Starting phenix.real_space_refine on Thu Jul 31 18:49:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7g_44305/07_2025/9b7g_44305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7g_44305/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7g_44305/07_2025/9b7g_44305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7g_44305/07_2025/9b7g_44305.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7g_44305/07_2025/9b7g_44305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7g_44305/07_2025/9b7g_44305.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: "K" 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: M, S, C, B, N, T, J, Q, I, R, O, U, L, P Time building chain proxies: 9.98, per 1000 atoms: 0.72 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=16, 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 C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 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 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: 4.03 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.06 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: 4.77 Time building geometry restraints manager: 4.75 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: 8634 22.19 - 44.39: 237 44.39 - 66.58: 51 66.58 - 88.77: 21 88.77 - 110.97: 12 Dihedral angle restraints: 8955 sinusoidal: 4056 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 8952 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: 2.03 - 2.61: 118 2.61 - 3.18: 11080 3.18 - 3.75: 20051 3.75 - 4.33: 29541 4.33 - 4.90: 49534 Nonbonded interactions: 110324 Sorted by model distance: nonbonded pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " model vdw 2.033 3.760 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 ... (remaining 110319 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: 0.10 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'S' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'P' } 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: 0.010 Normalize map: mean=0, sd=1: 11.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.430 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.950 ------------------------------------------------------------------------------- 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 14155 Z= 0.160 Angle : 0.602 6.542 19304 Z= 0.281 Chirality : 0.048 0.282 2238 Planarity : 0.004 0.044 2427 Dihedral : 11.945 110.967 5775 Min Nonbonded Distance : 2.033 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP B 421 HIS 0.002 0.000 HIS P 34 PHE 0.009 0.001 PHE Q 100D TYR 0.012 0.001 TYR Q 100F ARG 0.002 0.000 ARG P 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 21) link_NAG-ASN : angle 1.88814 ( 63) link_BETA1-4 : bond 0.00528 ( 12) link_BETA1-4 : angle 2.32370 ( 36) link_ALPHA1-3 : bond 0.00434 ( 3) link_ALPHA1-3 : angle 1.61663 ( 9) hydrogen bonds : bond 0.16240 ( 465) hydrogen bonds : angle 6.87695 ( 1386) link_BETA1-6 : bond 0.00616 ( 6) link_BETA1-6 : angle 1.32867 ( 18) SS BOND : bond 0.00156 ( 16) SS BOND : angle 1.40758 ( 32) covalent geometry : bond 0.00322 (14097) covalent geometry : angle 0.58075 (19146) *********************** 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 : 1.431 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: 0.6968 (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: 0.9971 time to fit residues: 302.3996 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 : 1.602 ------------------------------------------------------------------------------- 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 139 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4017 r_free = 0.4017 target = 0.169184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133562 restraints weight = 16913.810| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.10 r_work: 0.3633 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14155 Z= 0.200 Angle : 0.698 11.890 19304 Z= 0.354 Chirality : 0.050 0.204 2238 Planarity : 0.006 0.064 2427 Dihedral : 9.485 72.847 2699 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.43 % Allowed : 10.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1680 helix: 2.09 (0.35), residues: 198 sheet: 1.42 (0.24), residues: 426 loop : -0.49 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.006 0.001 HIS C 184 PHE 0.015 0.002 PHE B 125 TYR 0.017 0.002 TYR J 100F ARG 0.005 0.001 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 21) link_NAG-ASN : angle 2.24225 ( 63) link_BETA1-4 : bond 0.00401 ( 12) link_BETA1-4 : angle 2.99415 ( 36) link_ALPHA1-3 : bond 0.00786 ( 3) link_ALPHA1-3 : angle 2.20353 ( 9) hydrogen bonds : bond 0.05208 ( 465) hydrogen bonds : angle 5.53299 ( 1386) link_BETA1-6 : bond 0.00706 ( 6) link_BETA1-6 : angle 1.10987 ( 18) SS BOND : bond 0.00292 ( 16) SS BOND : angle 1.53386 ( 32) covalent geometry : bond 0.00484 (14097) covalent geometry : angle 0.67165 (19146) *********************** 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: 51 poor density : 160 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7177 (mttt) cc_final: 0.6302 (mtpm) REVERT: A 261 ARG cc_start: 0.7673 (ptt90) cc_final: 0.6854 (ptp-170) REVERT: A 406 ILE cc_start: 0.7572 (mp) cc_final: 0.7214 (mm) REVERT: L 72 SER cc_start: 0.7428 (OUTLIER) cc_final: 0.7185 (p) REVERT: L 93 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6378 (tttm) REVERT: B 27 LYS cc_start: 0.7275 (mttt) cc_final: 0.6524 (mtpm) REVERT: B 101 ASP cc_start: 0.8493 (p0) cc_final: 0.8279 (p0) REVERT: B 261 ARG cc_start: 0.7730 (ptt90) cc_final: 0.6916 (ptp-170) REVERT: J 93 THR cc_start: 0.7423 (p) cc_final: 0.7196 (p) REVERT: K 54 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7953 (mtm110) REVERT: K 93 LYS cc_start: 0.7317 (ttpp) cc_final: 0.6409 (tttm) REVERT: C 27 LYS cc_start: 0.6904 (mttt) cc_final: 0.6277 (mtpm) REVERT: C 261 ARG cc_start: 0.7728 (ptt90) cc_final: 0.7006 (ptp-170) REVERT: P 5 THR cc_start: 0.8162 (m) cc_final: 0.7879 (p) REVERT: P 93 LYS cc_start: 0.7500 (ttpp) cc_final: 0.7154 (ttpt) outliers start: 51 outliers final: 28 residues processed: 193 average time/residue: 0.9553 time to fit residues: 207.8943 Evaluate side-chains 181 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 100 optimal weight: 0.0050 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN K 79 GLN P 37 GLN P 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136143 restraints weight = 16954.929| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.09 r_work: 0.3664 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14155 Z= 0.122 Angle : 0.579 8.910 19304 Z= 0.294 Chirality : 0.046 0.191 2238 Planarity : 0.004 0.059 2427 Dihedral : 8.021 56.214 2691 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.89 % Allowed : 12.77 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1680 helix: 2.87 (0.35), residues: 198 sheet: 1.49 (0.24), residues: 417 loop : -0.42 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 127 HIS 0.002 0.001 HIS C 184 PHE 0.009 0.001 PHE B 125 TYR 0.011 0.001 TYR Q 100F ARG 0.003 0.000 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 21) link_NAG-ASN : angle 2.02960 ( 63) link_BETA1-4 : bond 0.00564 ( 12) link_BETA1-4 : angle 2.70321 ( 36) link_ALPHA1-3 : bond 0.00905 ( 3) link_ALPHA1-3 : angle 1.71685 ( 9) hydrogen bonds : bond 0.04231 ( 465) hydrogen bonds : angle 5.24397 ( 1386) link_BETA1-6 : bond 0.00714 ( 6) link_BETA1-6 : angle 1.04329 ( 18) SS BOND : bond 0.00094 ( 16) SS BOND : angle 0.97883 ( 32) covalent geometry : bond 0.00278 (14097) covalent geometry : angle 0.55346 (19146) *********************** 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 205 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7213 (mttt) cc_final: 0.6359 (mtpm) REVERT: A 197 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.6753 (pp30) REVERT: A 246 ASN cc_start: 0.7783 (t0) cc_final: 0.7226 (m-40) REVERT: A 261 ARG cc_start: 0.7573 (ptt90) cc_final: 0.6766 (ptp-170) REVERT: A 406 ILE cc_start: 0.7514 (mp) cc_final: 0.7149 (mm) REVERT: H 19 LYS cc_start: 0.8597 (tttt) cc_final: 0.8270 (tppt) REVERT: L 93 LYS cc_start: 0.7506 (ttpt) cc_final: 0.6401 (tttm) REVERT: B 27 LYS cc_start: 0.7280 (mttt) cc_final: 0.6555 (mtpm) REVERT: B 246 ASN cc_start: 0.7633 (t0) cc_final: 0.7007 (m-40) REVERT: B 261 ARG cc_start: 0.7645 (ptt90) cc_final: 0.6811 (ptp-170) REVERT: K 54 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7905 (mtm110) REVERT: K 93 LYS cc_start: 0.7371 (ttpp) cc_final: 0.6446 (tttm) REVERT: C 27 LYS cc_start: 0.7015 (mttt) cc_final: 0.6419 (mtpm) REVERT: C 246 ASN cc_start: 0.7659 (t0) cc_final: 0.7023 (m-40) REVERT: C 261 ARG cc_start: 0.7694 (ptt90) cc_final: 0.7003 (ptp-170) REVERT: P 5 THR cc_start: 0.8158 (m) cc_final: 0.7951 (p) REVERT: P 30 ASP cc_start: 0.7758 (m-30) cc_final: 0.6960 (t0) outliers start: 43 outliers final: 27 residues processed: 188 average time/residue: 1.0291 time to fit residues: 216.1284 Evaluate side-chains 175 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 100 VAL 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 144 SER 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 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 K residue 72 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 95 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 0.0070 chunk 157 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4016 r_free = 0.4016 target = 0.169056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133771 restraints weight = 16984.675| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.08 r_work: 0.3636 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14155 Z= 0.156 Angle : 0.630 9.796 19304 Z= 0.319 Chirality : 0.048 0.214 2238 Planarity : 0.005 0.063 2427 Dihedral : 7.137 55.444 2691 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.10 % Allowed : 11.96 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1680 helix: 2.83 (0.35), residues: 198 sheet: 1.47 (0.24), residues: 417 loop : -0.51 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.004 0.001 HIS C 184 PHE 0.012 0.002 PHE B 125 TYR 0.013 0.002 TYR J 100F ARG 0.004 0.000 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 21) link_NAG-ASN : angle 2.39370 ( 63) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 2.74996 ( 36) link_ALPHA1-3 : bond 0.01047 ( 3) link_ALPHA1-3 : angle 1.90641 ( 9) hydrogen bonds : bond 0.04674 ( 465) hydrogen bonds : angle 5.28006 ( 1386) link_BETA1-6 : bond 0.00739 ( 6) link_BETA1-6 : angle 1.05292 ( 18) SS BOND : bond 0.00180 ( 16) SS BOND : angle 1.27118 ( 32) covalent geometry : bond 0.00370 (14097) covalent geometry : angle 0.60123 (19146) *********************** 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 218 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 157 time to evaluate : 1.437 Fit side-chains REVERT: A 27 LYS cc_start: 0.7215 (mttt) cc_final: 0.6406 (mtpm) REVERT: A 246 ASN cc_start: 0.7743 (t0) cc_final: 0.7206 (m-40) REVERT: A 261 ARG cc_start: 0.7688 (ptt90) cc_final: 0.6862 (ptp-170) REVERT: A 406 ILE cc_start: 0.7554 (mp) cc_final: 0.7156 (mm) REVERT: H 19 LYS cc_start: 0.8596 (tttt) cc_final: 0.8218 (tppt) REVERT: L 72 SER cc_start: 0.7399 (OUTLIER) cc_final: 0.7182 (p) REVERT: L 93 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6404 (tttm) REVERT: L 94 SER cc_start: 0.7486 (OUTLIER) cc_final: 0.7163 (p) REVERT: B 27 LYS cc_start: 0.7248 (mttt) cc_final: 0.6533 (mtpm) REVERT: B 197 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: B 246 ASN cc_start: 0.7549 (t0) cc_final: 0.6971 (m-40) REVERT: B 261 ARG cc_start: 0.7658 (ptt90) cc_final: 0.6817 (ptp-170) REVERT: K 54 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7807 (mtm110) REVERT: K 93 LYS cc_start: 0.7469 (ttpp) cc_final: 0.6473 (tttm) REVERT: C 27 LYS cc_start: 0.7032 (mttt) cc_final: 0.6371 (mtpm) REVERT: C 246 ASN cc_start: 0.7633 (t0) cc_final: 0.7018 (m-40) REVERT: C 261 ARG cc_start: 0.7698 (ptt90) cc_final: 0.7019 (ptp-170) outliers start: 61 outliers final: 39 residues processed: 195 average time/residue: 1.0490 time to fit residues: 227.7051 Evaluate side-chains 194 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 20 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 56 SER 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 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 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 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 K residue 72 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 C residue 441 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 C 389 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131377 restraints weight = 17116.609| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.13 r_work: 0.3632 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14155 Z= 0.205 Angle : 0.694 10.870 19304 Z= 0.351 Chirality : 0.050 0.211 2238 Planarity : 0.005 0.068 2427 Dihedral : 7.018 56.782 2691 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.97 % Allowed : 13.51 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1680 helix: 2.46 (0.34), residues: 198 sheet: 1.41 (0.24), residues: 408 loop : -0.66 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 234 HIS 0.004 0.001 HIS C 184 PHE 0.015 0.002 PHE B 125 TYR 0.016 0.002 TYR Q 31A ARG 0.004 0.001 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.01024 ( 21) link_NAG-ASN : angle 2.78769 ( 63) link_BETA1-4 : bond 0.00439 ( 12) link_BETA1-4 : angle 2.88317 ( 36) link_ALPHA1-3 : bond 0.01007 ( 3) link_ALPHA1-3 : angle 2.43167 ( 9) hydrogen bonds : bond 0.05283 ( 465) hydrogen bonds : angle 5.41538 ( 1386) link_BETA1-6 : bond 0.00723 ( 6) link_BETA1-6 : angle 1.11294 ( 18) SS BOND : bond 0.00231 ( 16) SS BOND : angle 1.52517 ( 32) covalent geometry : bond 0.00494 (14097) covalent geometry : angle 0.66055 (19146) *********************** 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 211 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7269 (mttt) cc_final: 0.6464 (mtpm) REVERT: A 246 ASN cc_start: 0.7666 (t0) cc_final: 0.7152 (m-40) REVERT: A 261 ARG cc_start: 0.7695 (ptt90) cc_final: 0.6850 (ptp-170) REVERT: A 406 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7163 (mm) REVERT: L 93 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6436 (tttm) REVERT: L 94 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7296 (p) REVERT: B 27 LYS cc_start: 0.7298 (mttt) cc_final: 0.6585 (mtpm) REVERT: B 197 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: B 261 ARG cc_start: 0.7709 (ptt90) cc_final: 0.6876 (ptm160) REVERT: J 83 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7500 (mtt90) REVERT: K 93 LYS cc_start: 0.7547 (ttpp) cc_final: 0.6509 (tttm) REVERT: C 27 LYS cc_start: 0.7070 (mttt) cc_final: 0.6391 (mtpm) REVERT: C 246 ASN cc_start: 0.7627 (t0) cc_final: 0.7050 (m-40) REVERT: C 261 ARG cc_start: 0.7652 (ptt90) cc_final: 0.6953 (ptm160) outliers start: 59 outliers final: 41 residues processed: 189 average time/residue: 1.0347 time to fit residues: 217.8755 Evaluate side-chains 188 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 107 THR 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 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 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 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 K residue 72 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 C residue 441 ASP Chi-restraints excluded: chain Q residue 78 VAL 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 65 SER Chi-restraints excluded: chain P residue 93 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 144 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130868 restraints weight = 17156.729| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.13 r_work: 0.3623 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14155 Z= 0.222 Angle : 0.719 11.103 19304 Z= 0.363 Chirality : 0.051 0.231 2238 Planarity : 0.006 0.070 2427 Dihedral : 7.125 58.861 2691 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.70 % Allowed : 13.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1680 helix: 2.22 (0.34), residues: 198 sheet: 1.39 (0.25), residues: 402 loop : -0.75 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS C 184 PHE 0.015 0.002 PHE B 125 TYR 0.016 0.002 TYR Q 31A ARG 0.005 0.001 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.01164 ( 21) link_NAG-ASN : angle 3.01474 ( 63) link_BETA1-4 : bond 0.00402 ( 12) link_BETA1-4 : angle 2.91382 ( 36) link_ALPHA1-3 : bond 0.01009 ( 3) link_ALPHA1-3 : angle 2.22828 ( 9) hydrogen bonds : bond 0.05515 ( 465) hydrogen bonds : angle 5.50572 ( 1386) link_BETA1-6 : bond 0.00707 ( 6) link_BETA1-6 : angle 1.14991 ( 18) SS BOND : bond 0.00289 ( 16) SS BOND : angle 1.80568 ( 32) covalent geometry : bond 0.00540 (14097) covalent geometry : angle 0.68272 (19146) *********************** 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 214 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 144 time to evaluate : 1.510 Fit side-chains REVERT: A 27 LYS cc_start: 0.7271 (mttt) cc_final: 0.6467 (mtpm) REVERT: A 246 ASN cc_start: 0.7712 (t0) cc_final: 0.7225 (m-40) REVERT: A 261 ARG cc_start: 0.7693 (ptt90) cc_final: 0.6861 (ptp-170) REVERT: A 406 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7191 (mm) REVERT: H 62 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7079 (ttt180) REVERT: L 93 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6457 (tttm) REVERT: L 94 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7331 (p) REVERT: B 27 LYS cc_start: 0.7262 (mttt) cc_final: 0.6529 (mtpm) REVERT: B 197 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: B 246 ASN cc_start: 0.7558 (t0) cc_final: 0.7071 (m-40) REVERT: B 261 ARG cc_start: 0.7724 (ptt90) cc_final: 0.6886 (ptm160) REVERT: K 93 LYS cc_start: 0.7553 (ttpp) cc_final: 0.6516 (tttm) REVERT: C 27 LYS cc_start: 0.7079 (mttt) cc_final: 0.6401 (mtpm) REVERT: C 246 ASN cc_start: 0.7585 (t0) cc_final: 0.7039 (m-40) REVERT: C 261 ARG cc_start: 0.7704 (ptt90) cc_final: 0.7034 (ptm160) REVERT: Q 73 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5640 (mmt90) REVERT: P 61 ARG cc_start: 0.7036 (ttp-110) cc_final: 0.6799 (ttp-110) REVERT: P 93 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6347 (tptp) outliers start: 70 outliers final: 48 residues processed: 189 average time/residue: 1.1530 time to fit residues: 241.1680 Evaluate side-chains 195 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN 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 197 GLN 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 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 124 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 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 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 73 ARG Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain P residue 5 THR 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 93 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 chunk 40 optimal weight: 6.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 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 = 0.4020 r_free = 0.4020 target = 0.169304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135999 restraints weight = 17048.450| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.13 r_work: 0.3616 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14155 Z= 0.122 Angle : 0.597 8.417 19304 Z= 0.305 Chirality : 0.046 0.220 2238 Planarity : 0.005 0.063 2427 Dihedral : 6.675 58.200 2691 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.29 % Allowed : 14.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1680 helix: 2.79 (0.34), residues: 198 sheet: 1.65 (0.25), residues: 393 loop : -0.71 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 127 HIS 0.002 0.000 HIS B 156 PHE 0.009 0.001 PHE K 49 TYR 0.012 0.001 TYR Q 31A ARG 0.003 0.000 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00995 ( 21) link_NAG-ASN : angle 2.56040 ( 63) link_BETA1-4 : bond 0.00607 ( 12) link_BETA1-4 : angle 2.51240 ( 36) link_ALPHA1-3 : bond 0.01050 ( 3) link_ALPHA1-3 : angle 1.88977 ( 9) hydrogen bonds : bond 0.04374 ( 465) hydrogen bonds : angle 5.28704 ( 1386) link_BETA1-6 : bond 0.00750 ( 6) link_BETA1-6 : angle 1.07393 ( 18) SS BOND : bond 0.00167 ( 16) SS BOND : angle 1.24577 ( 32) covalent geometry : bond 0.00274 (14097) covalent geometry : angle 0.56637 (19146) *********************** 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 195 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7159 (mttt) cc_final: 0.6369 (mtpm) REVERT: A 246 ASN cc_start: 0.7600 (t0) cc_final: 0.7131 (m-40) REVERT: A 261 ARG cc_start: 0.7636 (ptt90) cc_final: 0.6762 (ptp-170) REVERT: A 406 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7063 (mm) REVERT: H 62 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7069 (ttt180) REVERT: L 93 LYS cc_start: 0.7423 (ttpt) cc_final: 0.6392 (tttm) REVERT: L 94 SER cc_start: 0.7547 (t) cc_final: 0.7234 (p) REVERT: B 27 LYS cc_start: 0.7194 (mttt) cc_final: 0.6472 (mtpm) REVERT: B 197 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: B 261 ARG cc_start: 0.7648 (ptt90) cc_final: 0.6767 (ptm160) REVERT: K 93 LYS cc_start: 0.7416 (ttpp) cc_final: 0.6430 (tttm) REVERT: C 27 LYS cc_start: 0.7063 (mttt) cc_final: 0.6356 (mtpm) REVERT: C 246 ASN cc_start: 0.7554 (t0) cc_final: 0.7000 (m-40) REVERT: C 261 ARG cc_start: 0.7631 (ptt90) cc_final: 0.6850 (ptm160) REVERT: Q 73 ARG cc_start: 0.6362 (OUTLIER) cc_final: 0.5593 (mmt90) REVERT: P 93 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6220 (tptp) outliers start: 49 outliers final: 36 residues processed: 177 average time/residue: 1.1046 time to fit residues: 217.0856 Evaluate side-chains 184 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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 277 CYS Chi-restraints excluded: chain A residue 406 ILE 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 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 100 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 J residue 56 SER Chi-restraints excluded: chain J residue 100 VAL 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 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 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 5 THR 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 65 SER Chi-restraints excluded: chain P residue 93 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 ASN K 79 GLN P 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135875 restraints weight = 17004.103| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.12 r_work: 0.3617 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14155 Z= 0.135 Angle : 0.607 8.610 19304 Z= 0.309 Chirality : 0.047 0.211 2238 Planarity : 0.005 0.062 2427 Dihedral : 6.422 59.678 2691 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.29 % Allowed : 14.99 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 1680 helix: 2.89 (0.34), residues: 198 sheet: 1.60 (0.25), residues: 396 loop : -0.73 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.002 0.001 HIS C 184 PHE 0.010 0.001 PHE B 120 TYR 0.013 0.002 TYR Q 31A ARG 0.003 0.000 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.01005 ( 21) link_NAG-ASN : angle 2.64593 ( 63) link_BETA1-4 : bond 0.00462 ( 12) link_BETA1-4 : angle 2.57556 ( 36) link_ALPHA1-3 : bond 0.01022 ( 3) link_ALPHA1-3 : angle 1.81976 ( 9) hydrogen bonds : bond 0.04426 ( 465) hydrogen bonds : angle 5.27215 ( 1386) link_BETA1-6 : bond 0.00732 ( 6) link_BETA1-6 : angle 1.05072 ( 18) SS BOND : bond 0.00191 ( 16) SS BOND : angle 1.23784 ( 32) covalent geometry : bond 0.00314 (14097) covalent geometry : angle 0.57524 (19146) *********************** 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 192 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7118 (mttt) cc_final: 0.6355 (mtpm) REVERT: A 246 ASN cc_start: 0.7656 (t0) cc_final: 0.7157 (m-40) REVERT: A 261 ARG cc_start: 0.7645 (ptt90) cc_final: 0.6782 (ptp-170) REVERT: A 406 ILE cc_start: 0.7519 (mp) cc_final: 0.7101 (mm) REVERT: H 62 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7057 (ttt180) REVERT: L 93 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6350 (tttm) REVERT: L 94 SER cc_start: 0.7564 (t) cc_final: 0.7251 (p) REVERT: B 27 LYS cc_start: 0.7217 (mttt) cc_final: 0.6526 (mtpm) REVERT: B 197 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: B 261 ARG cc_start: 0.7659 (ptt90) cc_final: 0.6780 (ptm160) REVERT: K 87 TYR cc_start: 0.7681 (m-80) cc_final: 0.7323 (m-80) REVERT: K 93 LYS cc_start: 0.7377 (ttpp) cc_final: 0.6382 (tttm) REVERT: C 27 LYS cc_start: 0.7061 (mttt) cc_final: 0.6361 (mtpm) REVERT: C 246 ASN cc_start: 0.7564 (t0) cc_final: 0.7015 (m-40) REVERT: C 261 ARG cc_start: 0.7640 (ptt90) cc_final: 0.6884 (ptm160) REVERT: Q 73 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5675 (mmt90) REVERT: P 93 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6221 (tptp) outliers start: 49 outliers final: 37 residues processed: 175 average time/residue: 1.1330 time to fit residues: 219.4551 Evaluate side-chains 180 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 441 ASP Chi-restraints excluded: chain H residue 62 ARG 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 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 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 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 78 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain P residue 5 THR 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 65 SER Chi-restraints excluded: chain P residue 93 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 129 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.167629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134381 restraints weight = 16952.352| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.12 r_work: 0.3598 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14155 Z= 0.173 Angle : 0.651 9.560 19304 Z= 0.330 Chirality : 0.048 0.214 2238 Planarity : 0.005 0.064 2427 Dihedral : 6.431 59.932 2691 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.83 % Allowed : 14.52 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1680 helix: 2.69 (0.34), residues: 198 sheet: 1.56 (0.25), residues: 396 loop : -0.81 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.003 0.001 HIS C 184 PHE 0.012 0.002 PHE B 125 TYR 0.014 0.002 TYR Q 31A ARG 0.004 0.000 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.01085 ( 21) link_NAG-ASN : angle 2.79777 ( 63) link_BETA1-4 : bond 0.00440 ( 12) link_BETA1-4 : angle 2.64025 ( 36) link_ALPHA1-3 : bond 0.00850 ( 3) link_ALPHA1-3 : angle 1.90348 ( 9) hydrogen bonds : bond 0.04820 ( 465) hydrogen bonds : angle 5.32700 ( 1386) link_BETA1-6 : bond 0.00716 ( 6) link_BETA1-6 : angle 1.06961 ( 18) SS BOND : bond 0.00230 ( 16) SS BOND : angle 1.43015 ( 32) covalent geometry : bond 0.00414 (14097) covalent geometry : angle 0.61873 (19146) *********************** 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 197 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7154 (mttt) cc_final: 0.6394 (mtpm) REVERT: A 246 ASN cc_start: 0.7649 (t0) cc_final: 0.7181 (m-40) REVERT: A 261 ARG cc_start: 0.7697 (ptt90) cc_final: 0.6838 (ptp-170) REVERT: A 406 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7139 (mm) REVERT: H 62 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7083 (ttt180) REVERT: L 93 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6392 (tttm) REVERT: L 94 SER cc_start: 0.7609 (t) cc_final: 0.7313 (p) REVERT: B 27 LYS cc_start: 0.7274 (mttt) cc_final: 0.6558 (mtpm) REVERT: B 197 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: B 261 ARG cc_start: 0.7694 (ptt90) cc_final: 0.6823 (ptm160) REVERT: J 83 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7498 (mtt90) REVERT: K 87 TYR cc_start: 0.7704 (m-80) cc_final: 0.7332 (m-80) REVERT: K 93 LYS cc_start: 0.7435 (ttpp) cc_final: 0.6440 (tttm) REVERT: C 27 LYS cc_start: 0.7113 (mttt) cc_final: 0.6411 (mtpm) REVERT: C 246 ASN cc_start: 0.7573 (t0) cc_final: 0.7047 (m-40) REVERT: C 261 ARG cc_start: 0.7642 (ptt90) cc_final: 0.6901 (ptm160) REVERT: Q 73 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5536 (mmt90) REVERT: P 93 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.6257 (tptp) outliers start: 57 outliers final: 46 residues processed: 178 average time/residue: 1.1284 time to fit residues: 222.8292 Evaluate side-chains 190 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 437 ILE Chi-restraints excluded: chain A residue 441 ASP 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 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 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 277 CYS Chi-restraints excluded: chain B residue 437 ILE 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 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 110 SER Chi-restraints excluded: chain P residue 5 THR 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 52 ASN Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 93 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 ASN K 79 GLN ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132425 restraints weight = 17047.702| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.08 r_work: 0.3618 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.202 14155 Z= 0.253 Angle : 0.921 59.175 19304 Z= 0.513 Chirality : 0.050 0.369 2238 Planarity : 0.006 0.137 2427 Dihedral : 6.462 59.898 2691 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.49 % Allowed : 14.52 % Favored : 81.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1680 helix: 2.65 (0.34), residues: 198 sheet: 1.56 (0.25), residues: 396 loop : -0.81 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.003 0.001 HIS C 184 PHE 0.013 0.002 PHE B 125 TYR 0.015 0.002 TYR Q 31A ARG 0.004 0.001 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.02176 ( 21) link_NAG-ASN : angle 3.71265 ( 63) link_BETA1-4 : bond 0.00423 ( 12) link_BETA1-4 : angle 2.68292 ( 36) link_ALPHA1-3 : bond 0.00646 ( 3) link_ALPHA1-3 : angle 1.93220 ( 9) hydrogen bonds : bond 0.04901 ( 465) hydrogen bonds : angle 5.33065 ( 1386) link_BETA1-6 : bond 0.00667 ( 6) link_BETA1-6 : angle 1.07004 ( 18) SS BOND : bond 0.00203 ( 16) SS BOND : angle 1.41352 ( 32) covalent geometry : bond 0.00560 (14097) covalent geometry : angle 0.88864 (19146) ********************** 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 189 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7190 (mttt) cc_final: 0.6430 (mtpm) REVERT: A 246 ASN cc_start: 0.7680 (t0) cc_final: 0.7192 (m-40) REVERT: A 261 ARG cc_start: 0.7709 (ptt90) cc_final: 0.6868 (ptp-170) REVERT: A 406 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7155 (mm) REVERT: H 62 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7100 (ttt180) REVERT: L 93 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6419 (tttm) REVERT: L 94 SER cc_start: 0.7630 (t) cc_final: 0.7337 (p) REVERT: B 27 LYS cc_start: 0.7299 (mttt) cc_final: 0.6586 (mtpm) REVERT: B 197 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: B 261 ARG cc_start: 0.7708 (ptt90) cc_final: 0.6851 (ptm160) REVERT: J 83 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7520 (mtt90) REVERT: K 87 TYR cc_start: 0.7720 (m-80) cc_final: 0.7353 (m-80) REVERT: K 93 LYS cc_start: 0.7452 (ttpp) cc_final: 0.6465 (tttm) REVERT: C 27 LYS cc_start: 0.7150 (mttt) cc_final: 0.6452 (mtpm) REVERT: C 246 ASN cc_start: 0.7574 (t0) cc_final: 0.7055 (m-40) REVERT: C 261 ARG cc_start: 0.7650 (ptt90) cc_final: 0.6917 (ptm160) REVERT: Q 73 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5557 (mmt90) REVERT: P 93 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6285 (tptp) outliers start: 52 outliers final: 44 residues processed: 172 average time/residue: 1.1966 time to fit residues: 228.0198 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 : 1.765 ------------------------------------------------------------------------------- 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 437 ILE Chi-restraints excluded: chain A residue 441 ASP 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 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 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 277 CYS Chi-restraints excluded: chain B residue 437 ILE 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 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 110 SER Chi-restraints excluded: chain P residue 5 THR 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 65 SER Chi-restraints excluded: chain P residue 93 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 155 optimal weight: 0.0060 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 79 GLN ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.167511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132416 restraints weight = 17210.586| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.09 r_work: 0.3618 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.257 14155 Z= 0.272 Angle : 0.924 59.174 19304 Z= 0.514 Chirality : 0.050 0.369 2238 Planarity : 0.006 0.137 2427 Dihedral : 6.462 59.898 2691 Min Nonbonded Distance : 1.488 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.36 % Allowed : 14.58 % Favored : 82.06 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1680 helix: 2.65 (0.34), residues: 198 sheet: 1.56 (0.25), residues: 396 loop : -0.81 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.003 0.001 HIS C 184 PHE 0.013 0.002 PHE B 125 TYR 0.015 0.002 TYR Q 31A ARG 0.004 0.001 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.05668 ( 21) link_NAG-ASN : angle 3.96748 ( 63) link_BETA1-4 : bond 0.00423 ( 12) link_BETA1-4 : angle 2.68292 ( 36) link_ALPHA1-3 : bond 0.00646 ( 3) link_ALPHA1-3 : angle 1.93222 ( 9) hydrogen bonds : bond 0.04901 ( 465) hydrogen bonds : angle 5.33065 ( 1386) link_BETA1-6 : bond 0.00667 ( 6) link_BETA1-6 : angle 1.07004 ( 18) SS BOND : bond 0.00203 ( 16) SS BOND : angle 1.41352 ( 32) covalent geometry : bond 0.00560 (14097) covalent geometry : angle 0.88864 (19146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11750.52 seconds wall clock time: 203 minutes 16.77 seconds (12196.77 seconds total)