Starting phenix.real_space_refine on Thu Sep 18 03:40:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7g_44305/09_2025/9b7g_44305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7g_44305/09_2025/9b7g_44305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b7g_44305/09_2025/9b7g_44305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7g_44305/09_2025/9b7g_44305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7g_44305/09_2025/9b7g_44305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7g_44305/09_2025/9b7g_44305.map" } resolution = 2.61 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 8634 2.51 5 N 2304 2.21 5 O 2814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 13800 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2733 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 326} Chain breaks: 1 Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 887 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 798 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, J, Q, K, P, I, R, M, S, N, T, O, U Time building chain proxies: 3.14, per 1000 atoms: 0.23 Number of scatterers: 13800 At special positions: 0 Unit cell: (118.57, 108.55, 145.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2814 8.00 N 2304 7.00 C 8634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA N 3 " - " MAN N 4 " " BMA T 3 " - " MAN T 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG D 1 " - " FUC D 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " " NAG I 1 " - " FUC I 2 " " NAG M 1 " - " FUC M 3 " " NAG R 1 " - " FUC R 2 " " NAG S 1 " - " FUC S 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 126 " " NAG A 603 " - " ASN A 285 " " NAG B 601 " - " ASN B 133 " " NAG B 602 " - " ASN B 126 " " NAG B 603 " - " ASN B 285 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 126 " " NAG C 603 " - " ASN C 285 " " NAG D 1 " - " ASN A 63 " " NAG E 1 " - " ASN A 158 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 246 " " NAG I 1 " - " ASN B 63 " " NAG M 1 " - " ASN B 158 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 246 " " NAG R 1 " - " ASN C 63 " " NAG S 1 " - " ASN C 158 " " NAG T 1 " - " ASN C 165 " " NAG U 1 " - " ASN C 246 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 623.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3132 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 42 sheets defined 15.3% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.648A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 404 through 441 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.580A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.509A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.649A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLY B 78 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 404 through 441 Processing helix chain 'J' and resid 60 through 64 removed outlier: 3.580A pdb=" N GLN J 64 " --> pdb=" O GLN J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.509A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.648A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 404 through 441 Processing helix chain 'Q' and resid 60 through 64 removed outlier: 3.580A pdb=" N GLN Q 64 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.509A pdb=" N THR Q 87 " --> pdb=" O SER Q 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.899A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.670A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.670A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AA7, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AA8, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA9, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AB1, first strand: chain 'H' and resid 54 through 58 removed outlier: 5.824A pdb=" N SER H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU H 52 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR H 100F" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 54 through 58 removed outlier: 5.824A pdb=" N SER H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU H 52 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.501A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.501A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.899A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 120 through 122 removed outlier: 6.671A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 120 through 122 removed outlier: 6.671A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 140 Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AC5, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AC6, first strand: chain 'J' and resid 54 through 58 removed outlier: 5.824A pdb=" N SER J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU J 52 " --> pdb=" O SER J 56 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR J 100F" --> pdb=" O GLY J 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 54 through 58 removed outlier: 5.824A pdb=" N SER J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU J 52 " --> pdb=" O SER J 56 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.501A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.501A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AD3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.899A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.671A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.671A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 136 through 140 Processing sheet with id=AD8, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AE1, first strand: chain 'Q' and resid 17 through 23 Processing sheet with id=AE2, first strand: chain 'Q' and resid 54 through 58 removed outlier: 5.823A pdb=" N SER Q 56 " --> pdb=" O LEU Q 52 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU Q 52 " --> pdb=" O SER Q 56 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR Q 100F" --> pdb=" O GLY Q 96 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 54 through 58 removed outlier: 5.823A pdb=" N SER Q 56 " --> pdb=" O LEU Q 52 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU Q 52 " --> pdb=" O SER Q 56 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AE5, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.501A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.501A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR P 86 " --> pdb=" O THR P 102 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4425 1.34 - 1.46: 3297 1.46 - 1.58: 6315 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 14097 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 14092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 18425 1.31 - 2.62: 539 2.62 - 3.93: 132 3.93 - 5.23: 32 5.23 - 6.54: 18 Bond angle restraints: 19146 Sorted by residual: angle pdb=" CA CYS J 22 " pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " ideal model delta sigma weight residual 114.40 108.59 5.81 2.30e+00 1.89e-01 6.38e+00 angle pdb=" CA CYS H 22 " pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " ideal model delta sigma weight residual 114.40 108.62 5.78 2.30e+00 1.89e-01 6.32e+00 angle pdb=" CA CYS Q 22 " pdb=" CB CYS Q 22 " pdb=" SG CYS Q 22 " ideal model delta sigma weight residual 114.40 108.63 5.77 2.30e+00 1.89e-01 6.29e+00 angle pdb=" C GLY K 50 " pdb=" N ASN K 51 " pdb=" CA ASN K 51 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.87e+00 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.85e+00 ... (remaining 19141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 8636 22.19 - 44.39: 241 44.39 - 66.58: 51 66.58 - 88.77: 21 88.77 - 110.97: 12 Dihedral angle restraints: 8961 sinusoidal: 4062 harmonic: 4899 Sorted by residual: dihedral pdb=" CB CYS Q 22 " pdb=" SG CYS Q 22 " pdb=" SG CYS Q 92 " pdb=" CB CYS Q 92 " ideal model delta sinusoidal sigma weight residual 93.00 127.62 -34.62 1 1.00e+01 1.00e-02 1.70e+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 93.00 127.60 -34.60 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " pdb=" CB CYS J 92 " ideal model delta sinusoidal sigma weight residual 93.00 127.58 -34.58 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 8958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1841 0.056 - 0.113: 326 0.113 - 0.169: 62 0.169 - 0.226: 3 0.226 - 0.282: 6 Chirality restraints: 2238 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2235 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 283 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO B 284 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 283 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO A 284 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 283 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 284 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 284 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 284 " 0.024 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2021 2.77 - 3.30: 12099 3.30 - 3.83: 22379 3.83 - 4.37: 26767 4.37 - 4.90: 47052 Nonbonded interactions: 110318 Sorted by model distance: nonbonded pdb=" OG SER C 47 " pdb=" O ASN C 285 " model vdw 2.231 3.040 nonbonded pdb=" OG SER B 47 " pdb=" O ASN B 285 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 47 " pdb=" O ASN A 285 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR C 28 " pdb=" O ASN C 31 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR B 28 " pdb=" O ASN B 31 " model vdw 2.301 3.040 ... (remaining 110313 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'O' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14157 Z= 0.160 Angle : 0.602 6.542 19308 Z= 0.281 Chirality : 0.048 0.282 2238 Planarity : 0.004 0.044 2427 Dihedral : 11.945 110.967 5775 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.81 % Allowed : 3.83 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.35 (0.20), residues: 1680 helix: 0.57 (0.35), residues: 198 sheet: 1.06 (0.24), residues: 444 loop : -0.16 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 61 TYR 0.012 0.001 TYR Q 100F PHE 0.009 0.001 PHE Q 100D TRP 0.008 0.001 TRP B 421 HIS 0.002 0.000 HIS P 34 Details of bonding type rmsd covalent geometry : bond 0.00322 (14097) covalent geometry : angle 0.58075 (19146) SS BOND : bond 0.00164 ( 18) SS BOND : angle 1.33083 ( 36) hydrogen bonds : bond 0.16240 ( 465) hydrogen bonds : angle 6.87695 ( 1386) link_ALPHA1-3 : bond 0.00434 ( 3) link_ALPHA1-3 : angle 1.61663 ( 9) link_BETA1-4 : bond 0.00528 ( 12) link_BETA1-4 : angle 2.32370 ( 36) link_BETA1-6 : bond 0.00616 ( 6) link_BETA1-6 : angle 1.32867 ( 18) link_NAG-ASN : bond 0.00770 ( 21) link_NAG-ASN : angle 1.88814 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 267 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7409 (mttt) cc_final: 0.6792 (mtpm) REVERT: A 261 ARG cc_start: 0.7548 (ptt90) cc_final: 0.7170 (ptp-170) REVERT: A 283 THR cc_start: 0.8150 (m) cc_final: 0.7791 (p) REVERT: A 285 ASN cc_start: 0.5813 (OUTLIER) cc_final: 0.4985 (t160) REVERT: B 27 LYS cc_start: 0.7519 (mttt) cc_final: 0.6969 (mtpm) REVERT: B 101 ASP cc_start: 0.8355 (p0) cc_final: 0.8073 (p0) REVERT: B 261 ARG cc_start: 0.7604 (ptt90) cc_final: 0.7247 (ptp-170) REVERT: B 285 ASN cc_start: 0.5541 (OUTLIER) cc_final: 0.4843 (t160) REVERT: K 93 LYS cc_start: 0.7802 (ttpp) cc_final: 0.7249 (tttm) REVERT: C 27 LYS cc_start: 0.7358 (mttt) cc_final: 0.6851 (mtpt) REVERT: C 261 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7240 (ptp-170) REVERT: C 285 ASN cc_start: 0.5427 (OUTLIER) cc_final: 0.4751 (t160) REVERT: P 93 LYS cc_start: 0.7799 (ttpp) cc_final: 0.7201 (tttm) outliers start: 12 outliers final: 1 residues processed: 272 average time/residue: 0.5319 time to fit residues: 160.0334 Evaluate side-chains 166 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 285 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN L 17 GLN L 34 HIS L 51 ASN L 79 GLN B 389 ASN J 105 GLN K 17 GLN K 34 HIS K 37 GLN K 51 ASN K 53 ASN C 389 ASN Q 105 GLN P 17 GLN P 34 HIS P 37 GLN P 51 ASN P 53 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132832 restraints weight = 16991.656| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.10 r_work: 0.3625 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14157 Z= 0.221 Angle : 0.722 12.325 19308 Z= 0.365 Chirality : 0.051 0.209 2238 Planarity : 0.006 0.065 2427 Dihedral : 9.565 73.155 2699 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.49 % Allowed : 10.48 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.44 (0.19), residues: 1680 helix: 1.96 (0.35), residues: 198 sheet: 1.41 (0.24), residues: 420 loop : -0.52 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 220 TYR 0.018 0.003 TYR J 100F PHE 0.017 0.002 PHE B 125 TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00536 (14097) covalent geometry : angle 0.69446 (19146) SS BOND : bond 0.00351 ( 18) SS BOND : angle 1.74438 ( 36) hydrogen bonds : bond 0.05440 ( 465) hydrogen bonds : angle 5.57263 ( 1386) link_ALPHA1-3 : bond 0.00768 ( 3) link_ALPHA1-3 : angle 2.18198 ( 9) link_BETA1-4 : bond 0.00571 ( 12) link_BETA1-4 : angle 2.93836 ( 36) link_BETA1-6 : bond 0.00691 ( 6) link_BETA1-6 : angle 1.16919 ( 18) link_NAG-ASN : bond 0.00761 ( 21) link_NAG-ASN : angle 2.37875 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7230 (mttt) cc_final: 0.6340 (mtpm) REVERT: A 261 ARG cc_start: 0.7686 (ptt90) cc_final: 0.6855 (ptp-170) REVERT: A 406 ILE cc_start: 0.7575 (mp) cc_final: 0.7214 (mm) REVERT: L 72 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7196 (p) REVERT: L 93 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6346 (tttm) REVERT: B 27 LYS cc_start: 0.7289 (mttt) cc_final: 0.6539 (mtpm) REVERT: B 101 ASP cc_start: 0.8458 (p0) cc_final: 0.8251 (p0) REVERT: B 261 ARG cc_start: 0.7744 (ptt90) cc_final: 0.6925 (ptp-170) REVERT: J 93 THR cc_start: 0.7458 (p) cc_final: 0.7241 (p) REVERT: K 54 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7987 (mtm110) REVERT: K 93 LYS cc_start: 0.7345 (ttpp) cc_final: 0.6446 (tttm) REVERT: C 27 LYS cc_start: 0.6943 (mttt) cc_final: 0.6318 (mtpm) REVERT: C 261 ARG cc_start: 0.7733 (ptt90) cc_final: 0.7012 (ptp-170) REVERT: P 93 LYS cc_start: 0.7473 (ttpp) cc_final: 0.7116 (ttpt) outliers start: 52 outliers final: 30 residues processed: 193 average time/residue: 0.4784 time to fit residues: 103.3635 Evaluate side-chains 179 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 72 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 93 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN B 435 HIS K 79 GLN P 37 GLN P 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133684 restraints weight = 17099.623| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.10 r_work: 0.3635 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14157 Z= 0.165 Angle : 0.636 10.374 19308 Z= 0.323 Chirality : 0.048 0.177 2238 Planarity : 0.005 0.063 2427 Dihedral : 8.191 57.362 2691 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.90 % Allowed : 11.96 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.47 (0.19), residues: 1680 helix: 2.49 (0.35), residues: 198 sheet: 1.18 (0.24), residues: 432 loop : -0.51 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 220 TYR 0.013 0.002 TYR Q 100F PHE 0.012 0.002 PHE B 125 TRP 0.010 0.002 TRP A 234 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00390 (14097) covalent geometry : angle 0.60859 (19146) SS BOND : bond 0.00180 ( 18) SS BOND : angle 1.26005 ( 36) hydrogen bonds : bond 0.04847 ( 465) hydrogen bonds : angle 5.39677 ( 1386) link_ALPHA1-3 : bond 0.00853 ( 3) link_ALPHA1-3 : angle 1.80211 ( 9) link_BETA1-4 : bond 0.00579 ( 12) link_BETA1-4 : angle 2.86247 ( 36) link_BETA1-6 : bond 0.00732 ( 6) link_BETA1-6 : angle 1.08614 ( 18) link_NAG-ASN : bond 0.00986 ( 21) link_NAG-ASN : angle 2.27174 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7292 (mttt) cc_final: 0.6464 (mtpm) REVERT: A 246 ASN cc_start: 0.7776 (t0) cc_final: 0.7215 (m-40) REVERT: A 261 ARG cc_start: 0.7650 (ptt90) cc_final: 0.6808 (ptp-170) REVERT: A 406 ILE cc_start: 0.7591 (mp) cc_final: 0.7212 (mm) REVERT: H 19 LYS cc_start: 0.8617 (tttt) cc_final: 0.8269 (tppt) REVERT: L 93 LYS cc_start: 0.7527 (ttpt) cc_final: 0.6405 (tttm) REVERT: L 94 SER cc_start: 0.7465 (OUTLIER) cc_final: 0.7142 (p) REVERT: B 27 LYS cc_start: 0.7295 (mttt) cc_final: 0.6565 (mtpm) REVERT: B 101 ASP cc_start: 0.8449 (p0) cc_final: 0.8231 (p0) REVERT: B 246 ASN cc_start: 0.7618 (t0) cc_final: 0.7026 (m-40) REVERT: B 261 ARG cc_start: 0.7660 (ptt90) cc_final: 0.6825 (ptp-170) REVERT: K 54 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7903 (mtm110) REVERT: K 93 LYS cc_start: 0.7444 (ttpp) cc_final: 0.6437 (tttm) REVERT: C 27 LYS cc_start: 0.7022 (mttt) cc_final: 0.6418 (mtpm) REVERT: C 246 ASN cc_start: 0.7675 (t0) cc_final: 0.7057 (m-40) REVERT: C 261 ARG cc_start: 0.7690 (ptt90) cc_final: 0.7003 (ptp-170) REVERT: P 30 ASP cc_start: 0.7768 (m-30) cc_final: 0.6978 (t0) REVERT: P 93 LYS cc_start: 0.7489 (ttpp) cc_final: 0.7127 (ttpt) outliers start: 58 outliers final: 39 residues processed: 200 average time/residue: 0.4929 time to fit residues: 109.4656 Evaluate side-chains 191 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 72 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS K 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.166353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130858 restraints weight = 17116.263| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.13 r_work: 0.3626 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14157 Z= 0.226 Angle : 0.732 11.990 19308 Z= 0.370 Chirality : 0.051 0.221 2238 Planarity : 0.006 0.069 2427 Dihedral : 7.497 59.708 2691 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.77 % Allowed : 11.63 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.31 (0.19), residues: 1680 helix: 2.27 (0.35), residues: 198 sheet: 1.35 (0.25), residues: 402 loop : -0.68 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 220 TYR 0.016 0.002 TYR Q 31A PHE 0.017 0.002 PHE B 125 TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00549 (14097) covalent geometry : angle 0.69698 (19146) SS BOND : bond 0.00302 ( 18) SS BOND : angle 1.66204 ( 36) hydrogen bonds : bond 0.05625 ( 465) hydrogen bonds : angle 5.56057 ( 1386) link_ALPHA1-3 : bond 0.01000 ( 3) link_ALPHA1-3 : angle 2.18014 ( 9) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 3.17066 ( 36) link_BETA1-6 : bond 0.00752 ( 6) link_BETA1-6 : angle 1.16506 ( 18) link_NAG-ASN : bond 0.01134 ( 21) link_NAG-ASN : angle 2.89840 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 153 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7300 (mttt) cc_final: 0.6482 (mtpm) REVERT: A 246 ASN cc_start: 0.7697 (t0) cc_final: 0.7169 (m-40) REVERT: A 261 ARG cc_start: 0.7719 (ptt90) cc_final: 0.6905 (ptp-170) REVERT: A 406 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7163 (mm) REVERT: H 62 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7049 (ttt180) REVERT: L 93 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6481 (tttm) REVERT: L 94 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7336 (p) REVERT: B 27 LYS cc_start: 0.7306 (mttt) cc_final: 0.6580 (mtpm) REVERT: B 197 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: B 261 ARG cc_start: 0.7728 (ptt90) cc_final: 0.6897 (ptp-170) REVERT: B 441 ASP cc_start: 0.4833 (OUTLIER) cc_final: 0.4527 (m-30) REVERT: J 83 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7510 (mtt90) REVERT: K 54 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7790 (mtm110) REVERT: K 93 LYS cc_start: 0.7540 (ttpp) cc_final: 0.6506 (tttm) REVERT: C 27 LYS cc_start: 0.7048 (mttt) cc_final: 0.6368 (mtpm) REVERT: C 246 ASN cc_start: 0.7606 (t0) cc_final: 0.7007 (m-40) REVERT: C 261 ARG cc_start: 0.7741 (ptt90) cc_final: 0.7062 (ptp-170) REVERT: P 93 LYS cc_start: 0.7389 (ttpp) cc_final: 0.7038 (ttpt) outliers start: 71 outliers final: 46 residues processed: 198 average time/residue: 0.5401 time to fit residues: 118.1884 Evaluate side-chains 193 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 93 optimal weight: 0.0770 chunk 151 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN K 79 GLN C 435 HIS P 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.168679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133563 restraints weight = 17149.568| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.09 r_work: 0.3633 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14157 Z= 0.141 Angle : 0.626 9.534 19308 Z= 0.317 Chirality : 0.047 0.210 2238 Planarity : 0.005 0.065 2427 Dihedral : 6.983 59.450 2691 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.03 % Allowed : 13.64 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.40 (0.19), residues: 1680 helix: 2.67 (0.35), residues: 198 sheet: 1.40 (0.25), residues: 411 loop : -0.71 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.013 0.002 TYR Q 31A PHE 0.010 0.002 PHE B 120 TRP 0.011 0.001 TRP C 127 HIS 0.003 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00328 (14097) covalent geometry : angle 0.59238 (19146) SS BOND : bond 0.00213 ( 18) SS BOND : angle 1.48468 ( 36) hydrogen bonds : bond 0.04631 ( 465) hydrogen bonds : angle 5.33805 ( 1386) link_ALPHA1-3 : bond 0.01062 ( 3) link_ALPHA1-3 : angle 2.06746 ( 9) link_BETA1-4 : bond 0.00497 ( 12) link_BETA1-4 : angle 2.76708 ( 36) link_BETA1-6 : bond 0.00754 ( 6) link_BETA1-6 : angle 1.07973 ( 18) link_NAG-ASN : bond 0.01055 ( 21) link_NAG-ASN : angle 2.62283 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7259 (mttt) cc_final: 0.6453 (mtpm) REVERT: A 246 ASN cc_start: 0.7660 (t0) cc_final: 0.7152 (m-40) REVERT: A 261 ARG cc_start: 0.7674 (ptt90) cc_final: 0.6833 (ptp-170) REVERT: A 406 ILE cc_start: 0.7543 (mp) cc_final: 0.7127 (mm) REVERT: H 62 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7060 (ttt-90) REVERT: L 93 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6437 (tttm) REVERT: L 94 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7249 (p) REVERT: B 27 LYS cc_start: 0.7297 (mttt) cc_final: 0.6580 (mtpm) REVERT: B 197 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: B 261 ARG cc_start: 0.7666 (ptt90) cc_final: 0.6823 (ptm160) REVERT: J 83 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7506 (mtt90) REVERT: K 54 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7722 (mtm110) REVERT: K 93 LYS cc_start: 0.7461 (ttpp) cc_final: 0.6486 (tttm) REVERT: C 27 LYS cc_start: 0.7031 (mttt) cc_final: 0.6368 (mtpm) REVERT: C 246 ASN cc_start: 0.7593 (t0) cc_final: 0.7022 (m-40) REVERT: C 261 ARG cc_start: 0.7631 (ptt90) cc_final: 0.6916 (ptm160) REVERT: Q 73 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5615 (mmt90) REVERT: P 30 ASP cc_start: 0.7726 (m-30) cc_final: 0.6925 (t0) outliers start: 60 outliers final: 42 residues processed: 188 average time/residue: 0.5621 time to fit residues: 116.5941 Evaluate side-chains 197 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 119 optimal weight: 0.0980 chunk 139 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN K 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137406 restraints weight = 16941.134| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.14 r_work: 0.3634 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14157 Z= 0.113 Angle : 0.567 7.981 19308 Z= 0.289 Chirality : 0.046 0.211 2238 Planarity : 0.005 0.061 2427 Dihedral : 6.456 59.675 2691 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.36 % Allowed : 14.45 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.57 (0.20), residues: 1680 helix: 3.04 (0.35), residues: 198 sheet: 1.42 (0.25), residues: 414 loop : -0.61 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 220 TYR 0.010 0.001 TYR Q 31A PHE 0.009 0.001 PHE B 120 TRP 0.011 0.001 TRP A 127 HIS 0.002 0.000 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00253 (14097) covalent geometry : angle 0.53948 (19146) SS BOND : bond 0.00209 ( 18) SS BOND : angle 1.07303 ( 36) hydrogen bonds : bond 0.04042 ( 465) hydrogen bonds : angle 5.12405 ( 1386) link_ALPHA1-3 : bond 0.01078 ( 3) link_ALPHA1-3 : angle 1.86730 ( 9) link_BETA1-4 : bond 0.00548 ( 12) link_BETA1-4 : angle 2.39644 ( 36) link_BETA1-6 : bond 0.00712 ( 6) link_BETA1-6 : angle 1.04885 ( 18) link_NAG-ASN : bond 0.00939 ( 21) link_NAG-ASN : angle 2.34479 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.528 Fit side-chains REVERT: A 27 LYS cc_start: 0.7199 (mttt) cc_final: 0.6409 (mtpm) REVERT: A 246 ASN cc_start: 0.7670 (t0) cc_final: 0.7160 (m-40) REVERT: A 261 ARG cc_start: 0.7630 (ptt90) cc_final: 0.6755 (ptp-170) REVERT: A 406 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7006 (mm) REVERT: L 93 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6373 (tttm) REVERT: L 94 SER cc_start: 0.7509 (t) cc_final: 0.7179 (p) REVERT: B 27 LYS cc_start: 0.7238 (mttt) cc_final: 0.6534 (mtpm) REVERT: B 197 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: B 246 ASN cc_start: 0.7517 (t0) cc_final: 0.6960 (m-40) REVERT: B 261 ARG cc_start: 0.7638 (ptt90) cc_final: 0.6762 (ptm160) REVERT: J 83 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7523 (mtt90) REVERT: K 32 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8548 (m-30) REVERT: K 93 LYS cc_start: 0.7309 (ttpp) cc_final: 0.6381 (tttm) REVERT: C 27 LYS cc_start: 0.7067 (mttt) cc_final: 0.6374 (mtpm) REVERT: C 246 ASN cc_start: 0.7565 (t0) cc_final: 0.6986 (m-40) REVERT: C 261 ARG cc_start: 0.7613 (ptt90) cc_final: 0.6834 (ptm160) REVERT: Q 73 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5639 (mmt90) REVERT: P 30 ASP cc_start: 0.7729 (m-30) cc_final: 0.6860 (t0) outliers start: 50 outliers final: 34 residues processed: 186 average time/residue: 0.5429 time to fit residues: 111.3368 Evaluate side-chains 188 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 72 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 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 389 ASN K 79 GLN P 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136552 restraints weight = 17021.551| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.14 r_work: 0.3620 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14157 Z= 0.130 Angle : 0.583 8.365 19308 Z= 0.297 Chirality : 0.046 0.218 2238 Planarity : 0.005 0.062 2427 Dihedral : 6.412 58.658 2691 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.76 % Allowed : 14.25 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.55 (0.20), residues: 1680 helix: 3.03 (0.34), residues: 198 sheet: 1.41 (0.25), residues: 414 loop : -0.62 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.012 0.001 TYR Q 31A PHE 0.009 0.001 PHE B 120 TRP 0.009 0.001 TRP C 127 HIS 0.002 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00302 (14097) covalent geometry : angle 0.55591 (19146) SS BOND : bond 0.00214 ( 18) SS BOND : angle 1.16180 ( 36) hydrogen bonds : bond 0.04197 ( 465) hydrogen bonds : angle 5.09995 ( 1386) link_ALPHA1-3 : bond 0.01034 ( 3) link_ALPHA1-3 : angle 1.93270 ( 9) link_BETA1-4 : bond 0.00427 ( 12) link_BETA1-4 : angle 2.38731 ( 36) link_BETA1-6 : bond 0.00713 ( 6) link_BETA1-6 : angle 1.03991 ( 18) link_NAG-ASN : bond 0.00926 ( 21) link_NAG-ASN : angle 2.35392 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7185 (mttt) cc_final: 0.6453 (mtpm) REVERT: A 246 ASN cc_start: 0.7684 (t0) cc_final: 0.7176 (m-40) REVERT: A 261 ARG cc_start: 0.7672 (ptt90) cc_final: 0.6805 (ptp-170) REVERT: A 406 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7062 (mm) REVERT: L 93 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6414 (tttm) REVERT: L 94 SER cc_start: 0.7560 (t) cc_final: 0.7237 (p) REVERT: B 27 LYS cc_start: 0.7263 (mttt) cc_final: 0.6570 (mtpm) REVERT: B 197 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: B 246 ASN cc_start: 0.7529 (t0) cc_final: 0.7002 (m-40) REVERT: B 261 ARG cc_start: 0.7670 (ptt90) cc_final: 0.6808 (ptm160) REVERT: J 83 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7578 (mtt90) REVERT: K 93 LYS cc_start: 0.7352 (ttpp) cc_final: 0.6427 (tttm) REVERT: C 27 LYS cc_start: 0.7103 (mttt) cc_final: 0.6411 (mtpm) REVERT: C 246 ASN cc_start: 0.7618 (t0) cc_final: 0.7032 (m-40) REVERT: C 261 ARG cc_start: 0.7630 (ptt90) cc_final: 0.6874 (ptm160) REVERT: Q 73 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.5634 (mmt90) outliers start: 56 outliers final: 43 residues processed: 180 average time/residue: 0.5665 time to fit residues: 111.8115 Evaluate side-chains 188 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN K 52 ASN K 79 GLN P 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132844 restraints weight = 16967.091| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.12 r_work: 0.3644 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14157 Z= 0.169 Angle : 0.634 9.498 19308 Z= 0.321 Chirality : 0.048 0.216 2238 Planarity : 0.005 0.064 2427 Dihedral : 6.571 59.949 2691 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.76 % Allowed : 14.25 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.45 (0.19), residues: 1680 helix: 2.81 (0.34), residues: 198 sheet: 1.56 (0.25), residues: 402 loop : -0.74 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.014 0.002 TYR J 100F PHE 0.012 0.002 PHE B 125 TRP 0.010 0.002 TRP B 234 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00404 (14097) covalent geometry : angle 0.60358 (19146) SS BOND : bond 0.00248 ( 18) SS BOND : angle 1.37793 ( 36) hydrogen bonds : bond 0.04692 ( 465) hydrogen bonds : angle 5.20502 ( 1386) link_ALPHA1-3 : bond 0.00919 ( 3) link_ALPHA1-3 : angle 2.03386 ( 9) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 2.55011 ( 36) link_BETA1-6 : bond 0.00702 ( 6) link_BETA1-6 : angle 1.05679 ( 18) link_NAG-ASN : bond 0.00972 ( 21) link_NAG-ASN : angle 2.56567 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.490 Fit side-chains REVERT: A 27 LYS cc_start: 0.7219 (mttt) cc_final: 0.6457 (mtpm) REVERT: A 246 ASN cc_start: 0.7670 (t0) cc_final: 0.7216 (m-40) REVERT: A 261 ARG cc_start: 0.7699 (ptt90) cc_final: 0.6848 (ptp-170) REVERT: A 406 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7117 (mm) REVERT: L 93 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6410 (tttm) REVERT: L 94 SER cc_start: 0.7623 (OUTLIER) cc_final: 0.7319 (p) REVERT: B 27 LYS cc_start: 0.7286 (mttt) cc_final: 0.6599 (mtpm) REVERT: B 197 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: B 246 ASN cc_start: 0.7534 (t0) cc_final: 0.7055 (m-40) REVERT: B 261 ARG cc_start: 0.7696 (ptt90) cc_final: 0.6848 (ptm160) REVERT: J 83 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7603 (mtt90) REVERT: K 93 LYS cc_start: 0.7452 (ttpp) cc_final: 0.6476 (tttm) REVERT: C 27 LYS cc_start: 0.7156 (mttt) cc_final: 0.6462 (mtpm) REVERT: C 246 ASN cc_start: 0.7613 (t0) cc_final: 0.7037 (m-40) REVERT: C 261 ARG cc_start: 0.7664 (ptt90) cc_final: 0.6940 (ptm160) REVERT: Q 73 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5661 (mmt90) outliers start: 56 outliers final: 47 residues processed: 178 average time/residue: 0.5724 time to fit residues: 112.1466 Evaluate side-chains 188 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 72 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 0.0570 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN K 52 ASN K 79 GLN P 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.170552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137215 restraints weight = 17084.208| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.21 r_work: 0.3627 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14157 Z= 0.111 Angle : 0.574 7.702 19308 Z= 0.292 Chirality : 0.045 0.232 2238 Planarity : 0.004 0.060 2427 Dihedral : 6.267 58.521 2691 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.49 % Allowed : 14.58 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.65 (0.20), residues: 1680 helix: 3.09 (0.34), residues: 198 sheet: 1.58 (0.25), residues: 408 loop : -0.59 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.010 0.001 TYR Q 31A PHE 0.008 0.001 PHE C 120 TRP 0.011 0.001 TRP A 127 HIS 0.002 0.000 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00246 (14097) covalent geometry : angle 0.54134 (19146) SS BOND : bond 0.00186 ( 18) SS BOND : angle 1.03482 ( 36) hydrogen bonds : bond 0.04078 ( 465) hydrogen bonds : angle 5.10295 ( 1386) link_ALPHA1-3 : bond 0.00985 ( 3) link_ALPHA1-3 : angle 1.60345 ( 9) link_BETA1-4 : bond 0.00583 ( 12) link_BETA1-4 : angle 2.41267 ( 36) link_BETA1-6 : bond 0.00719 ( 6) link_BETA1-6 : angle 1.04759 ( 18) link_NAG-ASN : bond 0.01075 ( 21) link_NAG-ASN : angle 2.72708 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.588 Fit side-chains REVERT: A 27 LYS cc_start: 0.7163 (mttt) cc_final: 0.6432 (mtpm) REVERT: A 246 ASN cc_start: 0.7608 (t0) cc_final: 0.7141 (m-40) REVERT: A 261 ARG cc_start: 0.7616 (ptt90) cc_final: 0.6755 (ptp-170) REVERT: A 406 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7064 (mm) REVERT: H 62 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7091 (ttt180) REVERT: L 93 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6345 (tttm) REVERT: L 94 SER cc_start: 0.7547 (t) cc_final: 0.7225 (p) REVERT: B 27 LYS cc_start: 0.7240 (mttt) cc_final: 0.6529 (mtpm) REVERT: B 197 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: B 246 ASN cc_start: 0.7491 (t0) cc_final: 0.6989 (m-40) REVERT: B 261 ARG cc_start: 0.7638 (ptt90) cc_final: 0.6762 (ptm160) REVERT: J 83 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7571 (mtt90) REVERT: K 54 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7792 (mtm110) REVERT: K 93 LYS cc_start: 0.7331 (ttpp) cc_final: 0.6397 (tttm) REVERT: C 27 LYS cc_start: 0.7045 (mttt) cc_final: 0.6360 (mtpm) REVERT: C 246 ASN cc_start: 0.7568 (t0) cc_final: 0.7009 (m-40) REVERT: C 261 ARG cc_start: 0.7613 (ptt90) cc_final: 0.6805 (ptm160) REVERT: Q 73 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5627 (mmt90) outliers start: 52 outliers final: 42 residues processed: 182 average time/residue: 0.5617 time to fit residues: 112.8604 Evaluate side-chains 191 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 84 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 407 GLN K 52 ASN K 79 GLN P 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137035 restraints weight = 16927.830| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.15 r_work: 0.3613 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14157 Z= 0.129 Angle : 0.592 8.215 19308 Z= 0.301 Chirality : 0.046 0.210 2238 Planarity : 0.005 0.061 2427 Dihedral : 6.187 57.729 2691 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.49 % Allowed : 14.65 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.63 (0.20), residues: 1680 helix: 3.07 (0.34), residues: 198 sheet: 1.67 (0.25), residues: 399 loop : -0.63 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.012 0.001 TYR Q 31A PHE 0.009 0.001 PHE A 120 TRP 0.011 0.001 TRP A 127 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00297 (14097) covalent geometry : angle 0.55925 (19146) SS BOND : bond 0.00211 ( 18) SS BOND : angle 1.14880 ( 36) hydrogen bonds : bond 0.04212 ( 465) hydrogen bonds : angle 5.10358 ( 1386) link_ALPHA1-3 : bond 0.00943 ( 3) link_ALPHA1-3 : angle 1.73510 ( 9) link_BETA1-4 : bond 0.00513 ( 12) link_BETA1-4 : angle 2.38918 ( 36) link_BETA1-6 : bond 0.00705 ( 6) link_BETA1-6 : angle 1.02884 ( 18) link_NAG-ASN : bond 0.01039 ( 21) link_NAG-ASN : angle 2.73245 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 0.488 Fit side-chains REVERT: A 27 LYS cc_start: 0.7176 (mttt) cc_final: 0.6451 (mtpm) REVERT: A 246 ASN cc_start: 0.7657 (t0) cc_final: 0.7160 (m-40) REVERT: A 261 ARG cc_start: 0.7664 (ptt90) cc_final: 0.6801 (ptp-170) REVERT: A 406 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7095 (mm) REVERT: H 62 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7067 (ttt180) REVERT: L 93 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6373 (tttm) REVERT: L 94 SER cc_start: 0.7577 (t) cc_final: 0.7263 (p) REVERT: B 27 LYS cc_start: 0.7250 (mttt) cc_final: 0.6546 (mtpm) REVERT: B 197 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: B 246 ASN cc_start: 0.7522 (t0) cc_final: 0.7002 (m-40) REVERT: B 261 ARG cc_start: 0.7672 (ptt90) cc_final: 0.6797 (ptm160) REVERT: J 83 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7596 (mtt90) REVERT: K 93 LYS cc_start: 0.7331 (ttpp) cc_final: 0.6412 (tttm) REVERT: C 27 LYS cc_start: 0.7073 (mttt) cc_final: 0.6383 (mtpm) REVERT: C 246 ASN cc_start: 0.7577 (t0) cc_final: 0.7018 (m-40) REVERT: C 261 ARG cc_start: 0.7622 (ptt90) cc_final: 0.6867 (ptm160) REVERT: Q 73 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.5701 (mmt90) outliers start: 52 outliers final: 45 residues processed: 173 average time/residue: 0.5533 time to fit residues: 105.5517 Evaluate side-chains 187 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 146 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 153 optimal weight: 0.0970 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN K 52 ASN K 79 GLN P 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136787 restraints weight = 17016.600| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.27 r_work: 0.3621 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 14157 Z= 0.222 Angle : 1.000 59.200 19308 Z= 0.593 Chirality : 0.049 0.569 2238 Planarity : 0.005 0.061 2427 Dihedral : 6.209 57.679 2691 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.56 % Allowed : 14.58 % Favored : 81.85 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.45 % 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: 0.63 (0.20), residues: 1680 helix: 3.08 (0.34), residues: 198 sheet: 1.67 (0.25), residues: 399 loop : -0.63 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.012 0.001 TYR Q 31A PHE 0.009 0.001 PHE B 120 TRP 0.010 0.001 TRP A 127 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00444 (14097) covalent geometry : angle 0.98476 (19146) SS BOND : bond 0.00223 ( 18) SS BOND : angle 1.13206 ( 36) hydrogen bonds : bond 0.04225 ( 465) hydrogen bonds : angle 5.10345 ( 1386) link_ALPHA1-3 : bond 0.01098 ( 3) link_ALPHA1-3 : angle 1.87862 ( 9) link_BETA1-4 : bond 0.00585 ( 12) link_BETA1-4 : angle 2.39205 ( 36) link_BETA1-6 : bond 0.00397 ( 6) link_BETA1-6 : angle 0.87933 ( 18) link_NAG-ASN : bond 0.01021 ( 21) link_NAG-ASN : angle 2.70842 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5534.60 seconds wall clock time: 95 minutes 12.66 seconds (5712.66 seconds total)