Starting phenix.real_space_refine on Thu Sep 18 14:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwe_47241/09_2025/9dwe_47241_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwe_47241/09_2025/9dwe_47241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dwe_47241/09_2025/9dwe_47241_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwe_47241/09_2025/9dwe_47241_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwe_47241/09_2025/9dwe_47241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwe_47241/09_2025/9dwe_47241.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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: 5 Type Number sf(0) Gaussians S 90 5.16 5 C 10899 2.51 5 N 2970 2.21 5 O 3438 1.98 5 H 3 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17400 Number of models: 1 Model: "" Number of chains: 15 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3987 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "M" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3984 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "N" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3984 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N SER H 17 " occ=0.59 ... (4 atoms not shown) pdb=" OG SER H 17 " occ=0.59 residue: pdb=" N SER H 24 " occ=0.85 ... (4 atoms not shown) pdb=" OG SER H 24 " occ=0.85 residue: pdb=" N SER I 17 " occ=0.56 ... (4 atoms not shown) pdb=" OG SER I 17 " occ=0.56 residue: pdb=" N SER I 24 " occ=0.79 ... (4 atoms not shown) pdb=" OG SER I 24 " occ=0.79 residue: pdb=" N SER J 17 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER J 17 " occ=0.54 residue: pdb=" N SER J 24 " occ=0.83 ... (4 atoms not shown) pdb=" OG SER J 24 " occ=0.83 Time building chain proxies: 4.59, per 1000 atoms: 0.26 Number of scatterers: 17400 At special positions: 0 Unit cell: (134.125, 129.05, 146.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 O 3438 8.00 N 2970 7.00 C 10899 6.00 H 3 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.02 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 476 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.02 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.02 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 312 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 487 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA2-3 " GAL D 1 " - " SIA D 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL E 1 " - " SIA E 2 " " GAL P 1 " - " SIA P 2 " NAG-ASN " NAG A 601 " - " ASN A 21 " " NAG A 602 " - " ASN A 33 " " NAG A 603 " - " ASN A 175 " " NAG A 604 " - " ASN A 296 " " NAG A 605 " - " ASN A 493 " " NAG B 601 " - " ASN B 21 " " NAG B 602 " - " ASN B 33 " " NAG B 603 " - " ASN B 175 " " NAG B 604 " - " ASN B 296 " " NAG B 605 " - " ASN B 493 " " NAG C 601 " - " ASN C 21 " " NAG C 602 " - " ASN C 33 " " NAG C 603 " - " ASN C 175 " " NAG C 604 " - " ASN C 296 " " NAG C 605 " - " ASN C 493 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 664.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 54 sheets defined 20.5% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 74 through 81 removed outlier: 4.009A pdb=" N ASP A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU A 79 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 376 through 398 removed outlier: 3.590A pdb=" N MET A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 466 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 497 through 513 removed outlier: 4.019A pdb=" N TYR A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.933A pdb=" N ASP B 78 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B 79 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.694A pdb=" N TRP B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 376 through 398 removed outlier: 3.646A pdb=" N MET B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 466 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 513 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.677A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.012A pdb=" N ASP C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU C 79 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 81 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.660A pdb=" N TRP C 132 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 376 through 398 removed outlier: 3.601A pdb=" N MET C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 466 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 497 through 513 removed outlier: 3.988A pdb=" N TYR C 501 " --> pdb=" O ASP C 497 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU C 503 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU C 504 " --> pdb=" O GLN C 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.651A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.651A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.527A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 375 removed outlier: 3.965A pdb=" N ASN A 367 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 362 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.880A pdb=" N LEU A 51 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS A 284 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.585A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 89 " --> pdb=" O MET A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.480A pdb=" N SER A 104 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TRP A 240 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS A 120 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 269 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 118 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.480A pdb=" N SER A 104 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TRP A 240 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU A 185 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AB7, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.631A pdb=" N CYS A 145 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AB9, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.018A pdb=" N CYS A 288 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.660A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.660A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.618A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.533A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 370 through 375 removed outlier: 3.504A pdb=" N GLY B 362 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.860A pdb=" N LEU B 51 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYS B 284 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.606A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 89 " --> pdb=" O MET B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.528A pdb=" N SER B 104 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TRP B 240 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU B 185 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR B 262 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS B 120 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS B 269 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 118 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.528A pdb=" N SER B 104 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TRP B 240 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU B 185 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 135 through 136 Processing sheet with id=AD7, first strand: chain 'B' and resid 142 through 147 removed outlier: 4.644A pdb=" N CYS B 145 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 170 through 175 Processing sheet with id=AD9, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AE1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.641A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.641A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.623A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.524A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 372 through 375 removed outlier: 3.518A pdb=" N GLY C 362 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AF1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AF2, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.867A pdb=" N LEU C 51 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS C 284 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.595A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 89 " --> pdb=" O MET C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.482A pdb=" N SER C 104 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TRP C 240 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS C 120 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS C 269 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 118 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.482A pdb=" N SER C 104 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TRP C 240 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU C 185 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AF7, first strand: chain 'C' and resid 142 through 147 removed outlier: 4.639A pdb=" N CYS C 145 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AF9, first strand: chain 'C' and resid 288 through 289 747 hydrogen bonds defined for protein. 1935 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: 4.00 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 3 1.17 - 1.33: 5026 1.33 - 1.49: 5544 1.49 - 1.66: 7082 1.66 - 1.82: 132 Bond restraints: 17787 Sorted by residual: bond pdb=" N GLY A 340 " pdb=" H GLY A 340 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CA GLY A 340 " pdb=" HA3 GLY A 340 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CA GLY A 340 " pdb=" HA2 GLY A 340 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C1 SIA P 2 " pdb=" O1A SIA P 2 " ideal model delta sigma weight residual 1.262 1.197 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 SIA E 2 " pdb=" O1A SIA E 2 " ideal model delta sigma weight residual 1.262 1.197 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 17782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 23486 2.12 - 4.24: 558 4.24 - 6.35: 39 6.35 - 8.47: 17 8.47 - 10.59: 11 Bond angle restraints: 24111 Sorted by residual: angle pdb=" C SER N 2 " pdb=" N ALA N 3 " pdb=" CA ALA N 3 " ideal model delta sigma weight residual 121.54 128.70 -7.16 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C SER M 2 " pdb=" N ALA M 3 " pdb=" CA ALA M 3 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C SER L 2 " pdb=" N ALA L 3 " pdb=" CA ALA L 3 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C1 SIA P 2 " pdb=" C2 SIA P 2 " pdb=" C3 SIA P 2 " ideal model delta sigma weight residual 115.48 104.89 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA ARG C 117 " pdb=" CB ARG C 117 " pdb=" CG ARG C 117 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 ... (remaining 24106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.52: 10419 26.52 - 53.05: 421 53.05 - 79.57: 52 79.57 - 106.09: 14 106.09 - 132.62: 1 Dihedral angle restraints: 10907 sinusoidal: 4628 harmonic: 6279 Sorted by residual: dihedral pdb=" C9 SIA E 2 " pdb=" C7 SIA E 2 " pdb=" C8 SIA E 2 " pdb=" O7 SIA E 2 " ideal model delta sinusoidal sigma weight residual -44.94 87.68 -132.62 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " pdb=" CB CYS I 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.68 35.32 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 58.04 34.96 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 10904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2575 0.120 - 0.240: 60 0.240 - 0.359: 3 0.359 - 0.479: 4 0.479 - 0.599: 1 Chirality restraints: 2643 Sorted by residual: chirality pdb=" C2 SIA P 2 " pdb=" O3 GAL P 1 " pdb=" C1 SIA P 2 " pdb=" O6 SIA P 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.70e+02 chirality pdb=" C2 SIA D 2 " pdb=" O3 GAL D 1 " pdb=" C1 SIA D 2 " pdb=" O6 SIA D 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.69e+02 chirality pdb=" C2 SIA E 2 " pdb=" O3 GAL E 1 " pdb=" C1 SIA E 2 " pdb=" O6 SIA E 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.74 0.24 2.00e-02 2.50e+03 1.46e+02 ... (remaining 2640 not shown) Planarity restraints: 3135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SIA P 2 " 0.016 2.00e-02 2.50e+03 4.79e-02 2.86e+01 pdb=" C11 SIA P 2 " -0.044 2.00e-02 2.50e+03 pdb=" C5 SIA P 2 " -0.058 2.00e-02 2.50e+03 pdb=" N5 SIA P 2 " 0.076 2.00e-02 2.50e+03 pdb=" O10 SIA P 2 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 290 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO C 291 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 291 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 291 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 SIA D 2 " 0.007 2.00e-02 2.50e+03 2.42e-02 7.31e+00 pdb=" C11 SIA D 2 " -0.022 2.00e-02 2.50e+03 pdb=" C5 SIA D 2 " -0.029 2.00e-02 2.50e+03 pdb=" N5 SIA D 2 " 0.039 2.00e-02 2.50e+03 pdb=" O10 SIA D 2 " 0.006 2.00e-02 2.50e+03 ... (remaining 3132 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 3 2.11 - 2.73: 1099 2.73 - 3.35: 18934 3.35 - 3.98: 38221 3.98 - 4.60: 53340 Nonbonded interactions: 111597 Sorted by model distance: nonbonded pdb=" O SER B 513 " pdb=" CZ ARG C 506 " model vdw 1.485 3.100 nonbonded pdb=" O SER B 513 " pdb=" NH1 ARG C 506 " model vdw 1.624 2.950 nonbonded pdb=" O SER B 513 " pdb=" NE ARG C 506 " model vdw 1.921 2.950 nonbonded pdb=" OH TYR A 101 " pdb=" O9 SIA E 2 " model vdw 2.279 2.800 nonbonded pdb=" OG1 THR B 290 " pdb=" O GLY B 293 " model vdw 2.279 2.800 ... (remaining 111592 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 8 through 332 or (resid 340 and (name N or name CA or name \ C or name O )) or resid 341 through 605)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.54 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: 12.330 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: 0.190 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 18.580 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.005 0.066 17826 Z= 0.228 Angle : 0.825 25.685 24207 Z= 0.410 Chirality : 0.054 0.599 2643 Planarity : 0.006 0.070 3120 Dihedral : 14.212 132.617 6831 Min Nonbonded Distance : 1.485 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.17), residues: 2163 helix: -0.46 (0.23), residues: 396 sheet: -0.06 (0.21), residues: 615 loop : -0.78 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 407 TYR 0.013 0.002 TYR A 496 PHE 0.032 0.002 PHE C 121 TRP 0.035 0.002 TRP B 70 HIS 0.009 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00482 (17784) covalent geometry : angle 0.75554 (24105) SS BOND : bond 0.00384 ( 24) SS BOND : angle 1.01421 ( 48) hydrogen bonds : bond 0.18375 ( 690) hydrogen bonds : angle 7.94420 ( 1935) link_BETA2-3 : bond 0.05950 ( 3) link_BETA2-3 : angle 7.04086 ( 9) link_NAG-ASN : bond 0.01456 ( 15) link_NAG-ASN : angle 7.05533 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8466 (mt0) cc_final: 0.8064 (tt0) REVERT: A 287 LYS cc_start: 0.8198 (mttm) cc_final: 0.7788 (mptt) REVERT: A 311 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8277 (mm-30) REVERT: A 507 LEU cc_start: 0.8018 (tp) cc_final: 0.7772 (mp) REVERT: M 79 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6547 (mt0) REVERT: I 3 GLN cc_start: 0.8453 (mt0) cc_final: 0.7994 (tt0) REVERT: B 287 LYS cc_start: 0.8108 (mttm) cc_final: 0.7713 (mptt) REVERT: B 311 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8220 (mm-30) REVERT: B 392 ASN cc_start: 0.8336 (m-40) cc_final: 0.8043 (m-40) REVERT: B 414 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8273 (mtm180) REVERT: B 470 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7362 (tttt) REVERT: B 500 GLN cc_start: 0.7953 (mt0) cc_final: 0.7745 (tt0) REVERT: B 508 LYS cc_start: 0.7429 (tttm) cc_final: 0.6812 (mmmt) REVERT: J 3 GLN cc_start: 0.8474 (mt0) cc_final: 0.7905 (mp10) REVERT: C 287 LYS cc_start: 0.8136 (mttm) cc_final: 0.7674 (mptt) REVERT: C 311 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8173 (mm-30) REVERT: C 414 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.8050 (mtm180) REVERT: C 417 GLU cc_start: 0.8628 (tt0) cc_final: 0.8347 (tt0) REVERT: C 501 TYR cc_start: 0.8740 (m-80) cc_final: 0.8227 (m-80) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.6779 time to fit residues: 309.2846 Evaluate side-chains 250 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 0.0050 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 230 ASN A 364 HIS A 365 HIS A 389 ASN B 97 ASN B 192 ASN B 389 ASN B 399 ASN C 97 ASN C 230 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135249 restraints weight = 19279.855| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.82 r_work: 0.3580 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17826 Z= 0.112 Angle : 0.537 20.155 24207 Z= 0.264 Chirality : 0.046 0.421 2643 Planarity : 0.004 0.045 3120 Dihedral : 7.518 124.126 2826 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.05 % Allowed : 9.36 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.18), residues: 2163 helix: 1.04 (0.26), residues: 396 sheet: 0.15 (0.21), residues: 609 loop : -0.46 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 506 TYR 0.012 0.001 TYR C 363 PHE 0.012 0.001 PHE A 342 TRP 0.009 0.001 TRP A 431 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00241 (17784) covalent geometry : angle 0.48656 (24105) SS BOND : bond 0.00197 ( 24) SS BOND : angle 0.75810 ( 48) hydrogen bonds : bond 0.03634 ( 690) hydrogen bonds : angle 5.62662 ( 1935) link_BETA2-3 : bond 0.00426 ( 3) link_BETA2-3 : angle 1.54262 ( 9) link_NAG-ASN : bond 0.00780 ( 15) link_NAG-ASN : angle 5.20119 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 SER cc_start: 0.7550 (m) cc_final: 0.7312 (p) REVERT: H 3 GLN cc_start: 0.8346 (mt0) cc_final: 0.7881 (tt0) REVERT: A 287 LYS cc_start: 0.7893 (mttm) cc_final: 0.7296 (mptt) REVERT: A 311 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7634 (mm-30) REVERT: A 356 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8581 (ttm) REVERT: A 507 LEU cc_start: 0.7806 (tp) cc_final: 0.7520 (mp) REVERT: M 24 SER cc_start: 0.7584 (m) cc_final: 0.7312 (p) REVERT: M 79 GLN cc_start: 0.6504 (mm-40) cc_final: 0.6156 (mt0) REVERT: I 3 GLN cc_start: 0.8298 (mt0) cc_final: 0.7741 (tt0) REVERT: B 180 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: B 287 LYS cc_start: 0.7756 (mttm) cc_final: 0.7174 (mptt) REVERT: B 311 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7629 (mm-30) REVERT: B 350 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: B 356 MET cc_start: 0.8878 (ttp) cc_final: 0.8632 (ttm) REVERT: B 414 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7520 (mtm180) REVERT: B 422 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7903 (mmtp) REVERT: B 470 LYS cc_start: 0.7639 (ttpt) cc_final: 0.6545 (tttt) REVERT: B 497 ASP cc_start: 0.7860 (t0) cc_final: 0.7604 (t0) REVERT: B 500 GLN cc_start: 0.7715 (mt0) cc_final: 0.7391 (tt0) REVERT: J 3 GLN cc_start: 0.8307 (mt0) cc_final: 0.7707 (tt0) REVERT: C 122 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: C 155 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: C 193 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8153 (p0) REVERT: C 202 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7604 (tppt) REVERT: C 237 ASP cc_start: 0.8431 (m-30) cc_final: 0.8173 (t0) REVERT: C 287 LYS cc_start: 0.7887 (mttm) cc_final: 0.7286 (mptt) REVERT: C 311 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7553 (mm-30) REVERT: C 398 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7686 (mtp) REVERT: C 414 ARG cc_start: 0.7718 (mmt-90) cc_final: 0.7278 (mtm180) REVERT: C 417 GLU cc_start: 0.8246 (tt0) cc_final: 0.7944 (tt0) REVERT: C 470 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6510 (tttt) REVERT: C 478 GLU cc_start: 0.8084 (tp30) cc_final: 0.7786 (tp30) REVERT: C 501 TYR cc_start: 0.8427 (m-80) cc_final: 0.7922 (m-80) outliers start: 57 outliers final: 27 residues processed: 310 average time/residue: 0.6367 time to fit residues: 219.2296 Evaluate side-chains 288 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 470 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 120 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 206 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN C 399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128031 restraints weight = 19522.288| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.86 r_work: 0.3437 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17826 Z= 0.249 Angle : 0.649 20.477 24207 Z= 0.308 Chirality : 0.049 0.404 2643 Planarity : 0.004 0.053 3120 Dihedral : 7.778 124.613 2826 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.80 % Allowed : 11.45 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.17), residues: 2163 helix: 1.03 (0.26), residues: 396 sheet: 0.07 (0.22), residues: 561 loop : -0.55 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 415 TYR 0.015 0.002 TYR I 100A PHE 0.019 0.002 PHE A 342 TRP 0.012 0.002 TRP B 70 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00576 (17784) covalent geometry : angle 0.57913 (24105) SS BOND : bond 0.00352 ( 24) SS BOND : angle 0.82771 ( 48) hydrogen bonds : bond 0.03918 ( 690) hydrogen bonds : angle 5.57196 ( 1935) link_BETA2-3 : bond 0.00342 ( 3) link_BETA2-3 : angle 1.73661 ( 9) link_NAG-ASN : bond 0.00568 ( 15) link_NAG-ASN : angle 6.76530 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 252 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LYS cc_start: 0.8039 (mttm) cc_final: 0.7494 (mptt) REVERT: A 311 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7737 (mm-30) REVERT: A 398 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7739 (mtp) REVERT: A 507 LEU cc_start: 0.7917 (tp) cc_final: 0.7621 (mp) REVERT: M 69 THR cc_start: 0.8354 (p) cc_final: 0.7869 (t) REVERT: B 122 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: B 180 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: B 287 LYS cc_start: 0.8021 (mttm) cc_final: 0.7458 (mptt) REVERT: B 311 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7749 (mm-30) REVERT: B 356 MET cc_start: 0.8913 (ttp) cc_final: 0.8707 (ttm) REVERT: B 414 ARG cc_start: 0.8486 (mmm160) cc_final: 0.7787 (mtm180) REVERT: B 422 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8118 (mmtp) REVERT: B 497 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8033 (t0) REVERT: B 500 GLN cc_start: 0.7835 (mt0) cc_final: 0.7451 (tt0) REVERT: N 53 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7155 (mp10) REVERT: C 15 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8971 (mp) REVERT: C 122 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: C 193 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8220 (p0) REVERT: C 202 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7749 (tppt) REVERT: C 269 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7923 (mmtm) REVERT: C 287 LYS cc_start: 0.8033 (mttm) cc_final: 0.7453 (mptt) REVERT: C 311 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7718 (mm-30) REVERT: C 398 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7779 (mtp) REVERT: C 414 ARG cc_start: 0.7992 (mmt-90) cc_final: 0.7570 (mtm180) REVERT: C 417 GLU cc_start: 0.8543 (tt0) cc_final: 0.8189 (tt0) REVERT: C 470 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6731 (tttt) REVERT: C 478 GLU cc_start: 0.8206 (tp30) cc_final: 0.7961 (tp30) REVERT: C 501 TYR cc_start: 0.8542 (m-80) cc_final: 0.8204 (m-80) outliers start: 71 outliers final: 40 residues processed: 281 average time/residue: 0.6644 time to fit residues: 206.9162 Evaluate side-chains 280 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 470 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 157 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 89 optimal weight: 0.0570 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 369 GLN A 399 ASN B 125 GLN B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130815 restraints weight = 19397.932| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.86 r_work: 0.3491 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17826 Z= 0.118 Angle : 0.517 18.641 24207 Z= 0.248 Chirality : 0.045 0.399 2643 Planarity : 0.003 0.036 3120 Dihedral : 7.227 118.454 2826 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.73 % Allowed : 14.13 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.18), residues: 2163 helix: 1.50 (0.26), residues: 396 sheet: 0.20 (0.21), residues: 597 loop : -0.36 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 415 TYR 0.008 0.001 TYR I 100A PHE 0.011 0.001 PHE A 342 TRP 0.010 0.001 TRP B 431 HIS 0.003 0.001 HIS C 302 Details of bonding type rmsd covalent geometry : bond 0.00263 (17784) covalent geometry : angle 0.45359 (24105) SS BOND : bond 0.00208 ( 24) SS BOND : angle 1.24760 ( 48) hydrogen bonds : bond 0.03239 ( 690) hydrogen bonds : angle 5.21059 ( 1935) link_BETA2-3 : bond 0.00170 ( 3) link_BETA2-3 : angle 1.13047 ( 9) link_NAG-ASN : bond 0.00517 ( 15) link_NAG-ASN : angle 5.63723 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 SER cc_start: 0.7645 (m) cc_final: 0.7422 (p) REVERT: L 69 THR cc_start: 0.8378 (p) cc_final: 0.7894 (t) REVERT: A 180 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: A 287 LYS cc_start: 0.7994 (mttm) cc_final: 0.7387 (mptt) REVERT: A 311 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7514 (mm-30) REVERT: A 398 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7479 (mtp) REVERT: A 470 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7429 (ttmt) REVERT: A 507 LEU cc_start: 0.7879 (tp) cc_final: 0.7548 (mp) REVERT: M 69 THR cc_start: 0.8330 (p) cc_final: 0.7806 (t) REVERT: B 122 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: B 287 LYS cc_start: 0.7927 (mttm) cc_final: 0.7316 (mptt) REVERT: B 311 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7570 (mm-30) REVERT: B 356 MET cc_start: 0.8880 (ttp) cc_final: 0.8661 (ttm) REVERT: B 414 ARG cc_start: 0.8418 (mmm160) cc_final: 0.7595 (mtm180) REVERT: B 422 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7916 (mmtp) REVERT: B 497 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7944 (t0) REVERT: B 500 GLN cc_start: 0.7761 (mt0) cc_final: 0.7403 (tt0) REVERT: N 53 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6975 (mp10) REVERT: C 122 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: C 269 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7854 (mmtm) REVERT: C 287 LYS cc_start: 0.8010 (mttm) cc_final: 0.7397 (mptt) REVERT: C 311 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7568 (mm-30) REVERT: C 414 ARG cc_start: 0.7872 (mmt-90) cc_final: 0.7408 (mtm180) REVERT: C 417 GLU cc_start: 0.8381 (tt0) cc_final: 0.7980 (tt0) REVERT: C 478 GLU cc_start: 0.8160 (tp30) cc_final: 0.7931 (tp30) REVERT: C 501 TYR cc_start: 0.8472 (m-80) cc_final: 0.8077 (m-80) REVERT: C 506 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6880 (ttp80) outliers start: 51 outliers final: 18 residues processed: 281 average time/residue: 0.6391 time to fit residues: 200.2195 Evaluate side-chains 265 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 507 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 186 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN B 48 ASN B 125 GLN B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN C 48 ASN C 250 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126055 restraints weight = 19375.827| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.87 r_work: 0.3379 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17826 Z= 0.274 Angle : 0.657 19.594 24207 Z= 0.313 Chirality : 0.050 0.412 2643 Planarity : 0.004 0.055 3120 Dihedral : 7.670 122.996 2826 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.98 % Allowed : 13.00 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.18), residues: 2163 helix: 1.21 (0.26), residues: 396 sheet: 0.12 (0.21), residues: 582 loop : -0.58 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 415 TYR 0.014 0.002 TYR A 496 PHE 0.019 0.002 PHE A 342 TRP 0.010 0.002 TRP B 431 HIS 0.008 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00641 (17784) covalent geometry : angle 0.58843 (24105) SS BOND : bond 0.00353 ( 24) SS BOND : angle 2.00296 ( 48) hydrogen bonds : bond 0.03775 ( 690) hydrogen bonds : angle 5.43357 ( 1935) link_BETA2-3 : bond 0.00403 ( 3) link_BETA2-3 : angle 1.59540 ( 9) link_NAG-ASN : bond 0.00536 ( 15) link_NAG-ASN : angle 6.48904 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 236 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8401 (ttp) REVERT: A 180 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: A 287 LYS cc_start: 0.8160 (mttm) cc_final: 0.7621 (mptt) REVERT: A 311 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7813 (mm-30) REVERT: A 398 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: A 470 LYS cc_start: 0.7999 (tttm) cc_final: 0.7626 (ttmt) REVERT: A 507 LEU cc_start: 0.8050 (tp) cc_final: 0.7765 (mp) REVERT: M 69 THR cc_start: 0.8421 (p) cc_final: 0.7937 (t) REVERT: B 122 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: B 271 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7953 (t70) REVERT: B 287 LYS cc_start: 0.8158 (mttm) cc_final: 0.7598 (mptt) REVERT: B 311 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7820 (mm-30) REVERT: B 398 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7679 (mmt) REVERT: B 500 GLN cc_start: 0.7931 (mt0) cc_final: 0.7502 (tt0) REVERT: N 53 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7168 (mp10) REVERT: N 69 THR cc_start: 0.8386 (p) cc_final: 0.7880 (t) REVERT: C 76 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8220 (mmp) REVERT: C 122 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: C 287 LYS cc_start: 0.8145 (mttm) cc_final: 0.7636 (mptt) REVERT: C 311 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7834 (mm-30) REVERT: C 398 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7850 (mtp) REVERT: C 470 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6866 (tttt) REVERT: C 501 TYR cc_start: 0.8720 (m-80) cc_final: 0.8412 (m-80) outliers start: 93 outliers final: 50 residues processed: 284 average time/residue: 0.6889 time to fit residues: 217.2362 Evaluate side-chains 283 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 470 LYS Chi-restraints excluded: chain C residue 507 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN B 48 ASN B 125 GLN B 176 ASN B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128059 restraints weight = 19232.427| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.96 r_work: 0.3438 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17826 Z= 0.150 Angle : 0.563 18.409 24207 Z= 0.268 Chirality : 0.047 0.553 2643 Planarity : 0.003 0.034 3120 Dihedral : 7.438 118.535 2826 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.85 % Allowed : 15.09 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.18), residues: 2163 helix: 1.47 (0.26), residues: 396 sheet: 0.14 (0.21), residues: 582 loop : -0.48 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 506 TYR 0.009 0.001 TYR A 496 PHE 0.012 0.001 PHE A 342 TRP 0.010 0.001 TRP C 431 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00339 (17784) covalent geometry : angle 0.48624 (24105) SS BOND : bond 0.00222 ( 24) SS BOND : angle 1.88370 ( 48) hydrogen bonds : bond 0.03308 ( 690) hydrogen bonds : angle 5.17092 ( 1935) link_BETA2-3 : bond 0.00206 ( 3) link_BETA2-3 : angle 1.11093 ( 9) link_NAG-ASN : bond 0.00542 ( 15) link_NAG-ASN : angle 6.31029 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 244 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8383 (p) cc_final: 0.7902 (t) REVERT: A 122 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: A 180 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: A 287 LYS cc_start: 0.8058 (mttm) cc_final: 0.7489 (mptt) REVERT: A 311 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7602 (mm-30) REVERT: A 398 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7535 (mtp) REVERT: A 507 LEU cc_start: 0.7908 (tp) cc_final: 0.7617 (mp) REVERT: M 69 THR cc_start: 0.8387 (p) cc_final: 0.7881 (t) REVERT: B 122 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: B 287 LYS cc_start: 0.8095 (mttm) cc_final: 0.7491 (mptt) REVERT: B 311 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7635 (mm-30) REVERT: B 414 ARG cc_start: 0.8409 (mmm160) cc_final: 0.7813 (mmt90) REVERT: B 500 GLN cc_start: 0.7854 (mt0) cc_final: 0.7428 (tt0) REVERT: N 53 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6956 (mp10) REVERT: N 69 THR cc_start: 0.8349 (p) cc_final: 0.7790 (t) REVERT: C 15 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8884 (mp) REVERT: C 76 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (mmp) REVERT: C 122 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: C 287 LYS cc_start: 0.8007 (mttm) cc_final: 0.7458 (mptt) REVERT: C 311 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7663 (mm-30) REVERT: C 414 ARG cc_start: 0.8369 (mmm160) cc_final: 0.7767 (mmt90) REVERT: C 421 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8062 (ttmt) REVERT: C 470 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6955 (tttt) REVERT: C 501 TYR cc_start: 0.8600 (m-80) cc_final: 0.8362 (m-80) outliers start: 72 outliers final: 40 residues processed: 283 average time/residue: 0.6561 time to fit residues: 207.4003 Evaluate side-chains 280 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 470 LYS Chi-restraints excluded: chain C residue 507 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 96 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 125 GLN A 250 HIS A 399 ASN A 464 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 250 HIS B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123689 restraints weight = 19398.504| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.86 r_work: 0.3352 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 17826 Z= 0.355 Angle : 0.729 19.799 24207 Z= 0.353 Chirality : 0.053 0.432 2643 Planarity : 0.005 0.072 3120 Dihedral : 8.163 126.284 2826 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.55 % Allowed : 14.98 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.18), residues: 2163 helix: 0.96 (0.26), residues: 396 sheet: -0.01 (0.21), residues: 582 loop : -0.83 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 506 TYR 0.016 0.002 TYR A 496 PHE 0.020 0.003 PHE A 342 TRP 0.011 0.002 TRP B 431 HIS 0.011 0.002 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00832 (17784) covalent geometry : angle 0.66633 (24105) SS BOND : bond 0.00559 ( 24) SS BOND : angle 2.40164 ( 48) hydrogen bonds : bond 0.04075 ( 690) hydrogen bonds : angle 5.66937 ( 1935) link_BETA2-3 : bond 0.00556 ( 3) link_BETA2-3 : angle 1.84292 ( 9) link_NAG-ASN : bond 0.00454 ( 15) link_NAG-ASN : angle 6.42276 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 227 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8430 (p) cc_final: 0.7972 (t) REVERT: A 76 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8347 (mmp) REVERT: A 122 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: A 287 LYS cc_start: 0.8132 (mttm) cc_final: 0.7584 (mmtt) REVERT: A 311 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7769 (mm-30) REVERT: A 507 LEU cc_start: 0.8062 (tp) cc_final: 0.7784 (mp) REVERT: M 24 SER cc_start: 0.8018 (m) cc_final: 0.7797 (p) REVERT: M 31 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7835 (mmp80) REVERT: M 69 THR cc_start: 0.8464 (p) cc_final: 0.7934 (t) REVERT: B 122 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: B 271 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.8009 (t70) REVERT: B 287 LYS cc_start: 0.8243 (mttm) cc_final: 0.7730 (mptt) REVERT: B 311 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7821 (mm-30) REVERT: B 493 ASN cc_start: 0.6829 (m-40) cc_final: 0.6605 (m-40) REVERT: N 69 THR cc_start: 0.8401 (p) cc_final: 0.7869 (t) REVERT: C 15 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8963 (mp) REVERT: C 76 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8309 (mmp) REVERT: C 122 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: C 287 LYS cc_start: 0.8135 (mttm) cc_final: 0.7693 (mmtm) REVERT: C 311 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7812 (mm-30) REVERT: C 398 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7883 (mtp) REVERT: C 421 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8216 (ttmt) REVERT: C 501 TYR cc_start: 0.8713 (m-80) cc_final: 0.8461 (m-80) REVERT: C 508 LYS cc_start: 0.7746 (mptt) cc_final: 0.7143 (tppt) outliers start: 85 outliers final: 53 residues processed: 274 average time/residue: 0.6464 time to fit residues: 198.1631 Evaluate side-chains 280 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 507 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 133 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 171 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 GLN A 399 ASN A 464 GLN B 125 GLN B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.161729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129031 restraints weight = 19160.270| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.87 r_work: 0.3438 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17826 Z= 0.115 Angle : 0.554 18.061 24207 Z= 0.270 Chirality : 0.046 0.357 2643 Planarity : 0.003 0.034 3120 Dihedral : 7.548 117.487 2826 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.57 % Allowed : 17.34 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -0.12 (0.18), residues: 2163 helix: 1.49 (0.26), residues: 396 sheet: -0.07 (0.22), residues: 573 loop : -0.58 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 506 TYR 0.008 0.001 TYR B 501 PHE 0.010 0.001 PHE C 121 TRP 0.012 0.001 TRP B 431 HIS 0.005 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00253 (17784) covalent geometry : angle 0.48634 (24105) SS BOND : bond 0.00398 ( 24) SS BOND : angle 2.95339 ( 48) hydrogen bonds : bond 0.03199 ( 690) hydrogen bonds : angle 5.26720 ( 1935) link_BETA2-3 : bond 0.00165 ( 3) link_BETA2-3 : angle 0.95233 ( 9) link_NAG-ASN : bond 0.00536 ( 15) link_NAG-ASN : angle 5.37967 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 36 TYR cc_start: 0.8083 (m-80) cc_final: 0.7832 (m-80) REVERT: L 69 THR cc_start: 0.8375 (p) cc_final: 0.7902 (t) REVERT: A 122 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 180 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: A 287 LYS cc_start: 0.8089 (mttm) cc_final: 0.7544 (mmtt) REVERT: A 311 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7743 (mm-30) REVERT: A 398 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7840 (mtp) REVERT: A 502 SER cc_start: 0.8417 (p) cc_final: 0.7707 (m) REVERT: A 507 LEU cc_start: 0.8073 (tp) cc_final: 0.7781 (mp) REVERT: M 24 SER cc_start: 0.7901 (m) cc_final: 0.7671 (p) REVERT: M 31 ARG cc_start: 0.8419 (mmp80) cc_final: 0.8092 (mmp-170) REVERT: M 69 THR cc_start: 0.8405 (p) cc_final: 0.7889 (t) REVERT: B 122 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: B 287 LYS cc_start: 0.8114 (mttm) cc_final: 0.7597 (mptt) REVERT: B 311 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7650 (mm-30) REVERT: N 53 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7048 (mp10) REVERT: N 61 ARG cc_start: 0.6735 (ptt90) cc_final: 0.6524 (ptt-90) REVERT: N 69 THR cc_start: 0.8397 (p) cc_final: 0.7859 (t) REVERT: C 15 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8896 (mp) REVERT: C 122 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: C 287 LYS cc_start: 0.8070 (mttm) cc_final: 0.7594 (mptt) REVERT: C 398 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7785 (mtp) REVERT: C 508 LYS cc_start: 0.7732 (mptt) cc_final: 0.7129 (tppt) outliers start: 48 outliers final: 25 residues processed: 283 average time/residue: 0.6337 time to fit residues: 200.9811 Evaluate side-chains 266 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 363 TYR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 502 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 144 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 chunk 173 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127432 restraints weight = 19305.790| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.92 r_work: 0.3410 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17826 Z= 0.222 Angle : 0.617 17.922 24207 Z= 0.301 Chirality : 0.048 0.381 2643 Planarity : 0.003 0.041 3120 Dihedral : 7.697 120.884 2826 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.16 % Allowed : 16.80 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.13 (0.18), residues: 2163 helix: 1.40 (0.26), residues: 396 sheet: 0.14 (0.22), residues: 558 loop : -0.68 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 506 TYR 0.012 0.001 TYR A 496 PHE 0.016 0.002 PHE A 342 TRP 0.010 0.001 TRP B 431 HIS 0.007 0.001 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00516 (17784) covalent geometry : angle 0.55661 (24105) SS BOND : bond 0.00444 ( 24) SS BOND : angle 3.15358 ( 48) hydrogen bonds : bond 0.03537 ( 690) hydrogen bonds : angle 5.34394 ( 1935) link_BETA2-3 : bond 0.00277 ( 3) link_BETA2-3 : angle 1.20309 ( 9) link_NAG-ASN : bond 0.00458 ( 15) link_NAG-ASN : angle 5.30911 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8424 (p) cc_final: 0.7944 (t) REVERT: A 76 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8384 (mmm) REVERT: A 122 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 180 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: A 287 LYS cc_start: 0.8078 (mttm) cc_final: 0.7583 (mmtt) REVERT: A 311 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7782 (mm-30) REVERT: A 398 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7671 (mtp) REVERT: A 403 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: A 502 SER cc_start: 0.8446 (p) cc_final: 0.7737 (m) REVERT: A 507 LEU cc_start: 0.8095 (tp) cc_final: 0.7806 (mp) REVERT: M 24 SER cc_start: 0.7950 (m) cc_final: 0.7733 (p) REVERT: M 69 THR cc_start: 0.8420 (p) cc_final: 0.7904 (t) REVERT: B 122 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: B 287 LYS cc_start: 0.8131 (mttm) cc_final: 0.7630 (mmtt) REVERT: B 311 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7745 (mm-30) REVERT: N 61 ARG cc_start: 0.6788 (ptt90) cc_final: 0.6520 (ptt-90) REVERT: N 69 THR cc_start: 0.8438 (p) cc_final: 0.7900 (t) REVERT: C 15 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8885 (mp) REVERT: C 122 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: C 287 LYS cc_start: 0.8054 (mttm) cc_final: 0.7636 (mmtm) REVERT: C 398 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7838 (mtp) REVERT: C 421 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: C 508 LYS cc_start: 0.7742 (mptt) cc_final: 0.7165 (tppt) outliers start: 59 outliers final: 37 residues processed: 273 average time/residue: 0.6441 time to fit residues: 196.6705 Evaluate side-chains 277 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 GLN A 125 GLN A 399 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126854 restraints weight = 19205.359| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.86 r_work: 0.3381 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17826 Z= 0.212 Angle : 0.657 29.565 24207 Z= 0.311 Chirality : 0.048 0.376 2643 Planarity : 0.003 0.035 3120 Dihedral : 7.624 120.068 2826 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.89 % Allowed : 17.07 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.13 (0.18), residues: 2163 helix: 1.38 (0.26), residues: 396 sheet: 0.17 (0.22), residues: 558 loop : -0.69 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 506 TYR 0.012 0.001 TYR A 496 PHE 0.015 0.002 PHE A 342 TRP 0.011 0.001 TRP B 431 HIS 0.006 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00490 (17784) covalent geometry : angle 0.56751 (24105) SS BOND : bond 0.00453 ( 24) SS BOND : angle 3.14265 ( 48) hydrogen bonds : bond 0.03472 ( 690) hydrogen bonds : angle 5.32623 ( 1935) link_BETA2-3 : bond 0.00209 ( 3) link_BETA2-3 : angle 1.11655 ( 9) link_NAG-ASN : bond 0.00423 ( 15) link_NAG-ASN : angle 6.97844 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8371 (mmm) REVERT: A 122 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: A 180 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: A 287 LYS cc_start: 0.8064 (mttm) cc_final: 0.7549 (mmtt) REVERT: A 311 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7724 (mm-30) REVERT: A 398 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7660 (mtp) REVERT: A 502 SER cc_start: 0.8404 (p) cc_final: 0.7675 (m) REVERT: A 507 LEU cc_start: 0.8039 (tp) cc_final: 0.7745 (mp) REVERT: M 24 SER cc_start: 0.7919 (m) cc_final: 0.7696 (p) REVERT: B 122 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: B 287 LYS cc_start: 0.8121 (mttm) cc_final: 0.7614 (mptt) REVERT: B 311 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7673 (mm-30) REVERT: B 466 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7917 (mtp180) REVERT: N 61 ARG cc_start: 0.6694 (ptt90) cc_final: 0.6412 (ptt-90) REVERT: N 69 THR cc_start: 0.8400 (p) cc_final: 0.7838 (t) REVERT: C 15 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8909 (mp) REVERT: C 122 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: C 287 LYS cc_start: 0.7991 (mttm) cc_final: 0.7561 (mmtm) REVERT: C 398 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7838 (mtp) REVERT: C 421 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8156 (ttmt) REVERT: C 508 LYS cc_start: 0.7692 (mptt) cc_final: 0.7090 (tppt) outliers start: 54 outliers final: 39 residues processed: 267 average time/residue: 0.6474 time to fit residues: 193.0059 Evaluate side-chains 270 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 163 optimal weight: 4.9990 chunk 76 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 GLN A 399 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 399 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.159997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127092 restraints weight = 19274.337| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.87 r_work: 0.3414 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17826 Z= 0.194 Angle : 0.618 17.930 24207 Z= 0.299 Chirality : 0.047 0.368 2643 Planarity : 0.003 0.034 3120 Dihedral : 7.550 119.087 2826 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.10 % Allowed : 16.85 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.07 (0.18), residues: 2163 helix: 1.44 (0.26), residues: 396 sheet: 0.23 (0.22), residues: 558 loop : -0.68 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 506 TYR 0.011 0.001 TYR C 496 PHE 0.015 0.002 PHE A 342 TRP 0.011 0.001 TRP B 431 HIS 0.005 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00447 (17784) covalent geometry : angle 0.54423 (24105) SS BOND : bond 0.00498 ( 24) SS BOND : angle 3.65573 ( 48) hydrogen bonds : bond 0.03405 ( 690) hydrogen bonds : angle 5.33209 ( 1935) link_BETA2-3 : bond 0.00204 ( 3) link_BETA2-3 : angle 1.03988 ( 9) link_NAG-ASN : bond 0.00428 ( 15) link_NAG-ASN : angle 5.66938 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7673.20 seconds wall clock time: 131 minutes 52.79 seconds (7912.79 seconds total)