Starting phenix.real_space_refine on Thu Feb 5 06:23:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mti_48610/02_2026/9mti_48610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mti_48610/02_2026/9mti_48610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mti_48610/02_2026/9mti_48610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mti_48610/02_2026/9mti_48610.map" model { file = "/net/cci-nas-00/data/ceres_data/9mti_48610/02_2026/9mti_48610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mti_48610/02_2026/9mti_48610.cif" } resolution = 2.98 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 9565 2.51 5 N 2686 2.21 5 O 2954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15274 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3873 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 489, 3849 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 469} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 489, 3849 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 469} Chain breaks: 1 bond proxies already assigned to first conformer: 3902 Chain: "B" Number of atoms: 3870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 489, 3846 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 489, 3846 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3899 Chain: "C" Number of atoms: 3865 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 489, 3849 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 469} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 489, 3849 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 469} Chain breaks: 1 bond proxies already assigned to first conformer: 3911 Chain: "H" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 486 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 633 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "J" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 707 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 86} Chain breaks: 2 Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 707 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 2 Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 701 Classifications: {'peptide': 92} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 85} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N ASER A 227 " occ=0.78 ... (10 atoms not shown) pdb=" OG BSER A 227 " occ=0.22 residue: pdb=" N AGLY A 228 " occ=0.78 ... (6 atoms not shown) pdb=" O BGLY A 228 " occ=0.22 residue: pdb=" N AMET A 260 " occ=0.28 ... (14 atoms not shown) pdb=" CE BMET A 260 " occ=0.72 residue: pdb=" N ASER A 369 " occ=0.82 ... (10 atoms not shown) pdb=" OG BSER A 369 " occ=0.18 residue: pdb=" N ASER B 227 " occ=0.69 ... (10 atoms not shown) pdb=" OG BSER B 227 " occ=0.31 residue: pdb=" N AGLY B 228 " occ=0.69 ... (6 atoms not shown) pdb=" O BGLY B 228 " occ=0.31 residue: pdb=" N AMET B 260 " occ=0.47 ... (14 atoms not shown) pdb=" CE BMET B 260 " occ=0.53 residue: pdb=" N ASER B 369 " occ=0.89 ... (10 atoms not shown) pdb=" OG BSER B 369 " occ=0.11 residue: pdb=" N ASER C 227 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER C 227 " occ=0.44 residue: pdb=" N AGLY C 228 " occ=0.56 ... (6 atoms not shown) pdb=" O BGLY C 228 " occ=0.44 residue: pdb=" N ASER C 369 " occ=0.88 ... (10 atoms not shown) pdb=" OG BSER C 369 " occ=0.12 Time building chain proxies: 5.68, per 1000 atoms: 0.37 Number of scatterers: 15274 At special positions: 0 Unit cell: (117.438, 122.728, 147.062, 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 69 16.00 O 2954 8.00 N 2686 7.00 C 9565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.06 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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: 1.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 47 sheets defined 20.8% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.873A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.814A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.632A pdb=" N THR A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 490 removed outlier: 3.896A pdb=" N ILE A 490 " --> pdb=" O ASP A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.504A pdb=" N ARG B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 456 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 385 Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 487 through 490 removed outlier: 3.983A pdb=" N ILE C 490 " --> pdb=" O ASP C 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 490' Processing helix chain 'C' and resid 491 through 501 Processing helix chain 'H' and resid 52A through 54 removed outlier: 3.541A pdb=" N TYR H 53 " --> pdb=" O SER H 52A" (cutoff:3.500A) Processing helix chain 'I' and resid 52A through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.603A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.854A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.043A pdb=" N VAL A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 256 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 134 removed outlier: 3.794A pdb=" N ASN A 133 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TRP A 153 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.613A pdb=" N GLY A 146 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.427A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.701A pdb=" N LYS A 391 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 366 removed outlier: 4.701A pdb=" N TYR B 351 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.630A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 53 " --> pdb=" O CYS B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.631A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 120 through 122 removed outlier: 6.670A pdb=" N GLY B 256 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 120 through 122 removed outlier: 6.670A pdb=" N GLY B 256 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'B' and resid 136 through 141 removed outlier: 3.631A pdb=" N GLY B 146 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA B 138 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N ALA B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.519A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.602A pdb=" N LYS B 391 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 365 Processing sheet with id=AC7, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.668A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AD3, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.615A pdb=" N GLY C 256 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.615A pdb=" N GLY C 256 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'C' and resid 136 through 141 removed outlier: 3.637A pdb=" N GLY C 146 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA C 138 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N ALA C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.686A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AD9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.518A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.518A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 58 through 59 removed outlier: 4.224A pdb=" N GLY I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.564A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 10 removed outlier: 6.596A pdb=" N SER L 20 " --> pdb=" O LEU L 9 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.737A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.737A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 45 through 49 removed outlier: 6.610A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 45 through 49 removed outlier: 6.610A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.639A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5108 1.35 - 1.47: 3910 1.47 - 1.60: 6504 1.60 - 1.72: 0 1.72 - 1.85: 92 Bond restraints: 15614 Sorted by residual: bond pdb=" CA ALA C 19 " pdb=" CB ALA C 19 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.64e-02 3.72e+03 1.12e+01 bond pdb=" CA PHE I 67 " pdb=" C PHE I 67 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.42e-02 4.96e+03 1.01e+01 bond pdb=" N GLY M 106 " pdb=" CA GLY M 106 " ideal model delta sigma weight residual 1.446 1.477 -0.031 9.70e-03 1.06e+04 1.00e+01 bond pdb=" N ILE C 437 " pdb=" CA ILE C 437 " ideal model delta sigma weight residual 1.463 1.494 -0.031 1.14e-02 7.69e+03 7.51e+00 bond pdb=" N VAL A 202 " pdb=" CA VAL A 202 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.36e+00 ... (remaining 15609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 20648 1.74 - 3.49: 456 3.49 - 5.23: 71 5.23 - 6.98: 11 6.98 - 8.72: 5 Bond angle restraints: 21191 Sorted by residual: angle pdb=" CA GLY M 106 " pdb=" C GLY M 106 " pdb=" O GLY M 106 " ideal model delta sigma weight residual 122.22 117.87 4.35 6.50e-01 2.37e+00 4.48e+01 angle pdb=" N GLN A 191 " pdb=" CA GLN A 191 " pdb=" CB GLN A 191 " ideal model delta sigma weight residual 110.01 118.34 -8.33 1.45e+00 4.76e-01 3.30e+01 angle pdb=" CA HIS A 75 " pdb=" C HIS A 75 " pdb=" O HIS A 75 " ideal model delta sigma weight residual 120.51 112.33 8.18 1.43e+00 4.89e-01 3.27e+01 angle pdb=" N GLN B 189 " pdb=" CA GLN B 189 " pdb=" C GLN B 189 " ideal model delta sigma weight residual 111.28 105.98 5.30 1.09e+00 8.42e-01 2.36e+01 angle pdb=" CA ASP A 73 " pdb=" CB ASP A 73 " pdb=" CG ASP A 73 " ideal model delta sigma weight residual 112.60 117.09 -4.49 1.00e+00 1.00e+00 2.01e+01 ... (remaining 21186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7875 17.96 - 35.92: 982 35.92 - 53.87: 321 53.87 - 71.83: 84 71.83 - 89.79: 29 Dihedral angle restraints: 9291 sinusoidal: 3659 harmonic: 5632 Sorted by residual: dihedral pdb=" CB CYS B 64 " pdb=" SG CYS B 64 " pdb=" SG CYS B 76 " pdb=" CB CYS B 76 " ideal model delta sinusoidal sigma weight residual -86.00 -174.77 88.77 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -169.99 83.99 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CD ARG A 321 " pdb=" NE ARG A 321 " pdb=" CZ ARG A 321 " pdb=" NH1 ARG A 321 " ideal model delta sinusoidal sigma weight residual 0.00 -62.27 62.27 1 1.00e+01 1.00e-02 5.13e+01 ... (remaining 9288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1742 0.043 - 0.087: 388 0.087 - 0.130: 155 0.130 - 0.173: 7 0.173 - 0.216: 6 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA GLN A 189 " pdb=" N GLN A 189 " pdb=" C GLN A 189 " pdb=" CB GLN A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE C 437 " pdb=" N ILE C 437 " pdb=" C ILE C 437 " pdb=" CB ILE C 437 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA LEU C 439 " pdb=" N LEU C 439 " pdb=" C LEU C 439 " pdb=" CB LEU C 439 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2295 not shown) Planarity restraints: 2774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " 0.969 9.50e-02 1.11e+02 4.34e-01 1.14e+02 pdb=" NE ARG A 321 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 405 " -0.715 9.50e-02 1.11e+02 3.21e-01 6.27e+01 pdb=" NE ARG A 405 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 405 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 405 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 405 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 383 " -0.520 9.50e-02 1.11e+02 2.33e-01 3.33e+01 pdb=" NE ARG C 383 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG C 383 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 383 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 383 " -0.018 2.00e-02 2.50e+03 ... (remaining 2771 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2310 2.76 - 3.30: 13356 3.30 - 3.83: 25750 3.83 - 4.37: 30137 4.37 - 4.90: 53568 Nonbonded interactions: 125121 Sorted by model distance: nonbonded pdb=" OG SER L 25 " pdb=" O GLN L 27 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR B 283 " pdb=" O GLY B 286 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR N 7 " pdb=" OG SER N 22 " model vdw 2.244 3.040 nonbonded pdb=" O ASN B 96 " pdb=" ND2 ASN B 96 " model vdw 2.264 3.120 nonbonded pdb=" OG1 THR A 283 " pdb=" O GLY A 286 " model vdw 2.272 3.040 ... (remaining 125116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 226 or resid 229 through 259 or re \ sid 261 through 368 or resid 370 through 502)) selection = (chain 'B' and (resid 11 through 226 or resid 229 through 259 or resid 261 throu \ gh 368 or resid 370 through 502)) selection = (chain 'C' and (resid 11 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 226 or resid 229 through 259 or re \ sid 261 through 368 or resid 370 through 502)) } ncs_group { reference = (chain 'H' and (resid 32 through 49 or resid 52B through 65 or resid 85 through \ 109)) selection = chain 'M' } ncs_group { reference = (chain 'J' and (resid 3 through 11 or resid 19 through 104)) selection = (chain 'L' and (resid 3 through 11 or resid 19 through 104)) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.900 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.003 0.060 15636 Z= 0.188 Angle : 0.622 8.722 21235 Z= 0.378 Chirality : 0.043 0.216 2298 Planarity : 0.012 0.434 2774 Dihedral : 18.456 89.790 5631 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.39 % Rotamer: Outliers : 2.07 % Allowed : 30.94 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1936 helix: 2.74 (0.26), residues: 363 sheet: 0.01 (0.23), residues: 476 loop : -1.26 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 61 TYR 0.012 0.001 TYR A 105 PHE 0.018 0.001 PHE B 500 TRP 0.013 0.001 TRP B 222 HIS 0.007 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00329 (15614) covalent geometry : angle 0.61933 (21191) SS BOND : bond 0.00591 ( 22) SS BOND : angle 1.47659 ( 44) hydrogen bonds : bond 0.13746 ( 619) hydrogen bonds : angle 6.75422 ( 1765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 340 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 14 CYS cc_start: 0.6886 (m) cc_final: 0.6521 (m) REVERT: A 191 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.6936 (tt0) REVERT: B 188 ASN cc_start: 0.7885 (m-40) cc_final: 0.7682 (m110) REVERT: B 238 LYS cc_start: 0.7945 (mmtp) cc_final: 0.7710 (mmtt) REVERT: C 331 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8519 (mp) REVERT: J 98 PHE cc_start: 0.8783 (m-80) cc_final: 0.8465 (m-80) outliers start: 30 outliers final: 20 residues processed: 363 average time/residue: 0.6117 time to fit residues: 243.1128 Evaluate side-chains 354 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 105 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN B 80 GLN B 226 GLN B 248 ASN B 407 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 18 HIS ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106046 restraints weight = 93827.069| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.22 r_work: 0.3035 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 15636 Z= 0.310 Angle : 0.649 11.797 21235 Z= 0.338 Chirality : 0.046 0.179 2298 Planarity : 0.006 0.053 2774 Dihedral : 5.439 49.362 2173 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.03 % Favored : 94.87 % Rotamer: Outliers : 4.32 % Allowed : 26.67 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1936 helix: 2.66 (0.25), residues: 363 sheet: 0.07 (0.23), residues: 482 loop : -1.38 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 62 TYR 0.035 0.002 TYR B 195 PHE 0.018 0.002 PHE A 467 TRP 0.015 0.002 TRP B 222 HIS 0.011 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00736 (15614) covalent geometry : angle 0.64456 (21191) SS BOND : bond 0.00615 ( 22) SS BOND : angle 1.77055 ( 44) hydrogen bonds : bond 0.05078 ( 619) hydrogen bonds : angle 5.12609 ( 1765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 VAL cc_start: 0.8630 (m) cc_final: 0.8378 (t) REVERT: C 193 ASN cc_start: 0.8153 (t0) cc_final: 0.7886 (t0) REVERT: C 266 SER cc_start: 0.8948 (p) cc_final: 0.8606 (m) REVERT: C 356 GLN cc_start: 0.8328 (tt0) cc_final: 0.8116 (tt0) REVERT: C 408 ASP cc_start: 0.7398 (m-30) cc_final: 0.7054 (m-30) REVERT: J 30 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8113 (mtpp) REVERT: J 98 PHE cc_start: 0.8795 (m-80) cc_final: 0.8324 (m-80) REVERT: L 73 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7210 (tt) outliers start: 67 outliers final: 37 residues processed: 391 average time/residue: 0.6634 time to fit residues: 284.1658 Evaluate side-chains 377 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 338 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 186 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 159 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 190 optimal weight: 0.0170 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 0.2980 chunk 161 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 248 ASN B 80 GLN B 137 ASN B 226 GLN B 407 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 248 ASN C 250 ASN C 356 GLN C 454 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104931 restraints weight = 81873.911| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.07 r_work: 0.3057 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15636 Z= 0.112 Angle : 0.525 10.010 21235 Z= 0.274 Chirality : 0.041 0.231 2298 Planarity : 0.005 0.053 2774 Dihedral : 4.377 40.681 2151 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 3.17 % Allowed : 28.32 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 1936 helix: 3.11 (0.25), residues: 363 sheet: 0.11 (0.23), residues: 499 loop : -1.24 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.024 0.001 TYR B 195 PHE 0.015 0.001 PHE B 353 TRP 0.013 0.001 TRP B 222 HIS 0.010 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00265 (15614) covalent geometry : angle 0.52163 (21191) SS BOND : bond 0.00347 ( 22) SS BOND : angle 1.46693 ( 44) hydrogen bonds : bond 0.03984 ( 619) hydrogen bonds : angle 4.66292 ( 1765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.7454 (p0) cc_final: 0.7171 (p0) REVERT: A 328 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8025 (p) REVERT: B 259 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8313 (mmmm) REVERT: B 415 ASP cc_start: 0.7693 (t0) cc_final: 0.7228 (t0) REVERT: B 497 ASN cc_start: 0.8208 (t0) cc_final: 0.7985 (t0) REVERT: B 498 ASN cc_start: 0.8160 (m-40) cc_final: 0.7931 (m110) REVERT: C 20 VAL cc_start: 0.8610 (m) cc_final: 0.8338 (t) REVERT: C 193 ASN cc_start: 0.8157 (t0) cc_final: 0.7849 (t0) REVERT: C 266 SER cc_start: 0.8896 (p) cc_final: 0.8564 (m) REVERT: C 408 ASP cc_start: 0.7396 (m-30) cc_final: 0.7056 (m-30) REVERT: J 30 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: J 98 PHE cc_start: 0.8837 (m-80) cc_final: 0.8346 (m-80) REVERT: M 38 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7239 (ttp-170) REVERT: N 33 LEU cc_start: 0.8400 (tt) cc_final: 0.8158 (tt) outliers start: 48 outliers final: 30 residues processed: 375 average time/residue: 0.6904 time to fit residues: 282.6112 Evaluate side-chains 371 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 338 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 157 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 250 ASN B 80 GLN B 226 GLN B 248 ASN B 407 GLN B 454 GLN C 250 ASN C 424 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105105 restraints weight = 93615.327| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.04 r_work: 0.2981 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 15636 Z= 0.369 Angle : 0.699 11.936 21235 Z= 0.363 Chirality : 0.049 0.354 2298 Planarity : 0.006 0.059 2774 Dihedral : 5.061 49.764 2149 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 4.99 % Allowed : 26.55 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 1936 helix: 2.74 (0.25), residues: 363 sheet: 0.12 (0.24), residues: 478 loop : -1.40 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 57 TYR 0.029 0.003 TYR B 195 PHE 0.019 0.003 PHE C 79 TRP 0.015 0.002 TRP A 234 HIS 0.010 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00878 (15614) covalent geometry : angle 0.68661 (21191) SS BOND : bond 0.00763 ( 22) SS BOND : angle 2.98228 ( 44) hydrogen bonds : bond 0.05190 ( 619) hydrogen bonds : angle 5.08549 ( 1765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 334 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7822 (mtt-85) cc_final: 0.7599 (mtt-85) REVERT: A 268 MET cc_start: 0.8389 (ttm) cc_final: 0.8176 (ttp) REVERT: A 479 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6128 (tm-30) REVERT: B 380 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7316 (ttmm) REVERT: B 408 ASP cc_start: 0.7366 (m-30) cc_final: 0.7027 (m-30) REVERT: B 443 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: B 498 ASN cc_start: 0.8219 (m-40) cc_final: 0.7973 (m-40) REVERT: C 20 VAL cc_start: 0.8555 (m) cc_final: 0.8328 (t) REVERT: C 70 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7951 (tt) REVERT: C 193 ASN cc_start: 0.8200 (t0) cc_final: 0.7973 (t160) REVERT: C 266 SER cc_start: 0.8981 (p) cc_final: 0.8574 (m) REVERT: C 408 ASP cc_start: 0.7390 (m-30) cc_final: 0.6937 (m-30) REVERT: C 414 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7595 (tp30) REVERT: J 30 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8113 (mtpp) outliers start: 78 outliers final: 53 residues processed: 385 average time/residue: 0.6194 time to fit residues: 261.9959 Evaluate side-chains 379 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 321 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 44 optimal weight: 0.0270 chunk 150 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 154 optimal weight: 0.0000 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 189 GLN A 248 ASN B 80 GLN B 137 ASN B 226 GLN B 248 ASN B 407 GLN C 18 HIS C 248 ASN C 250 ASN C 356 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108231 restraints weight = 95828.066| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 4.28 r_work: 0.3037 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15636 Z= 0.126 Angle : 0.553 12.975 21235 Z= 0.288 Chirality : 0.042 0.298 2298 Planarity : 0.005 0.059 2774 Dihedral : 4.498 48.175 2149 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 3.59 % Allowed : 28.32 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1936 helix: 3.13 (0.25), residues: 363 sheet: 0.16 (0.23), residues: 498 loop : -1.31 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 383 TYR 0.023 0.001 TYR B 195 PHE 0.016 0.001 PHE B 353 TRP 0.014 0.001 TRP B 222 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00300 (15614) covalent geometry : angle 0.54503 (21191) SS BOND : bond 0.00552 ( 22) SS BOND : angle 2.07614 ( 44) hydrogen bonds : bond 0.03980 ( 619) hydrogen bonds : angle 4.64993 ( 1765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 330 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8403 (mtm-85) REVERT: B 415 ASP cc_start: 0.7767 (t0) cc_final: 0.7263 (t0) REVERT: B 497 ASN cc_start: 0.8249 (t0) cc_final: 0.7990 (t0) REVERT: B 498 ASN cc_start: 0.8238 (m-40) cc_final: 0.7963 (m110) REVERT: C 15 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8068 (mp) REVERT: C 20 VAL cc_start: 0.8618 (m) cc_final: 0.8353 (t) REVERT: C 266 SER cc_start: 0.8931 (p) cc_final: 0.8555 (m) REVERT: C 356 GLN cc_start: 0.8338 (tt0) cc_final: 0.8134 (tt0) REVERT: C 408 ASP cc_start: 0.7417 (m-30) cc_final: 0.7050 (m-30) REVERT: C 414 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7603 (tp30) REVERT: J 30 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: L 7 THR cc_start: 0.7830 (m) cc_final: 0.7400 (p) REVERT: N 33 LEU cc_start: 0.8442 (tt) cc_final: 0.8189 (tp) outliers start: 55 outliers final: 37 residues processed: 364 average time/residue: 0.6810 time to fit residues: 271.4017 Evaluate side-chains 363 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 324 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 130 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 80 GLN B 137 ASN B 226 GLN B 407 GLN C 250 ASN C 424 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105255 restraints weight = 87268.627| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.05 r_work: 0.2986 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 15636 Z= 0.299 Angle : 0.668 12.376 21235 Z= 0.347 Chirality : 0.048 0.390 2298 Planarity : 0.006 0.061 2774 Dihedral : 4.946 54.044 2149 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.87 % Favored : 94.08 % Rotamer: Outliers : 4.26 % Allowed : 27.65 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 1936 helix: 2.85 (0.25), residues: 363 sheet: 0.21 (0.24), residues: 481 loop : -1.48 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 383 TYR 0.029 0.002 TYR B 195 PHE 0.020 0.002 PHE C 332 TRP 0.018 0.002 TRP A 234 HIS 0.009 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00713 (15614) covalent geometry : angle 0.65512 (21191) SS BOND : bond 0.00776 ( 22) SS BOND : angle 2.98606 ( 44) hydrogen bonds : bond 0.04813 ( 619) hydrogen bonds : angle 4.92627 ( 1765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 332 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8451 (ttm) cc_final: 0.8231 (ttp) REVERT: A 382 ASN cc_start: 0.8171 (m110) cc_final: 0.7816 (m-40) REVERT: A 479 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: B 408 ASP cc_start: 0.7476 (m-30) cc_final: 0.7092 (m-30) REVERT: B 415 ASP cc_start: 0.7814 (t0) cc_final: 0.7324 (t0) REVERT: B 461 ASP cc_start: 0.7911 (t0) cc_final: 0.7703 (t0) REVERT: B 498 ASN cc_start: 0.8255 (m-40) cc_final: 0.7959 (m-40) REVERT: C 20 VAL cc_start: 0.8619 (m) cc_final: 0.8381 (t) REVERT: C 70 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7988 (tt) REVERT: C 266 SER cc_start: 0.8967 (p) cc_final: 0.8586 (m) REVERT: C 408 ASP cc_start: 0.7425 (m-30) cc_final: 0.6871 (m-30) REVERT: C 414 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7642 (tp30) REVERT: J 30 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8109 (mtpp) outliers start: 65 outliers final: 48 residues processed: 377 average time/residue: 0.6815 time to fit residues: 280.8092 Evaluate side-chains 378 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 327 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 190 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 454 GLN B 80 GLN B 137 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 248 ASN B 407 GLN C 248 ASN C 250 ASN C 356 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107866 restraints weight = 91277.636| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 4.32 r_work: 0.3031 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15636 Z= 0.139 Angle : 0.565 11.378 21235 Z= 0.295 Chirality : 0.043 0.276 2298 Planarity : 0.005 0.061 2774 Dihedral : 4.548 53.474 2149 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 3.90 % Allowed : 27.77 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1936 helix: 3.13 (0.25), residues: 363 sheet: 0.23 (0.23), residues: 502 loop : -1.39 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 383 TYR 0.026 0.001 TYR B 195 PHE 0.014 0.001 PHE B 353 TRP 0.014 0.001 TRP B 222 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00333 (15614) covalent geometry : angle 0.55783 (21191) SS BOND : bond 0.00558 ( 22) SS BOND : angle 2.06384 ( 44) hydrogen bonds : bond 0.04035 ( 619) hydrogen bonds : angle 4.66332 ( 1765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8415 (ttm) cc_final: 0.8197 (ttp) REVERT: A 382 ASN cc_start: 0.8112 (m110) cc_final: 0.7762 (m-40) REVERT: A 479 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6355 (tm-30) REVERT: B 415 ASP cc_start: 0.7773 (t0) cc_final: 0.7314 (t0) REVERT: B 497 ASN cc_start: 0.8288 (t0) cc_final: 0.8041 (t0) REVERT: B 498 ASN cc_start: 0.8245 (m-40) cc_final: 0.7954 (m110) REVERT: C 15 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7912 (mp) REVERT: C 20 VAL cc_start: 0.8623 (m) cc_final: 0.8364 (t) REVERT: C 266 SER cc_start: 0.8931 (p) cc_final: 0.8548 (m) REVERT: C 408 ASP cc_start: 0.7445 (m-30) cc_final: 0.7072 (m-30) REVERT: C 414 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7636 (tp30) REVERT: J 30 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8020 (mtpp) REVERT: L 7 THR cc_start: 0.7810 (m) cc_final: 0.7378 (p) REVERT: N 30 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7679 (mtpp) REVERT: N 33 LEU cc_start: 0.8408 (tt) cc_final: 0.8175 (tp) outliers start: 59 outliers final: 40 residues processed: 368 average time/residue: 0.6711 time to fit residues: 270.2852 Evaluate side-chains 370 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 165 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 47 optimal weight: 0.0000 chunk 98 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN B 137 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN C 250 ASN C 356 GLN C 424 ASN N 27DHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104711 restraints weight = 90895.029| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.41 r_work: 0.3056 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15636 Z= 0.128 Angle : 0.559 10.597 21235 Z= 0.289 Chirality : 0.042 0.237 2298 Planarity : 0.005 0.062 2774 Dihedral : 4.419 54.575 2149 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 3.41 % Allowed : 28.50 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.19), residues: 1936 helix: 3.23 (0.25), residues: 363 sheet: 0.25 (0.23), residues: 502 loop : -1.36 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 383 TYR 0.026 0.001 TYR B 195 PHE 0.014 0.001 PHE B 500 TRP 0.014 0.001 TRP B 222 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00307 (15614) covalent geometry : angle 0.55318 (21191) SS BOND : bond 0.00508 ( 22) SS BOND : angle 1.81192 ( 44) hydrogen bonds : bond 0.03909 ( 619) hydrogen bonds : angle 4.58562 ( 1765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 327 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8395 (ttm) cc_final: 0.8186 (ttp) REVERT: A 382 ASN cc_start: 0.8103 (m110) cc_final: 0.7741 (m-40) REVERT: B 415 ASP cc_start: 0.7737 (t0) cc_final: 0.7355 (t0) REVERT: B 497 ASN cc_start: 0.8291 (t0) cc_final: 0.8039 (t0) REVERT: B 498 ASN cc_start: 0.8219 (m-40) cc_final: 0.7940 (m110) REVERT: C 20 VAL cc_start: 0.8544 (m) cc_final: 0.8285 (t) REVERT: C 266 SER cc_start: 0.8919 (p) cc_final: 0.8548 (m) REVERT: C 408 ASP cc_start: 0.7481 (m-30) cc_final: 0.7113 (m-30) REVERT: C 414 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7593 (tp30) REVERT: J 30 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7977 (mtpp) REVERT: L 7 THR cc_start: 0.7812 (m) cc_final: 0.7387 (p) REVERT: N 33 LEU cc_start: 0.8409 (tt) cc_final: 0.8178 (tp) outliers start: 51 outliers final: 40 residues processed: 360 average time/residue: 0.7010 time to fit residues: 275.4473 Evaluate side-chains 374 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 27 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 158 optimal weight: 0.4980 chunk 120 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 80 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN C 250 ASN C 356 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107820 restraints weight = 90466.381| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.31 r_work: 0.2994 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15636 Z= 0.160 Angle : 0.577 10.555 21235 Z= 0.299 Chirality : 0.043 0.260 2298 Planarity : 0.005 0.065 2774 Dihedral : 4.530 56.637 2149 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 3.29 % Allowed : 28.50 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1936 helix: 3.05 (0.25), residues: 366 sheet: 0.23 (0.23), residues: 502 loop : -1.36 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 383 TYR 0.029 0.002 TYR B 195 PHE 0.020 0.002 PHE B 500 TRP 0.015 0.001 TRP A 234 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00384 (15614) covalent geometry : angle 0.57041 (21191) SS BOND : bond 0.00565 ( 22) SS BOND : angle 2.00153 ( 44) hydrogen bonds : bond 0.04100 ( 619) hydrogen bonds : angle 4.63293 ( 1765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 323 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8425 (ttm) cc_final: 0.8212 (ttp) REVERT: A 382 ASN cc_start: 0.8062 (m110) cc_final: 0.7700 (m-40) REVERT: B 380 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7222 (ttmm) REVERT: B 415 ASP cc_start: 0.7729 (t0) cc_final: 0.7342 (t0) REVERT: B 461 ASP cc_start: 0.7913 (t0) cc_final: 0.7686 (t0) REVERT: B 497 ASN cc_start: 0.8300 (t0) cc_final: 0.8053 (t0) REVERT: B 498 ASN cc_start: 0.8225 (m-40) cc_final: 0.7941 (m110) REVERT: C 20 VAL cc_start: 0.8501 (m) cc_final: 0.8266 (t) REVERT: C 266 SER cc_start: 0.8943 (p) cc_final: 0.8547 (m) REVERT: C 408 ASP cc_start: 0.7473 (m-30) cc_final: 0.7086 (m-30) REVERT: C 414 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7618 (tp30) REVERT: C 457 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6961 (tm-30) REVERT: L 7 THR cc_start: 0.7787 (m) cc_final: 0.7351 (p) REVERT: N 33 LEU cc_start: 0.8403 (tt) cc_final: 0.8173 (tp) outliers start: 49 outliers final: 43 residues processed: 356 average time/residue: 0.6922 time to fit residues: 269.4231 Evaluate side-chains 366 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 322 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 95 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 80 GLN B 137 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN C 22 ASN C 250 ASN C 356 GLN C 424 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108938 restraints weight = 88323.268| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 4.11 r_work: 0.3061 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15636 Z= 0.139 Angle : 0.560 10.271 21235 Z= 0.291 Chirality : 0.043 0.243 2298 Planarity : 0.005 0.067 2774 Dihedral : 4.466 58.155 2149 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 2.86 % Allowed : 28.87 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 1936 helix: 3.15 (0.25), residues: 363 sheet: 0.26 (0.23), residues: 502 loop : -1.34 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 383 TYR 0.030 0.001 TYR B 195 PHE 0.022 0.001 PHE B 500 TRP 0.015 0.001 TRP A 234 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00332 (15614) covalent geometry : angle 0.55435 (21191) SS BOND : bond 0.00523 ( 22) SS BOND : angle 1.85649 ( 44) hydrogen bonds : bond 0.03975 ( 619) hydrogen bonds : angle 4.60479 ( 1765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7470 (mmt-90) REVERT: A 101 ASP cc_start: 0.7618 (p0) cc_final: 0.7372 (p0) REVERT: A 201 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.8014 (ttp-110) REVERT: A 361 THR cc_start: 0.8491 (p) cc_final: 0.8265 (m) REVERT: A 382 ASN cc_start: 0.8079 (m110) cc_final: 0.7721 (m-40) REVERT: A 439 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8035 (pp) REVERT: B 268 MET cc_start: 0.8749 (ttm) cc_final: 0.8488 (ttp) REVERT: B 380 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7282 (ttmm) REVERT: B 461 ASP cc_start: 0.7837 (t0) cc_final: 0.7630 (t0) REVERT: B 497 ASN cc_start: 0.8316 (t0) cc_final: 0.8054 (t0) REVERT: B 498 ASN cc_start: 0.8198 (m-40) cc_final: 0.7894 (m110) REVERT: C 266 SER cc_start: 0.8898 (p) cc_final: 0.8534 (m) REVERT: C 368 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8097 (ttmm) REVERT: C 408 ASP cc_start: 0.7441 (m-30) cc_final: 0.7067 (m-30) REVERT: C 414 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7560 (tp30) REVERT: L 7 THR cc_start: 0.7798 (m) cc_final: 0.7387 (p) REVERT: N 33 LEU cc_start: 0.8392 (tt) cc_final: 0.8154 (tp) outliers start: 42 outliers final: 40 residues processed: 349 average time/residue: 0.6924 time to fit residues: 264.2950 Evaluate side-chains 362 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 8 optimal weight: 0.0470 chunk 174 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 117 optimal weight: 0.0040 overall best weight: 0.3490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN C 250 ASN C 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105017 restraints weight = 100348.883| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.68 r_work: 0.3053 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15636 Z= 0.113 Angle : 0.549 9.847 21235 Z= 0.285 Chirality : 0.042 0.272 2298 Planarity : 0.005 0.067 2774 Dihedral : 4.352 59.222 2148 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.68 % Allowed : 29.29 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1936 helix: 3.24 (0.25), residues: 360 sheet: 0.31 (0.23), residues: 492 loop : -1.30 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 383 TYR 0.014 0.001 TYR J 49 PHE 0.024 0.001 PHE B 500 TRP 0.013 0.001 TRP B 222 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00269 (15614) covalent geometry : angle 0.54421 (21191) SS BOND : bond 0.00461 ( 22) SS BOND : angle 1.62721 ( 44) hydrogen bonds : bond 0.03806 ( 619) hydrogen bonds : angle 4.55630 ( 1765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6345.32 seconds wall clock time: 108 minutes 57.87 seconds (6537.87 seconds total)