Starting phenix.real_space_refine on Fri Mar 6 12:00:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vn1_21247/03_2026/6vn1_21247.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vn1_21247/03_2026/6vn1_21247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vn1_21247/03_2026/6vn1_21247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vn1_21247/03_2026/6vn1_21247.map" model { file = "/net/cci-nas-00/data/ceres_data/6vn1_21247/03_2026/6vn1_21247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vn1_21247/03_2026/6vn1_21247.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14058 atoms to isotropic. 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 99 5.16 5 C 12333 2.51 5 N 3366 2.21 5 O 3726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19524 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 957 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4719 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: M, N, I, J, B, C Time building chain proxies: 4.35, per 1000 atoms: 0.22 Number of scatterers: 19524 At special positions: 0 Unit cell: (136.74, 150.52, 178.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3726 8.00 N 3366 7.00 C 12333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 645 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 540 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 645 " distance=2.04 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 645 " distance=2.04 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: 1.27 Conformation dependent library (CDL) restraints added in 926.4 milliseconds 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 54 sheets defined 17.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'H' and resid 26 through 30 removed outlier: 3.848A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER H 30 " --> pdb=" O GLY H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 26 through 30' Processing helix chain 'H' and resid 108 through 112 removed outlier: 3.632A pdb=" N PHE H 112 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 5.275A pdb=" N ASP A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.538A pdb=" N ILE A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 removed outlier: 4.678A pdb=" N GLU A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 554 removed outlier: 4.244A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.544A pdb=" N LEU A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.848A pdb=" N PHE I 29 " --> pdb=" O GLY I 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER I 30 " --> pdb=" O GLY I 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 26 through 30' Processing helix chain 'I' and resid 108 through 112 removed outlier: 3.633A pdb=" N PHE I 112 " --> pdb=" O PRO I 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 5.275A pdb=" N ASP B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.539A pdb=" N ILE B 412 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 434 removed outlier: 4.678A pdb=" N GLU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 554 removed outlier: 4.244A pdb=" N ALA B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.545A pdb=" N LEU B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'J' and resid 26 through 30 removed outlier: 3.849A pdb=" N PHE J 29 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER J 30 " --> pdb=" O GLY J 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 26 through 30' Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.631A pdb=" N PHE J 112 " --> pdb=" O PRO J 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 removed outlier: 5.274A pdb=" N ASP C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 408 through 412 removed outlier: 3.539A pdb=" N ILE C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 434 removed outlier: 4.679A pdb=" N GLU C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 554 removed outlier: 4.244A pdb=" N ALA C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 566 removed outlier: 3.545A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 729 Processing sheet with id=AA1, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AA3, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 46 through 51 removed outlier: 3.523A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 69 through 72 Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 574 removed outlier: 6.865A pdb=" N ILE A 130 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE B 679 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG A 132 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS A 373 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 157 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 379 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY A 151 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS A 373 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 157 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 379 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY A 151 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 186 through 197 removed outlier: 5.709A pdb=" N ILE A 188 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP A 180 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 241 through 242 removed outlier: 7.332A pdb=" N LYS A 166 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN A 360 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AB5, first strand: chain 'A' and resid 216 through 221 Processing sheet with id=AB6, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AB7, first strand: chain 'A' and resid 591 through 595 Processing sheet with id=AB8, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AB9, first strand: chain 'A' and resid 650 through 655 removed outlier: 3.660A pdb=" N ARG A 669 " --> pdb=" O TYR A 661 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU A 663 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 677 through 679 removed outlier: 3.862A pdb=" N GLY A 677 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 19 through 20 Processing sheet with id=AC3, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=AC4, first strand: chain 'M' and resid 33 through 35 Processing sheet with id=AC5, first strand: chain 'M' and resid 48 through 49 Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'I' and resid 46 through 51 removed outlier: 3.522A pdb=" N ARG I 38 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 69 through 72 Processing sheet with id=AC9, first strand: chain 'B' and resid 573 through 574 removed outlier: 6.890A pdb=" N ILE B 130 " --> pdb=" O GLY C 677 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 679 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARG B 132 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS B 373 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS B 157 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP B 379 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY B 151 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS B 373 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS B 157 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP B 379 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY B 151 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 186 through 197 removed outlier: 5.710A pdb=" N ILE B 188 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP B 180 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 241 through 242 removed outlier: 7.332A pdb=" N LYS B 166 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASN B 360 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 212 through 214 Processing sheet with id=AD6, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AD7, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AD8, first strand: chain 'B' and resid 591 through 595 Processing sheet with id=AD9, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AE1, first strand: chain 'B' and resid 650 through 655 removed outlier: 3.660A pdb=" N ARG B 669 " --> pdb=" O TYR B 661 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU B 663 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AE3, first strand: chain 'N' and resid 23 through 24 Processing sheet with id=AE4, first strand: chain 'N' and resid 33 through 35 Processing sheet with id=AE5, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'J' and resid 46 through 51 removed outlier: 3.523A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 69 through 72 Processing sheet with id=AE9, first strand: chain 'C' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS C 373 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS C 157 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP C 379 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY C 151 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS C 373 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS C 157 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP C 379 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY C 151 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 186 through 197 removed outlier: 5.710A pdb=" N ILE C 188 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP C 180 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 241 through 242 removed outlier: 7.333A pdb=" N LYS C 166 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN C 360 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 212 through 214 Processing sheet with id=AF5, first strand: chain 'C' and resid 216 through 221 Processing sheet with id=AF6, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AF7, first strand: chain 'C' and resid 591 through 595 Processing sheet with id=AF8, first strand: chain 'C' and resid 607 through 609 Processing sheet with id=AF9, first strand: chain 'C' and resid 650 through 655 removed outlier: 3.660A pdb=" N ARG C 669 " --> pdb=" O TYR C 661 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU C 663 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1806 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: 3.54 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6336 1.34 - 1.46: 4482 1.46 - 1.58: 9006 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 19980 Sorted by residual: bond pdb=" N GLU B 513 " pdb=" CA GLU B 513 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.01e+00 bond pdb=" N GLU C 513 " pdb=" CA GLU C 513 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.74e+00 bond pdb=" N GLU A 513 " pdb=" CA GLU A 513 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.66e+00 bond pdb=" N GLY B 127 " pdb=" CA GLY B 127 " ideal model delta sigma weight residual 1.449 1.469 -0.020 1.45e-02 4.76e+03 1.95e+00 bond pdb=" C LYS M 42 " pdb=" N ALA M 43 " ideal model delta sigma weight residual 1.339 1.262 0.077 5.57e-02 3.22e+02 1.91e+00 ... (remaining 19975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 25936 1.38 - 2.75: 1032 2.75 - 4.13: 143 4.13 - 5.50: 19 5.50 - 6.88: 11 Bond angle restraints: 27141 Sorted by residual: angle pdb=" N GLU B 513 " pdb=" CA GLU B 513 " pdb=" C GLU B 513 " ideal model delta sigma weight residual 111.36 107.65 3.71 1.09e+00 8.42e-01 1.16e+01 angle pdb=" N GLU C 513 " pdb=" CA GLU C 513 " pdb=" C GLU C 513 " ideal model delta sigma weight residual 111.36 107.71 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" N GLU A 513 " pdb=" CA GLU A 513 " pdb=" C GLU A 513 " ideal model delta sigma weight residual 111.36 107.71 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" C GLY M 99 " pdb=" N GLN M 100 " pdb=" CA GLN M 100 " ideal model delta sigma weight residual 120.95 125.56 -4.61 1.78e+00 3.16e-01 6.71e+00 angle pdb=" C GLY L 99 " pdb=" N GLN L 100 " pdb=" CA GLN L 100 " ideal model delta sigma weight residual 120.95 125.55 -4.60 1.78e+00 3.16e-01 6.67e+00 ... (remaining 27136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 10902 17.68 - 35.36: 861 35.36 - 53.04: 159 53.04 - 70.72: 24 70.72 - 88.40: 24 Dihedral angle restraints: 11970 sinusoidal: 4776 harmonic: 7194 Sorted by residual: dihedral pdb=" CB CYS C 369 " pdb=" SG CYS C 369 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual 93.00 149.03 -56.03 1 1.00e+01 1.00e-02 4.24e+01 dihedral pdb=" CB CYS A 369 " pdb=" SG CYS A 369 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CB CYS B 369 " pdb=" SG CYS B 369 " pdb=" SG CYS B 417 " pdb=" CB CYS B 417 " ideal model delta sinusoidal sigma weight residual 93.00 148.98 -55.98 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 11967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1758 0.033 - 0.067: 795 0.067 - 0.100: 327 0.100 - 0.133: 114 0.133 - 0.166: 21 Chirality restraints: 3015 Sorted by residual: chirality pdb=" CB ILE M 21 " pdb=" CA ILE M 21 " pdb=" CG1 ILE M 21 " pdb=" CG2 ILE M 21 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB ILE N 21 " pdb=" CA ILE N 21 " pdb=" CG1 ILE N 21 " pdb=" CG2 ILE N 21 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CB ILE L 21 " pdb=" CA ILE L 21 " pdb=" CG1 ILE L 21 " pdb=" CG2 ILE L 21 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 3012 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER M 7 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO M 8 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO M 8 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 8 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 7 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO N 8 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO N 8 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO N 8 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO L 8 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.035 5.00e-02 4.00e+02 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 391 2.68 - 3.23: 17672 3.23 - 3.79: 29466 3.79 - 4.34: 42589 4.34 - 4.90: 72040 Nonbonded interactions: 162158 Sorted by model distance: nonbonded pdb=" OD1 ASP N 82 " pdb=" OH TYR N 86 " model vdw 2.123 3.040 nonbonded pdb=" OD1 ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.123 3.040 nonbonded pdb=" OD1 ASP M 82 " pdb=" OH TYR M 86 " model vdw 2.123 3.040 nonbonded pdb=" O ILE N 21 " pdb=" NE2 GLN N 100 " model vdw 2.181 3.120 nonbonded pdb=" O ILE M 21 " pdb=" NE2 GLN M 100 " model vdw 2.182 3.120 ... (remaining 162153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.320 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 20001 Z= 0.251 Angle : 0.628 6.877 27183 Z= 0.354 Chirality : 0.047 0.166 3015 Planarity : 0.004 0.064 3480 Dihedral : 13.280 88.402 7287 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.36 (0.15), residues: 2430 helix: -0.38 (0.29), residues: 309 sheet: -2.56 (0.18), residues: 687 loop : -2.56 (0.13), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.020 0.002 TYR C 682 PHE 0.023 0.002 PHE C 165 TRP 0.015 0.001 TRP A 359 HIS 0.009 0.002 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00611 (19980) covalent geometry : angle 0.62710 (27141) SS BOND : bond 0.00312 ( 21) SS BOND : angle 0.96051 ( 42) hydrogen bonds : bond 0.19196 ( 620) hydrogen bonds : angle 9.47369 ( 1806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.815 Fit side-chains REVERT: A 120 TYR cc_start: 0.8336 (m-80) cc_final: 0.8010 (m-80) REVERT: A 236 GLN cc_start: 0.7497 (mt0) cc_final: 0.7206 (mt0) REVERT: A 270 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: A 291 ASP cc_start: 0.8009 (p0) cc_final: 0.7403 (p0) REVERT: A 416 GLN cc_start: 0.8021 (mp10) cc_final: 0.7231 (pm20) REVERT: A 504 ARG cc_start: 0.8162 (ptt180) cc_final: 0.7962 (ptt180) REVERT: A 516 MET cc_start: 0.8284 (mtp) cc_final: 0.7987 (mtm) REVERT: A 632 ASP cc_start: 0.7613 (m-30) cc_final: 0.7394 (m-30) REVERT: A 708 ASP cc_start: 0.7926 (t70) cc_final: 0.7352 (t0) REVERT: M 53 ILE cc_start: 0.8842 (mm) cc_final: 0.8538 (mp) REVERT: B 120 TYR cc_start: 0.8361 (m-80) cc_final: 0.8154 (m-80) REVERT: B 260 TYR cc_start: 0.8707 (t80) cc_final: 0.8395 (t80) REVERT: B 270 ARG cc_start: 0.7586 (mmm-85) cc_final: 0.7340 (mmm160) REVERT: B 339 ARG cc_start: 0.7797 (mtt-85) cc_final: 0.7568 (mtp85) REVERT: B 526 GLU cc_start: 0.7421 (tt0) cc_final: 0.7200 (tm-30) REVERT: B 599 MET cc_start: 0.8896 (mtp) cc_final: 0.8615 (mtm) REVERT: B 632 ASP cc_start: 0.7577 (m-30) cc_final: 0.7274 (m-30) REVERT: B 708 ASP cc_start: 0.7850 (t70) cc_final: 0.7360 (t0) REVERT: B 716 GLU cc_start: 0.7795 (tp30) cc_final: 0.7453 (tp30) REVERT: N 53 ILE cc_start: 0.8793 (mm) cc_final: 0.8577 (mp) REVERT: J 100 ILE cc_start: 0.8767 (mt) cc_final: 0.8535 (mm) REVERT: C 291 ASP cc_start: 0.8043 (p0) cc_final: 0.7628 (p0) REVERT: C 416 GLN cc_start: 0.7822 (mp10) cc_final: 0.7226 (pm20) REVERT: C 516 MET cc_start: 0.8280 (mtp) cc_final: 0.7907 (mtp) REVERT: C 666 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7277 (mtp-110) REVERT: C 708 ASP cc_start: 0.8045 (t70) cc_final: 0.7472 (t0) outliers start: 0 outliers final: 1 residues processed: 307 average time/residue: 0.6184 time to fit residues: 213.0318 Evaluate side-chains 229 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 696 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 4.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN L 90 GLN A 223 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 628 GLN M 79 GLN M 90 GLN B 147 ASN B 223 ASN B 543 GLN B 597 ASN B 628 GLN N 79 GLN N 89 GLN N 90 GLN C 147 ASN C 223 ASN ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 648 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.181021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144739 restraints weight = 20481.380| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.89 r_work: 0.3443 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20001 Z= 0.179 Angle : 0.584 6.682 27183 Z= 0.316 Chirality : 0.046 0.192 3015 Planarity : 0.005 0.061 3480 Dihedral : 5.006 35.067 2742 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.13 % Allowed : 11.06 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.16), residues: 2430 helix: 0.98 (0.31), residues: 309 sheet: -2.13 (0.18), residues: 717 loop : -1.97 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 699 TYR 0.013 0.002 TYR A 652 PHE 0.022 0.002 PHE A 165 TRP 0.011 0.001 TRP A 359 HIS 0.006 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00426 (19980) covalent geometry : angle 0.58313 (27141) SS BOND : bond 0.00416 ( 21) SS BOND : angle 0.86391 ( 42) hydrogen bonds : bond 0.04353 ( 620) hydrogen bonds : angle 6.47130 ( 1806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 92 LYS cc_start: 0.7597 (tttm) cc_final: 0.7372 (ttpt) REVERT: H 60 TYR cc_start: 0.7296 (m-80) cc_final: 0.7012 (m-80) REVERT: A 120 TYR cc_start: 0.8680 (m-80) cc_final: 0.8345 (m-80) REVERT: A 291 ASP cc_start: 0.8564 (p0) cc_final: 0.8171 (p0) REVERT: A 416 GLN cc_start: 0.8111 (mp10) cc_final: 0.7236 (pm20) REVERT: A 504 ARG cc_start: 0.8145 (ptt180) cc_final: 0.7927 (ptt180) REVERT: A 582 SER cc_start: 0.8845 (t) cc_final: 0.8596 (p) REVERT: A 708 ASP cc_start: 0.8347 (t70) cc_final: 0.7733 (t0) REVERT: M 53 ILE cc_start: 0.8855 (mm) cc_final: 0.8526 (mp) REVERT: M 70 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5966 (tp30) REVERT: I 120 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: B 120 TYR cc_start: 0.8655 (m-80) cc_final: 0.8434 (m-80) REVERT: B 260 TYR cc_start: 0.8888 (t80) cc_final: 0.8528 (t80) REVERT: B 291 ASP cc_start: 0.8544 (p0) cc_final: 0.8073 (p0) REVERT: B 526 GLU cc_start: 0.8424 (tt0) cc_final: 0.8175 (tm-30) REVERT: B 554 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8070 (t80) REVERT: B 599 MET cc_start: 0.8958 (mtp) cc_final: 0.8640 (mtm) REVERT: B 632 ASP cc_start: 0.7907 (m-30) cc_final: 0.7567 (m-30) REVERT: B 694 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: B 708 ASP cc_start: 0.8288 (t70) cc_final: 0.7739 (t0) REVERT: N 53 ILE cc_start: 0.8809 (mm) cc_final: 0.8560 (mp) REVERT: N 70 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5847 (tp30) REVERT: J 52 MET cc_start: 0.6783 (mtp) cc_final: 0.6541 (mtp) REVERT: J 120 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: C 225 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8219 (tppt) REVERT: C 238 MET cc_start: 0.8322 (mmm) cc_final: 0.7984 (mmm) REVERT: C 291 ASP cc_start: 0.8509 (p0) cc_final: 0.8253 (p0) REVERT: C 416 GLN cc_start: 0.7806 (mp10) cc_final: 0.7171 (pm20) REVERT: C 439 VAL cc_start: 0.8096 (p) cc_final: 0.7883 (m) REVERT: C 513 GLU cc_start: 0.7801 (mp0) cc_final: 0.7573 (mp0) REVERT: C 516 MET cc_start: 0.8993 (mtp) cc_final: 0.8653 (mtp) REVERT: C 554 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8158 (t80) REVERT: C 666 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7830 (mtp-110) REVERT: C 708 ASP cc_start: 0.8497 (t70) cc_final: 0.7916 (t0) outliers start: 46 outliers final: 18 residues processed: 285 average time/residue: 0.6536 time to fit residues: 209.1664 Evaluate side-chains 258 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 206 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN A 411 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN B 411 GLN B 568 GLN N 89 GLN C 543 GLN C 648 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144829 restraints weight = 20524.358| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.87 r_work: 0.3450 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20001 Z= 0.167 Angle : 0.555 6.629 27183 Z= 0.300 Chirality : 0.045 0.189 3015 Planarity : 0.004 0.062 3480 Dihedral : 4.846 34.392 2739 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.92 % Allowed : 12.87 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.16), residues: 2430 helix: 1.39 (0.32), residues: 309 sheet: -1.89 (0.18), residues: 723 loop : -1.71 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 285 TYR 0.016 0.001 TYR A 430 PHE 0.020 0.001 PHE A 165 TRP 0.010 0.001 TRP A 359 HIS 0.005 0.001 HIS C 649 Details of bonding type rmsd covalent geometry : bond 0.00397 (19980) covalent geometry : angle 0.55279 (27141) SS BOND : bond 0.00410 ( 21) SS BOND : angle 1.37624 ( 42) hydrogen bonds : bond 0.04116 ( 620) hydrogen bonds : angle 6.02681 ( 1806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 257 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5831 (tp30) REVERT: L 92 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7235 (ttpt) REVERT: H 60 TYR cc_start: 0.7332 (m-80) cc_final: 0.7048 (m-80) REVERT: H 93 MET cc_start: 0.7947 (ttm) cc_final: 0.7577 (ttt) REVERT: A 291 ASP cc_start: 0.8532 (p0) cc_final: 0.8136 (p0) REVERT: A 322 MET cc_start: 0.8924 (mmm) cc_final: 0.8580 (mmm) REVERT: A 416 GLN cc_start: 0.8019 (mp10) cc_final: 0.7177 (pm20) REVERT: A 504 ARG cc_start: 0.8144 (ptt180) cc_final: 0.7814 (ptt180) REVERT: A 554 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8233 (t80) REVERT: A 582 SER cc_start: 0.8864 (t) cc_final: 0.8640 (p) REVERT: A 708 ASP cc_start: 0.8343 (t70) cc_final: 0.7750 (t0) REVERT: M 53 ILE cc_start: 0.8870 (mm) cc_final: 0.8564 (mp) REVERT: B 260 TYR cc_start: 0.8847 (t80) cc_final: 0.8532 (t80) REVERT: B 291 ASP cc_start: 0.8585 (p0) cc_final: 0.8141 (p0) REVERT: B 439 VAL cc_start: 0.8198 (p) cc_final: 0.7962 (m) REVERT: B 554 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 583 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8022 (m-40) REVERT: B 599 MET cc_start: 0.8921 (mtp) cc_final: 0.8647 (mtm) REVERT: B 632 ASP cc_start: 0.7888 (m-30) cc_final: 0.7536 (m-30) REVERT: B 708 ASP cc_start: 0.8309 (t70) cc_final: 0.7747 (t0) REVERT: N 47 MET cc_start: 0.7943 (mmm) cc_final: 0.7650 (tpt) REVERT: J 52 MET cc_start: 0.6905 (mtp) cc_final: 0.6697 (mtp) REVERT: C 225 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8242 (tptt) REVERT: C 238 MET cc_start: 0.8295 (mmm) cc_final: 0.8006 (mmm) REVERT: C 291 ASP cc_start: 0.8446 (p0) cc_final: 0.8162 (p0) REVERT: C 339 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7596 (mtt-85) REVERT: C 416 GLN cc_start: 0.7816 (mp10) cc_final: 0.7249 (pm20) REVERT: C 513 GLU cc_start: 0.7760 (mp0) cc_final: 0.7362 (mp0) REVERT: C 516 MET cc_start: 0.8996 (mtp) cc_final: 0.8649 (mtp) REVERT: C 554 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8160 (t80) REVERT: C 666 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7822 (mtp-110) REVERT: C 708 ASP cc_start: 0.8443 (t70) cc_final: 0.7837 (t0) outliers start: 63 outliers final: 31 residues processed: 296 average time/residue: 0.6048 time to fit residues: 202.6260 Evaluate side-chains 274 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 92 LYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN H 120 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN J 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.180255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141902 restraints weight = 20694.913| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.80 r_work: 0.3475 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20001 Z= 0.158 Angle : 0.538 5.941 27183 Z= 0.292 Chirality : 0.045 0.194 3015 Planarity : 0.004 0.060 3480 Dihedral : 4.782 33.962 2739 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.12 % Allowed : 13.29 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.16), residues: 2430 helix: 1.56 (0.32), residues: 309 sheet: -1.60 (0.19), residues: 705 loop : -1.53 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 569 TYR 0.015 0.001 TYR I 95 PHE 0.019 0.001 PHE A 165 TRP 0.011 0.001 TRP A 359 HIS 0.005 0.001 HIS A 649 Details of bonding type rmsd covalent geometry : bond 0.00375 (19980) covalent geometry : angle 0.53639 (27141) SS BOND : bond 0.00399 ( 21) SS BOND : angle 1.15591 ( 42) hydrogen bonds : bond 0.03940 ( 620) hydrogen bonds : angle 5.81013 ( 1806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 238 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5677 (tp30) REVERT: H 60 TYR cc_start: 0.7338 (m-80) cc_final: 0.7063 (m-80) REVERT: H 120 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: A 291 ASP cc_start: 0.8485 (p0) cc_final: 0.8054 (p0) REVERT: A 322 MET cc_start: 0.8851 (mmm) cc_final: 0.8527 (mmm) REVERT: A 416 GLN cc_start: 0.7999 (mp10) cc_final: 0.7263 (pm20) REVERT: A 504 ARG cc_start: 0.8085 (ptt180) cc_final: 0.7802 (ptt180) REVERT: A 554 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8198 (t80) REVERT: A 582 SER cc_start: 0.8757 (t) cc_final: 0.8513 (p) REVERT: A 583 ASN cc_start: 0.8529 (m-40) cc_final: 0.8296 (m110) REVERT: A 708 ASP cc_start: 0.8301 (t70) cc_final: 0.7612 (t0) REVERT: M 53 ILE cc_start: 0.8839 (mm) cc_final: 0.8538 (mp) REVERT: M 70 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5946 (tp30) REVERT: M 82 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: B 260 TYR cc_start: 0.8766 (t80) cc_final: 0.8467 (t80) REVERT: B 291 ASP cc_start: 0.8577 (p0) cc_final: 0.8167 (p0) REVERT: B 439 VAL cc_start: 0.8157 (p) cc_final: 0.7946 (m) REVERT: B 513 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: B 554 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8061 (t80) REVERT: B 599 MET cc_start: 0.8891 (mtp) cc_final: 0.8613 (mtm) REVERT: B 632 ASP cc_start: 0.7817 (m-30) cc_final: 0.7461 (m-30) REVERT: B 694 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: B 708 ASP cc_start: 0.8197 (t70) cc_final: 0.7651 (t0) REVERT: N 47 MET cc_start: 0.7858 (mmm) cc_final: 0.7583 (tpt) REVERT: N 70 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.5912 (tp30) REVERT: N 82 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: C 139 CYS cc_start: 0.4990 (OUTLIER) cc_final: 0.4184 (t) REVERT: C 225 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8207 (tptt) REVERT: C 238 MET cc_start: 0.8258 (mmm) cc_final: 0.7958 (mmm) REVERT: C 291 ASP cc_start: 0.8377 (p0) cc_final: 0.8095 (p0) REVERT: C 406 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: C 416 GLN cc_start: 0.7749 (mp10) cc_final: 0.6973 (pm20) REVERT: C 513 GLU cc_start: 0.7640 (mp0) cc_final: 0.7221 (mp0) REVERT: C 554 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8156 (t80) REVERT: C 666 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7738 (mtp-110) REVERT: C 708 ASP cc_start: 0.8402 (t70) cc_final: 0.7858 (t0) outliers start: 89 outliers final: 46 residues processed: 295 average time/residue: 0.5884 time to fit residues: 196.4247 Evaluate side-chains 286 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 115 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 206 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN C 388 ASN C 411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142601 restraints weight = 20682.181| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.77 r_work: 0.3490 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20001 Z= 0.127 Angle : 0.519 9.265 27183 Z= 0.284 Chirality : 0.044 0.198 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.608 32.405 2739 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.43 % Allowed : 14.35 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2430 helix: 1.35 (0.32), residues: 327 sheet: -1.47 (0.18), residues: 750 loop : -1.36 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 699 TYR 0.015 0.001 TYR I 95 PHE 0.016 0.001 PHE A 165 TRP 0.010 0.001 TRP A 359 HIS 0.004 0.001 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00293 (19980) covalent geometry : angle 0.51606 (27141) SS BOND : bond 0.00573 ( 21) SS BOND : angle 1.55015 ( 42) hydrogen bonds : bond 0.03777 ( 620) hydrogen bonds : angle 5.56761 ( 1806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 245 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5633 (tp30) REVERT: H 60 TYR cc_start: 0.7388 (m-80) cc_final: 0.7073 (m-80) REVERT: H 93 MET cc_start: 0.7843 (ttm) cc_final: 0.7511 (ttt) REVERT: A 291 ASP cc_start: 0.8412 (p0) cc_final: 0.8030 (p0) REVERT: A 322 MET cc_start: 0.8863 (mmm) cc_final: 0.8533 (mmm) REVERT: A 406 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7036 (mm-30) REVERT: A 416 GLN cc_start: 0.7620 (mp10) cc_final: 0.7078 (pm20) REVERT: A 504 ARG cc_start: 0.8096 (ptt180) cc_final: 0.7830 (ptt180) REVERT: A 554 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 582 SER cc_start: 0.8763 (t) cc_final: 0.8512 (p) REVERT: A 583 ASN cc_start: 0.8519 (m-40) cc_final: 0.8291 (m110) REVERT: A 708 ASP cc_start: 0.8307 (t70) cc_final: 0.7705 (t0) REVERT: M 53 ILE cc_start: 0.8805 (mm) cc_final: 0.8511 (mp) REVERT: M 70 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5853 (tp30) REVERT: M 82 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: M 89 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: B 291 ASP cc_start: 0.8500 (p0) cc_final: 0.8025 (p0) REVERT: B 416 GLN cc_start: 0.7838 (mp10) cc_final: 0.7300 (pm20) REVERT: B 417 CYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6789 (p) REVERT: B 439 VAL cc_start: 0.8146 (p) cc_final: 0.7937 (m) REVERT: B 513 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: B 554 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8042 (t80) REVERT: B 618 SER cc_start: 0.8213 (m) cc_final: 0.8004 (p) REVERT: B 666 ARG cc_start: 0.8296 (mtp-110) cc_final: 0.7940 (mtp85) REVERT: B 708 ASP cc_start: 0.8158 (t70) cc_final: 0.7611 (t0) REVERT: N 47 MET cc_start: 0.7820 (mmm) cc_final: 0.7565 (tpt) REVERT: N 70 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5792 (tp30) REVERT: N 82 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: J 81 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6320 (tmm) REVERT: J 93 MET cc_start: 0.7555 (ttp) cc_final: 0.7019 (ttt) REVERT: C 238 MET cc_start: 0.8230 (mmm) cc_final: 0.7947 (mmm) REVERT: C 291 ASP cc_start: 0.8317 (p0) cc_final: 0.7953 (p0) REVERT: C 339 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7389 (mtt-85) REVERT: C 406 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6782 (mm-30) REVERT: C 416 GLN cc_start: 0.7725 (mp10) cc_final: 0.6969 (pm20) REVERT: C 513 GLU cc_start: 0.7618 (mp0) cc_final: 0.7099 (mp0) REVERT: C 554 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8104 (t80) REVERT: C 678 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8475 (ttp) REVERT: C 708 ASP cc_start: 0.8360 (t70) cc_final: 0.7809 (t0) outliers start: 74 outliers final: 32 residues processed: 293 average time/residue: 0.5681 time to fit residues: 188.1177 Evaluate side-chains 282 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 194 optimal weight: 0.0070 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 126 optimal weight: 0.3980 chunk 115 optimal weight: 0.2980 chunk 189 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.185118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147005 restraints weight = 20668.588| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.69 r_work: 0.3512 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20001 Z= 0.113 Angle : 0.507 10.536 27183 Z= 0.274 Chirality : 0.044 0.205 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.495 31.704 2739 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.47 % Allowed : 15.09 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 2430 helix: 1.44 (0.32), residues: 327 sheet: -1.25 (0.19), residues: 753 loop : -1.22 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 38 TYR 0.013 0.001 TYR I 95 PHE 0.014 0.001 PHE A 165 TRP 0.014 0.001 TRP C 539 HIS 0.004 0.001 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00259 (19980) covalent geometry : angle 0.50439 (27141) SS BOND : bond 0.00344 ( 21) SS BOND : angle 1.41122 ( 42) hydrogen bonds : bond 0.03502 ( 620) hydrogen bonds : angle 5.39055 ( 1806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5642 (tp30) REVERT: H 60 TYR cc_start: 0.7426 (m-80) cc_final: 0.7178 (m-80) REVERT: H 93 MET cc_start: 0.7868 (ttm) cc_final: 0.7505 (ttt) REVERT: A 225 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8454 (mtpt) REVERT: A 291 ASP cc_start: 0.8361 (p0) cc_final: 0.7981 (p0) REVERT: A 322 MET cc_start: 0.8920 (mmm) cc_final: 0.8586 (mmm) REVERT: A 406 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6895 (mm-30) REVERT: A 416 GLN cc_start: 0.8030 (mp10) cc_final: 0.7450 (pm20) REVERT: A 420 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: A 504 ARG cc_start: 0.8053 (ptt180) cc_final: 0.7802 (ptt180) REVERT: A 554 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8069 (t80) REVERT: A 582 SER cc_start: 0.8769 (t) cc_final: 0.8550 (p) REVERT: A 583 ASN cc_start: 0.8484 (m-40) cc_final: 0.8250 (m110) REVERT: A 694 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: A 708 ASP cc_start: 0.8304 (t70) cc_final: 0.7737 (t0) REVERT: M 70 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5763 (tp30) REVERT: M 82 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: M 89 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: B 389 PHE cc_start: 0.8445 (m-80) cc_final: 0.8222 (m-10) REVERT: B 416 GLN cc_start: 0.7613 (mp10) cc_final: 0.7323 (pm20) REVERT: B 417 CYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6740 (p) REVERT: B 554 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8013 (t80) REVERT: B 599 MET cc_start: 0.8318 (mtp) cc_final: 0.8043 (mtm) REVERT: B 666 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7985 (mtp85) REVERT: B 694 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: B 708 ASP cc_start: 0.8093 (t70) cc_final: 0.7549 (t0) REVERT: N 47 MET cc_start: 0.7826 (mmm) cc_final: 0.7560 (tpt) REVERT: N 70 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5769 (tp30) REVERT: N 82 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: J 81 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6354 (tmm) REVERT: J 93 MET cc_start: 0.7472 (ttp) cc_final: 0.7268 (ttt) REVERT: C 238 MET cc_start: 0.8320 (mmm) cc_final: 0.8107 (mmm) REVERT: C 339 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7337 (mtt-85) REVERT: C 388 ASN cc_start: 0.8117 (m-40) cc_final: 0.7877 (m110) REVERT: C 406 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: C 416 GLN cc_start: 0.7816 (mp10) cc_final: 0.7262 (pm20) REVERT: C 420 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7138 (tp30) REVERT: C 513 GLU cc_start: 0.7543 (mp0) cc_final: 0.7231 (mp0) REVERT: C 554 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8068 (t80) REVERT: C 582 SER cc_start: 0.8970 (t) cc_final: 0.8651 (p) REVERT: C 678 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8569 (ttp) REVERT: C 708 ASP cc_start: 0.8375 (t70) cc_final: 0.7806 (t0) outliers start: 75 outliers final: 39 residues processed: 290 average time/residue: 0.5753 time to fit residues: 188.6916 Evaluate side-chains 289 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 230 optimal weight: 0.1980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN M 90 GLN N 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.180189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142202 restraints weight = 21097.346| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.65 r_work: 0.3490 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 20001 Z= 0.262 Angle : 0.631 15.365 27183 Z= 0.334 Chirality : 0.048 0.191 3015 Planarity : 0.005 0.059 3480 Dihedral : 5.060 38.123 2739 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.26 % Allowed : 15.09 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.17), residues: 2430 helix: 1.49 (0.32), residues: 309 sheet: -1.26 (0.19), residues: 717 loop : -1.23 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 547 TYR 0.018 0.002 TYR I 95 PHE 0.025 0.002 PHE C 165 TRP 0.011 0.002 TRP B 359 HIS 0.006 0.001 HIS C 649 Details of bonding type rmsd covalent geometry : bond 0.00637 (19980) covalent geometry : angle 0.62411 (27141) SS BOND : bond 0.00516 ( 21) SS BOND : angle 2.36800 ( 42) hydrogen bonds : bond 0.04568 ( 620) hydrogen bonds : angle 5.85948 ( 1806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 237 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5673 (tp30) REVERT: H 60 TYR cc_start: 0.7376 (m-80) cc_final: 0.7111 (m-80) REVERT: H 93 MET cc_start: 0.7916 (ttm) cc_final: 0.7595 (ttm) REVERT: A 416 GLN cc_start: 0.8016 (mp10) cc_final: 0.7337 (pm20) REVERT: A 504 ARG cc_start: 0.8114 (ptt180) cc_final: 0.7816 (ptt180) REVERT: A 554 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8196 (t80) REVERT: A 582 SER cc_start: 0.8768 (t) cc_final: 0.8545 (p) REVERT: A 694 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: A 708 ASP cc_start: 0.8311 (t70) cc_final: 0.7756 (t0) REVERT: M 53 ILE cc_start: 0.8883 (mm) cc_final: 0.8511 (mp) REVERT: M 70 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5879 (tp30) REVERT: M 82 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: B 389 PHE cc_start: 0.8595 (m-80) cc_final: 0.8333 (m-10) REVERT: B 416 GLN cc_start: 0.7751 (mp10) cc_final: 0.7257 (pm20) REVERT: B 554 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 582 SER cc_start: 0.8902 (t) cc_final: 0.8688 (p) REVERT: B 599 MET cc_start: 0.8678 (mtp) cc_final: 0.8394 (mtm) REVERT: B 708 ASP cc_start: 0.8158 (t70) cc_final: 0.7606 (t0) REVERT: N 47 MET cc_start: 0.7898 (mmm) cc_final: 0.7583 (tpt) REVERT: N 53 ILE cc_start: 0.8679 (mm) cc_final: 0.8292 (mt) REVERT: N 70 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.5826 (tp30) REVERT: N 82 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: J 81 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6452 (tmm) REVERT: C 238 MET cc_start: 0.8385 (mmm) cc_final: 0.8044 (mmm) REVERT: C 291 ASP cc_start: 0.8487 (p0) cc_final: 0.8145 (p0) REVERT: C 389 PHE cc_start: 0.8617 (m-80) cc_final: 0.8380 (m-10) REVERT: C 416 GLN cc_start: 0.7747 (mp10) cc_final: 0.7292 (pm20) REVERT: C 420 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: C 513 GLU cc_start: 0.7730 (mp0) cc_final: 0.7322 (mp0) REVERT: C 554 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8201 (t80) REVERT: C 582 SER cc_start: 0.8900 (t) cc_final: 0.8558 (p) REVERT: C 708 ASP cc_start: 0.8448 (t70) cc_final: 0.7920 (t0) outliers start: 92 outliers final: 46 residues processed: 303 average time/residue: 0.5644 time to fit residues: 193.5687 Evaluate side-chains 286 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 55 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 0.0980 chunk 188 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.183310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147435 restraints weight = 20727.933| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.98 r_work: 0.3451 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20001 Z= 0.149 Angle : 0.553 14.355 27183 Z= 0.295 Chirality : 0.045 0.209 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.773 32.920 2739 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.38 % Allowed : 16.44 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2430 helix: 1.27 (0.31), residues: 327 sheet: -1.18 (0.19), residues: 759 loop : -1.17 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 547 TYR 0.016 0.001 TYR I 60 PHE 0.019 0.001 PHE A 165 TRP 0.013 0.001 TRP B 539 HIS 0.004 0.001 HIS C 649 Details of bonding type rmsd covalent geometry : bond 0.00352 (19980) covalent geometry : angle 0.54764 (27141) SS BOND : bond 0.00396 ( 21) SS BOND : angle 2.08932 ( 42) hydrogen bonds : bond 0.03855 ( 620) hydrogen bonds : angle 5.55086 ( 1806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5704 (tp30) REVERT: H 60 TYR cc_start: 0.7402 (m-80) cc_final: 0.7172 (m-80) REVERT: H 93 MET cc_start: 0.7890 (ttm) cc_final: 0.7640 (ttm) REVERT: A 416 GLN cc_start: 0.8069 (mp10) cc_final: 0.7411 (pm20) REVERT: A 504 ARG cc_start: 0.8098 (ptt180) cc_final: 0.7862 (ptt180) REVERT: A 554 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8209 (t80) REVERT: A 582 SER cc_start: 0.8814 (t) cc_final: 0.8613 (p) REVERT: A 583 ASN cc_start: 0.8587 (m-40) cc_final: 0.8344 (m110) REVERT: A 708 ASP cc_start: 0.8366 (t70) cc_final: 0.7811 (t0) REVERT: M 70 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5851 (tp30) REVERT: M 82 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: M 89 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: I 93 MET cc_start: 0.7870 (ttm) cc_final: 0.7648 (tmm) REVERT: B 389 PHE cc_start: 0.8574 (m-80) cc_final: 0.8292 (m-10) REVERT: B 554 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8053 (t80) REVERT: B 599 MET cc_start: 0.8569 (mtp) cc_final: 0.8251 (mtm) REVERT: B 618 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7989 (p) REVERT: B 708 ASP cc_start: 0.8186 (t70) cc_final: 0.7609 (t0) REVERT: N 47 MET cc_start: 0.7866 (mmm) cc_final: 0.7575 (tpt) REVERT: N 70 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5872 (tp30) REVERT: N 82 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: J 81 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6211 (tmm) REVERT: J 93 MET cc_start: 0.7708 (ttp) cc_final: 0.7372 (ttt) REVERT: C 238 MET cc_start: 0.8461 (mmm) cc_final: 0.8192 (mmm) REVERT: C 389 PHE cc_start: 0.8594 (m-80) cc_final: 0.8368 (m-10) REVERT: C 406 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: C 416 GLN cc_start: 0.7794 (mp10) cc_final: 0.7295 (pm20) REVERT: C 420 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7409 (tp30) REVERT: C 513 GLU cc_start: 0.7706 (mp0) cc_final: 0.7311 (mp0) REVERT: C 554 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8212 (t80) REVERT: C 582 SER cc_start: 0.8943 (t) cc_final: 0.8670 (p) REVERT: C 678 MET cc_start: 0.8957 (ttm) cc_final: 0.8591 (ttp) REVERT: C 708 ASP cc_start: 0.8469 (t70) cc_final: 0.7913 (t0) outliers start: 73 outliers final: 42 residues processed: 296 average time/residue: 0.5597 time to fit residues: 188.4674 Evaluate side-chains 287 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 223 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.0020 chunk 86 optimal weight: 2.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.182839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146103 restraints weight = 20605.205| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.00 r_work: 0.3454 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20001 Z= 0.151 Angle : 0.555 14.957 27183 Z= 0.294 Chirality : 0.045 0.232 3015 Planarity : 0.004 0.057 3480 Dihedral : 4.748 33.501 2739 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.96 % Allowed : 17.27 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.17), residues: 2430 helix: 1.32 (0.32), residues: 327 sheet: -1.12 (0.19), residues: 759 loop : -1.12 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 569 TYR 0.019 0.001 TYR B 667 PHE 0.019 0.001 PHE A 165 TRP 0.014 0.001 TRP J 36 HIS 0.004 0.001 HIS C 649 Details of bonding type rmsd covalent geometry : bond 0.00358 (19980) covalent geometry : angle 0.55197 (27141) SS BOND : bond 0.00400 ( 21) SS BOND : angle 1.66949 ( 42) hydrogen bonds : bond 0.03864 ( 620) hydrogen bonds : angle 5.54073 ( 1806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5716 (tp30) REVERT: H 60 TYR cc_start: 0.7424 (m-80) cc_final: 0.7158 (m-80) REVERT: H 93 MET cc_start: 0.7882 (ttm) cc_final: 0.7627 (ttm) REVERT: A 416 GLN cc_start: 0.8022 (mp10) cc_final: 0.7301 (pm20) REVERT: A 420 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: A 504 ARG cc_start: 0.8071 (ptt180) cc_final: 0.7790 (ptt180) REVERT: A 554 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8209 (t80) REVERT: A 582 SER cc_start: 0.8717 (t) cc_final: 0.8501 (p) REVERT: A 583 ASN cc_start: 0.8580 (m-40) cc_final: 0.8331 (m110) REVERT: A 708 ASP cc_start: 0.8354 (t70) cc_final: 0.7738 (t0) REVERT: M 70 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5810 (tp30) REVERT: M 82 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: M 89 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: I 93 MET cc_start: 0.7839 (ttm) cc_final: 0.7596 (tmm) REVERT: B 389 PHE cc_start: 0.8560 (m-80) cc_final: 0.8274 (m-10) REVERT: B 554 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8083 (t80) REVERT: B 568 GLN cc_start: 0.8258 (tt0) cc_final: 0.8009 (pp30) REVERT: B 599 MET cc_start: 0.8606 (mtp) cc_final: 0.8287 (mtm) REVERT: B 618 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 708 ASP cc_start: 0.8178 (t70) cc_final: 0.7673 (t0) REVERT: N 47 MET cc_start: 0.7947 (mmm) cc_final: 0.7696 (tpt) REVERT: N 70 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.5864 (tp30) REVERT: N 82 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: J 81 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6244 (tmm) REVERT: J 93 MET cc_start: 0.7673 (ttp) cc_final: 0.7464 (ttt) REVERT: C 238 MET cc_start: 0.8438 (mmm) cc_final: 0.8172 (mmm) REVERT: C 389 PHE cc_start: 0.8546 (m-80) cc_final: 0.8338 (m-10) REVERT: C 416 GLN cc_start: 0.7763 (mp10) cc_final: 0.7286 (pm20) REVERT: C 420 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: C 513 GLU cc_start: 0.7714 (mp0) cc_final: 0.7376 (mp0) REVERT: C 554 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8152 (t80) REVERT: C 582 SER cc_start: 0.8932 (t) cc_final: 0.8664 (p) REVERT: C 708 ASP cc_start: 0.8444 (t70) cc_final: 0.7882 (t0) outliers start: 64 outliers final: 43 residues processed: 282 average time/residue: 0.5737 time to fit residues: 183.9847 Evaluate side-chains 283 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 167 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 152 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.181828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145720 restraints weight = 20837.069| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.10 r_work: 0.3434 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20001 Z= 0.194 Angle : 0.598 15.798 27183 Z= 0.313 Chirality : 0.046 0.228 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.919 35.482 2739 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.92 % Allowed : 17.36 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.17), residues: 2430 helix: 1.20 (0.31), residues: 327 sheet: -1.17 (0.18), residues: 780 loop : -1.19 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 547 TYR 0.023 0.002 TYR B 667 PHE 0.022 0.002 PHE B 165 TRP 0.015 0.001 TRP J 36 HIS 0.005 0.001 HIS C 649 Details of bonding type rmsd covalent geometry : bond 0.00468 (19980) covalent geometry : angle 0.59417 (27141) SS BOND : bond 0.00454 ( 21) SS BOND : angle 1.77434 ( 42) hydrogen bonds : bond 0.04167 ( 620) hydrogen bonds : angle 5.69623 ( 1806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 236 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5769 (tp30) REVERT: H 60 TYR cc_start: 0.7421 (m-80) cc_final: 0.7173 (m-80) REVERT: H 93 MET cc_start: 0.7931 (ttm) cc_final: 0.7660 (ttm) REVERT: A 416 GLN cc_start: 0.8098 (mp10) cc_final: 0.7453 (pm20) REVERT: A 420 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: A 504 ARG cc_start: 0.8112 (ptt180) cc_final: 0.7867 (ptt180) REVERT: A 554 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8214 (t80) REVERT: A 582 SER cc_start: 0.8724 (t) cc_final: 0.8510 (p) REVERT: A 583 ASN cc_start: 0.8591 (m-40) cc_final: 0.8347 (m110) REVERT: A 708 ASP cc_start: 0.8382 (t70) cc_final: 0.7848 (t0) REVERT: M 70 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.5867 (tp30) REVERT: M 82 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: I 93 MET cc_start: 0.7855 (ttm) cc_final: 0.7604 (tmm) REVERT: B 389 PHE cc_start: 0.8595 (m-80) cc_final: 0.8309 (m-10) REVERT: B 554 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8098 (t80) REVERT: B 568 GLN cc_start: 0.8282 (tt0) cc_final: 0.7981 (pp30) REVERT: B 599 MET cc_start: 0.8707 (mtp) cc_final: 0.8401 (mtm) REVERT: B 618 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7987 (p) REVERT: B 708 ASP cc_start: 0.8217 (t70) cc_final: 0.7723 (t0) REVERT: N 47 MET cc_start: 0.7904 (mmm) cc_final: 0.7640 (tpt) REVERT: N 70 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.5823 (tp30) REVERT: N 82 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: J 81 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6292 (tmm) REVERT: J 93 MET cc_start: 0.7651 (ttp) cc_final: 0.7447 (ttt) REVERT: C 238 MET cc_start: 0.8462 (mmm) cc_final: 0.8174 (mmm) REVERT: C 291 ASP cc_start: 0.8448 (p0) cc_final: 0.8117 (p0) REVERT: C 389 PHE cc_start: 0.8584 (m-80) cc_final: 0.8365 (m-10) REVERT: C 416 GLN cc_start: 0.7762 (mp10) cc_final: 0.7269 (pm20) REVERT: C 420 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: C 513 GLU cc_start: 0.7822 (mp0) cc_final: 0.7427 (mp0) REVERT: C 554 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8209 (t80) REVERT: C 582 SER cc_start: 0.8929 (t) cc_final: 0.8660 (p) REVERT: C 708 ASP cc_start: 0.8507 (t70) cc_final: 0.7992 (t0) outliers start: 63 outliers final: 42 residues processed: 282 average time/residue: 0.5788 time to fit residues: 185.7915 Evaluate side-chains 284 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 56 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 0.0670 chunk 110 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.181866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143380 restraints weight = 20832.306| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.77 r_work: 0.3468 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20001 Z= 0.182 Angle : 0.586 15.950 27183 Z= 0.308 Chirality : 0.046 0.232 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.903 34.696 2739 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.19 % Allowed : 17.22 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.17), residues: 2430 helix: 1.16 (0.31), residues: 327 sheet: -1.15 (0.18), residues: 780 loop : -1.17 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.023 0.002 TYR B 667 PHE 0.021 0.002 PHE B 165 TRP 0.015 0.001 TRP J 36 HIS 0.005 0.001 HIS C 649 Details of bonding type rmsd covalent geometry : bond 0.00437 (19980) covalent geometry : angle 0.58000 (27141) SS BOND : bond 0.00437 ( 21) SS BOND : angle 2.14764 ( 42) hydrogen bonds : bond 0.04065 ( 620) hydrogen bonds : angle 5.63712 ( 1806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7642.02 seconds wall clock time: 130 minutes 37.68 seconds (7837.68 seconds total)