT: H 670 MET cc_start: 0.5090 (tmm) cc_final: 0.4476 (pp-130) REVERT: I 308 MET cc_start: 0.7621 (tpp) cc_final: 0.7156 (tmm) REVERT: I 324 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7568 (tp40) REVERT: I 383 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8727 (tt) REVERT: I 437 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.7993 (m) REVERT: I 493 ASP cc_start: 0.5925 (m-30) cc_final: 0.4828 (p0) REVERT: J 309 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8630 (mm) REVERT: J 493 ASP cc_start: 0.5807 (m-30) cc_final: 0.4763 (p0) REVERT: K 493 ASP cc_start: 0.5921 (m-30) cc_final: 0.4892 (p0) REVERT: K 598 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8667 (mptt) REVERT: K 670 MET cc_start: 0.5280 (OUTLIER) cc_final: 0.4872 (pp-130) REVERT: L 437 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.7910 (m) REVERT: L 493 ASP cc_start: 0.5804 (m-30) cc_final: 0.4776 (p0) REVERT: L 532 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8582 (mt) REVERT: M 493 ASP cc_start: 0.5668 (OUTLIER) cc_final: 0.4676 (p0) REVERT: N 493 ASP cc_start: 0.5824 (m-30) cc_final: 0.4738 (p0) REVERT: N 670 MET cc_start: 0.5244 (tmm) cc_final: 0.4871 (tmm) REVERT: O 493 ASP cc_start: 0.5898 (m-30) cc_final: 0.4811 (p0) REVERT: O 541 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7821 (mtp180) REVERT: O 598 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8706 (mptt) outliers start: 135 outliers final: 81 residues processed: 425 average time/residue: 0.4559 time to fit residues: 242.0249 Evaluate side-chains 408 residues out of total 4755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 300 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain F residue 637 LYS Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 541 ARG Chi-restraints excluded: chain G residue 585 LEU Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain H residue 369 GLU Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 437 SER Chi-restraints excluded: chain H residue 541 ARG Chi-restraints excluded: chain I residue 324 GLN Chi-restraints excluded: chain I residue 383 ILE Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 437 SER Chi-restraints excluded: chain I residue 585 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 321 THR Chi-restraints excluded: chain J residue 369 GLU Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain J residue 605 ILE Chi-restraints excluded: chain J residue 646 SER Chi-restraints excluded: chain K residue 369 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 585 LEU Chi-restraints excluded: chain K residue 598 LYS Chi-restraints excluded: chain K residue 670 MET Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 397 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 655 ASP Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 397 THR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 605 ILE Chi-restraints excluded: chain M residue 646 SER Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 437 SER Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain N residue 646 SER Chi-restraints excluded: chain O residue 321 THR Chi-restraints excluded: chain O residue 369 GLU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 541 ARG Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 605 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 310 optimal weight: 9.9990 chunk 231 optimal weight: 0.0000 chunk 19 optimal weight: 0.9990 chunk 493 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 429 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 509 optimal weight: 7.9990 chunk 433 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN F 266 ASN G 595 GLN I 266 ASN L 266 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.134919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102131 restraints weight = 57892.666| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.79 r_work: 0.3256 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 43425 Z= 0.114 Angle : 0.524 7.114 58725 Z= 0.291 Chirality : 0.046 0.175 7050 Planarity : 0.004 0.042 7650 Dihedral : 5.130 17.914 5955 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.08 % Allowed : 28.66 % Favored : 69.25 % 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 (0.11), residues: 5550 helix: 1.75 (0.14), residues: 1335 sheet: 0.00 (0.10), residues: 2685 loop : -2.42 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 411 TYR 0.010 0.001 TYR L 403 PHE 0.016 0.002 PHE E 474 TRP 0.003 0.001 TRP L 443 HIS 0.002 0.001 HIS O 659 Details of bonding type rmsd covalent geometry : bond 0.00238 (43425) covalent geometry : angle 0.52395 (58725) hydrogen bonds : bond 0.04849 ( 1754) hydrogen bonds : angle 5.15419 ( 4956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17206.58 seconds wall clock time: 292 minutes 40.89 seconds (17560.89 seconds total)