Starting phenix.real_space_refine on Wed Mar 4 13:06:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uye_20947/03_2026/6uye_20947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uye_20947/03_2026/6uye_20947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uye_20947/03_2026/6uye_20947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uye_20947/03_2026/6uye_20947.map" model { file = "/net/cci-nas-00/data/ceres_data/6uye_20947/03_2026/6uye_20947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uye_20947/03_2026/6uye_20947.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.074 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 51 5.16 5 C 8676 2.51 5 N 2262 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13692 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1808 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 12, 'TRANS': 218} Chain breaks: 2 Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 730 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" 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: "O" 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: "A" 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 Restraints were copied for chains: B, C, E, F, H, I, K, L, P, S, Q, T, R, U Time building chain proxies: 2.39, per 1000 atoms: 0.17 Number of scatterers: 13692 At special positions: 0 Unit cell: (120.51, 122.57, 123.6, 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 51 16.00 O 2703 8.00 N 2262 7.00 C 8676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA P 3 " - " MAN P 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 301 " - " ASN A 228 " " NAG A 309 " - " ASN A 238 " " NAG B 301 " - " ASN B 228 " " NAG B 309 " - " ASN B 238 " " NAG C 301 " - " ASN C 228 " " NAG C 309 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN A 268 " " NAG O 1 " - " ASN D 563 " " NAG P 1 " - " ASN B 257 " " NAG Q 1 " - " ASN B 268 " " NAG R 1 " - " ASN E 563 " " NAG S 1 " - " ASN C 257 " " NAG T 1 " - " ASN C 268 " " NAG U 1 " - " ASN F 563 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 585.3 milliseconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 15.1% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 553 through 575 removed outlier: 3.711A pdb=" N ASN D 563 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.582A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.636A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.724A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.224A pdb=" N SER J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 553 through 575 removed outlier: 3.711A pdb=" N ASN E 563 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.581A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.635A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.724A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.223A pdb=" N SER K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 553 through 575 removed outlier: 3.711A pdb=" N ASN F 563 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.582A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.636A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.724A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.224A pdb=" N SER L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 removed outlier: 3.702A pdb=" N ILE A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 184 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 64 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 3.601A pdb=" N GLY A 87 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 89 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 161 removed outlier: 6.580A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 114 removed outlier: 6.549A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 142 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 14.972A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU A 235 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 242 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.500A pdb=" N LEU G 18 " --> pdb=" O MET G 83 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU G 81 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.088A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.457A pdb=" N CYS G 96 " --> pdb=" O TRP G 121 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP G 121 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS G 98 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.574A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.488A pdb=" N VAL J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.701A pdb=" N ILE B 38 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 184 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 64 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 89 removed outlier: 3.601A pdb=" N GLY B 87 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 89 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 160 through 161 removed outlier: 6.562A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB6, first strand: chain 'B' and resid 108 through 114 removed outlier: 6.549A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 142 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 14.971A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 235 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 242 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.500A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.088A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.458A pdb=" N CYS H 96 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP H 121 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS H 98 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.575A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.487A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 45 removed outlier: 3.702A pdb=" N ILE C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 184 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 64 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 86 through 89 removed outlier: 3.601A pdb=" N GLY C 87 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C 89 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 160 through 161 removed outlier: 6.580A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AC7, first strand: chain 'C' and resid 108 through 114 removed outlier: 6.549A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 142 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 14.971A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU C 235 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 242 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.500A pdb=" N LEU I 18 " --> pdb=" O MET I 83 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.088A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.457A pdb=" N CYS I 96 " --> pdb=" O TRP I 121 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP I 121 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS I 98 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.575A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.487A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2433 1.32 - 1.44: 3874 1.44 - 1.56: 7622 1.56 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 13998 Sorted by residual: bond pdb=" CA HIS H 35 " pdb=" CB HIS H 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.14e+00 bond pdb=" CA HIS G 35 " pdb=" CB HIS G 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.09e+00 bond pdb=" CA HIS I 35 " pdb=" CB HIS I 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.07e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 13993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 17946 2.22 - 4.45: 904 4.45 - 6.67: 117 6.67 - 8.89: 26 8.89 - 11.12: 6 Bond angle restraints: 18999 Sorted by residual: angle pdb=" C ASP A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 120.43 125.49 -5.06 9.60e-01 1.09e+00 2.78e+01 angle pdb=" C ASP B 78 " pdb=" N VAL B 79 " pdb=" CA VAL B 79 " ideal model delta sigma weight residual 120.43 125.48 -5.05 9.60e-01 1.09e+00 2.77e+01 angle pdb=" C ASP C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta sigma weight residual 120.43 125.44 -5.01 9.60e-01 1.09e+00 2.73e+01 angle pdb=" C SER G 113 " pdb=" N TYR G 114 " pdb=" CA TYR G 114 " ideal model delta sigma weight residual 122.17 114.35 7.82 1.54e+00 4.22e-01 2.58e+01 angle pdb=" C SER H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta sigma weight residual 122.17 114.40 7.77 1.54e+00 4.22e-01 2.55e+01 ... (remaining 18994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 8415 21.54 - 43.07: 195 43.07 - 64.61: 39 64.61 - 86.14: 45 86.14 - 107.68: 24 Dihedral angle restraints: 8718 sinusoidal: 3900 harmonic: 4818 Sorted by residual: dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 138.49 41.51 0 5.00e+00 4.00e-02 6.89e+01 dihedral pdb=" CA PHE J 94 " pdb=" C PHE J 94 " pdb=" N PRO J 95 " pdb=" CA PRO J 95 " ideal model delta harmonic sigma weight residual 180.00 138.50 41.50 0 5.00e+00 4.00e-02 6.89e+01 dihedral pdb=" CA PHE K 94 " pdb=" C PHE K 94 " pdb=" N PRO K 95 " pdb=" CA PRO K 95 " ideal model delta harmonic sigma weight residual 180.00 138.51 41.49 0 5.00e+00 4.00e-02 6.89e+01 ... (remaining 8715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1545 0.059 - 0.118: 525 0.118 - 0.178: 105 0.178 - 0.237: 18 0.237 - 0.296: 12 Chirality restraints: 2205 Sorted by residual: chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2202 not shown) Planarity restraints: 2385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " 0.061 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO L 95 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE K 94 " 0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO K 95 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO K 95 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO K 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 94 " 0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO J 95 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO J 95 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO J 95 " 0.051 5.00e-02 4.00e+02 ... (remaining 2382 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3466 2.79 - 3.32: 11173 3.32 - 3.84: 22703 3.84 - 4.37: 24183 4.37 - 4.90: 42826 Nonbonded interactions: 104351 Sorted by model distance: nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 97 " model vdw 2.260 3.040 nonbonded pdb=" O ILE K 2 " pdb=" OG1 THR K 97 " model vdw 2.261 3.040 nonbonded pdb=" O ILE J 2 " pdb=" OG1 THR J 97 " model vdw 2.261 3.040 nonbonded pdb=" ND2 ASN C 278 " pdb=" O TRP I 108 " model vdw 2.299 3.120 nonbonded pdb=" O ALA D 562 " pdb=" OG1 THR D 566 " model vdw 2.323 3.040 ... (remaining 104346 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.010 0.069 14052 Z= 0.460 Angle : 1.154 16.482 19146 Z= 0.607 Chirality : 0.063 0.296 2205 Planarity : 0.007 0.092 2370 Dihedral : 13.382 107.679 5601 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.18), residues: 1644 helix: -2.26 (0.28), residues: 171 sheet: -1.62 (0.20), residues: 591 loop : -2.27 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 596 TYR 0.030 0.004 TYR B 109 PHE 0.027 0.004 PHE C 176 TRP 0.031 0.004 TRP C 104 HIS 0.013 0.002 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.01025 (13998) covalent geometry : angle 1.11496 (18999) SS BOND : bond 0.00659 ( 15) SS BOND : angle 1.23633 ( 30) hydrogen bonds : bond 0.23518 ( 429) hydrogen bonds : angle 9.56156 ( 1143) link_ALPHA1-3 : bond 0.00629 ( 6) link_ALPHA1-3 : angle 1.94754 ( 18) link_ALPHA1-6 : bond 0.00177 ( 3) link_ALPHA1-6 : angle 1.52075 ( 9) link_BETA1-4 : bond 0.00833 ( 15) link_BETA1-4 : angle 2.93093 ( 45) link_NAG-ASN : bond 0.01111 ( 15) link_NAG-ASN : angle 5.47245 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8364 (p0) cc_final: 0.7979 (p0) REVERT: A 235 GLU cc_start: 0.8108 (tt0) cc_final: 0.7690 (tm-30) REVERT: A 291 TRP cc_start: 0.6138 (p90) cc_final: 0.5447 (p90) REVERT: D 587 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7998 (ttm-80) REVERT: G 34 MET cc_start: 0.8211 (mmm) cc_final: 0.7914 (mmm) REVERT: G 54 ASP cc_start: 0.8402 (p0) cc_final: 0.8105 (p0) REVERT: G 68 PHE cc_start: 0.6833 (m-10) cc_final: 0.6193 (m-10) REVERT: G 119 ASP cc_start: 0.8208 (p0) cc_final: 0.7943 (p0) REVERT: J 28 ASP cc_start: 0.8110 (t0) cc_final: 0.7881 (t0) REVERT: J 37 GLN cc_start: 0.8406 (tt0) cc_final: 0.7811 (tm-30) REVERT: J 104 LEU cc_start: 0.8964 (tp) cc_final: 0.8746 (tt) REVERT: J 108 ARG cc_start: 0.3432 (mtt180) cc_final: 0.1297 (ttp80) REVERT: B 117 ASP cc_start: 0.8377 (p0) cc_final: 0.8058 (p0) REVERT: B 229 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7484 (pp20) REVERT: B 235 GLU cc_start: 0.8125 (tt0) cc_final: 0.7733 (tm-30) REVERT: B 280 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7528 (mp0) REVERT: B 291 TRP cc_start: 0.6110 (p90) cc_final: 0.5467 (p90) REVERT: E 587 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7826 (ttm-80) REVERT: E 588 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7823 (mmmm) REVERT: H 36 TRP cc_start: 0.7741 (m100) cc_final: 0.6682 (m100) REVERT: H 54 ASP cc_start: 0.8415 (p0) cc_final: 0.7922 (p0) REVERT: H 57 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8112 (tptm) REVERT: H 68 PHE cc_start: 0.6897 (m-10) cc_final: 0.6283 (m-80) REVERT: H 119 ASP cc_start: 0.8366 (p0) cc_final: 0.8154 (p0) REVERT: K 37 GLN cc_start: 0.8513 (tt0) cc_final: 0.8167 (tm-30) REVERT: K 71 PHE cc_start: 0.7910 (m-10) cc_final: 0.7663 (m-10) REVERT: K 108 ARG cc_start: 0.3098 (mtt180) cc_final: 0.0693 (ptt90) REVERT: C 56 LYS cc_start: 0.7486 (mmtm) cc_final: 0.7268 (mmmt) REVERT: C 117 ASP cc_start: 0.8384 (p0) cc_final: 0.8089 (p0) REVERT: C 235 GLU cc_start: 0.8120 (tt0) cc_final: 0.7645 (tm-30) REVERT: C 291 TRP cc_start: 0.6106 (p90) cc_final: 0.5472 (p90) REVERT: F 527 ILE cc_start: 0.5793 (mm) cc_final: 0.5113 (mm) REVERT: F 587 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7924 (ttm-80) REVERT: I 34 MET cc_start: 0.8244 (mmm) cc_final: 0.7844 (mmm) REVERT: I 36 TRP cc_start: 0.7700 (m100) cc_final: 0.6720 (m100) REVERT: I 38 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7725 (ttm-80) REVERT: I 54 ASP cc_start: 0.8390 (p0) cc_final: 0.7895 (p0) REVERT: I 68 PHE cc_start: 0.6774 (m-10) cc_final: 0.6081 (m-10) REVERT: I 94 TYR cc_start: 0.6507 (m-10) cc_final: 0.6253 (m-10) REVERT: I 104 TYR cc_start: 0.8253 (m-10) cc_final: 0.7956 (m-10) REVERT: L 49 TYR cc_start: 0.8000 (p90) cc_final: 0.7554 (p90) REVERT: L 67 SER cc_start: 0.7996 (t) cc_final: 0.7464 (p) REVERT: L 71 PHE cc_start: 0.7798 (m-10) cc_final: 0.7202 (m-10) REVERT: L 108 ARG cc_start: 0.3197 (mtt180) cc_final: 0.0521 (ptt90) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.1395 time to fit residues: 100.4713 Evaluate side-chains 322 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN D 516 HIS D 595 GLN J 6 GLN J 38 GLN E 516 HIS E 595 GLN K 38 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN F 516 HIS ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.119940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092177 restraints weight = 27329.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095462 restraints weight = 15419.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.097668 restraints weight = 10587.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099135 restraints weight = 8262.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099992 restraints weight = 6993.027| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14052 Z= 0.166 Angle : 0.766 8.311 19146 Z= 0.379 Chirality : 0.048 0.188 2205 Planarity : 0.005 0.049 2370 Dihedral : 11.933 77.509 2622 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.91 % Allowed : 11.72 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.20), residues: 1644 helix: 0.14 (0.40), residues: 174 sheet: -1.47 (0.19), residues: 648 loop : -1.51 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.025 0.002 TYR I 115 PHE 0.017 0.002 PHE A 290 TRP 0.014 0.001 TRP G 121 HIS 0.002 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00378 (13998) covalent geometry : angle 0.74160 (18999) SS BOND : bond 0.00316 ( 15) SS BOND : angle 1.58514 ( 30) hydrogen bonds : bond 0.03636 ( 429) hydrogen bonds : angle 6.93337 ( 1143) link_ALPHA1-3 : bond 0.00962 ( 6) link_ALPHA1-3 : angle 2.30723 ( 18) link_ALPHA1-6 : bond 0.00951 ( 3) link_ALPHA1-6 : angle 1.28941 ( 9) link_BETA1-4 : bond 0.00398 ( 15) link_BETA1-4 : angle 2.32355 ( 45) link_NAG-ASN : bond 0.00438 ( 15) link_NAG-ASN : angle 2.80896 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 384 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7391 (mmmt) cc_final: 0.6882 (mptt) REVERT: A 117 ASP cc_start: 0.8332 (p0) cc_final: 0.7956 (p0) REVERT: A 122 LEU cc_start: 0.8670 (mp) cc_final: 0.8439 (mt) REVERT: A 140 LYS cc_start: 0.8884 (tttt) cc_final: 0.8658 (ttmm) REVERT: A 235 GLU cc_start: 0.8070 (tt0) cc_final: 0.7420 (tm-30) REVERT: A 291 TRP cc_start: 0.5843 (p90) cc_final: 0.5302 (p90) REVERT: D 587 ARG cc_start: 0.8532 (mtp85) cc_final: 0.8148 (ttm110) REVERT: G 34 MET cc_start: 0.8175 (mmm) cc_final: 0.7834 (mmm) REVERT: G 54 ASP cc_start: 0.8181 (p0) cc_final: 0.7758 (p0) REVERT: G 119 ASP cc_start: 0.8309 (p0) cc_final: 0.7895 (t70) REVERT: J 4 MET cc_start: 0.6919 (ttm) cc_final: 0.6521 (ttm) REVERT: J 24 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.6776 (mmm-85) REVERT: J 70 ASP cc_start: 0.8367 (t0) cc_final: 0.7844 (t70) REVERT: J 90 GLN cc_start: 0.8661 (pp30) cc_final: 0.8053 (pp30) REVERT: J 104 LEU cc_start: 0.8942 (tp) cc_final: 0.8508 (tt) REVERT: J 108 ARG cc_start: 0.3745 (mtt180) cc_final: 0.1538 (ptt90) REVERT: B 56 LYS cc_start: 0.7367 (mmmt) cc_final: 0.7005 (mptt) REVERT: B 117 ASP cc_start: 0.8303 (p0) cc_final: 0.7954 (p0) REVERT: B 235 GLU cc_start: 0.8203 (tt0) cc_final: 0.7586 (tm-30) REVERT: B 291 TRP cc_start: 0.6037 (p90) cc_final: 0.5631 (p90) REVERT: E 587 ARG cc_start: 0.8370 (mtp85) cc_final: 0.7881 (ttm-80) REVERT: H 36 TRP cc_start: 0.7624 (m100) cc_final: 0.6730 (m100) REVERT: H 54 ASP cc_start: 0.8271 (p0) cc_final: 0.7774 (p0) REVERT: H 57 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8192 (mmtp) REVERT: K 90 GLN cc_start: 0.8800 (pp30) cc_final: 0.8148 (pp30) REVERT: K 92 LYS cc_start: 0.8647 (tttm) cc_final: 0.8424 (tttm) REVERT: K 108 ARG cc_start: 0.3597 (mtt180) cc_final: 0.1183 (ptt90) REVERT: C 117 ASP cc_start: 0.8253 (p0) cc_final: 0.7960 (p0) REVERT: C 229 GLU cc_start: 0.7762 (pp20) cc_final: 0.7426 (pp20) REVERT: C 235 GLU cc_start: 0.8188 (tt0) cc_final: 0.7558 (tm-30) REVERT: C 291 TRP cc_start: 0.5974 (p90) cc_final: 0.5435 (p90) REVERT: F 527 ILE cc_start: 0.5694 (mm) cc_final: 0.5158 (mm) REVERT: F 587 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8080 (ttm-80) REVERT: I 36 TRP cc_start: 0.7658 (m100) cc_final: 0.6766 (m100) REVERT: I 48 MET cc_start: 0.6024 (mtp) cc_final: 0.5501 (mtp) REVERT: I 54 ASP cc_start: 0.8223 (p0) cc_final: 0.7745 (p0) REVERT: I 104 TYR cc_start: 0.8209 (m-10) cc_final: 0.7885 (m-10) REVERT: L 2 ILE cc_start: 0.6913 (pt) cc_final: 0.6696 (pt) REVERT: L 67 SER cc_start: 0.7951 (t) cc_final: 0.7644 (p) REVERT: L 104 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8092 (tt) REVERT: L 108 ARG cc_start: 0.3372 (mtt180) cc_final: 0.0973 (ptt90) outliers start: 27 outliers final: 18 residues processed: 399 average time/residue: 0.1365 time to fit residues: 75.0548 Evaluate side-chains 335 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 316 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 595 GLN J 37 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091384 restraints weight = 27552.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094350 restraints weight = 16303.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096366 restraints weight = 11576.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097703 restraints weight = 9218.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098461 restraints weight = 7905.525| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14052 Z= 0.177 Angle : 0.740 8.714 19146 Z= 0.361 Chirality : 0.047 0.181 2205 Planarity : 0.005 0.055 2370 Dihedral : 10.467 71.816 2622 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.47 % Allowed : 14.19 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1644 helix: 0.56 (0.41), residues: 180 sheet: -1.23 (0.20), residues: 648 loop : -1.32 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 136 TYR 0.021 0.002 TYR I 115 PHE 0.016 0.002 PHE D 592 TRP 0.013 0.001 TRP G 36 HIS 0.005 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00409 (13998) covalent geometry : angle 0.72068 (18999) SS BOND : bond 0.00566 ( 15) SS BOND : angle 1.23061 ( 30) hydrogen bonds : bond 0.03448 ( 429) hydrogen bonds : angle 6.37736 ( 1143) link_ALPHA1-3 : bond 0.01017 ( 6) link_ALPHA1-3 : angle 1.69918 ( 18) link_ALPHA1-6 : bond 0.00873 ( 3) link_ALPHA1-6 : angle 1.30541 ( 9) link_BETA1-4 : bond 0.00375 ( 15) link_BETA1-4 : angle 2.08322 ( 45) link_NAG-ASN : bond 0.00241 ( 15) link_NAG-ASN : angle 2.67432 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7535 (mmmt) cc_final: 0.7124 (mptt) REVERT: A 117 ASP cc_start: 0.8331 (p0) cc_final: 0.7978 (p0) REVERT: A 140 LYS cc_start: 0.8901 (tttt) cc_final: 0.8687 (ttmm) REVERT: A 235 GLU cc_start: 0.8075 (tt0) cc_final: 0.7568 (tm-30) REVERT: D 587 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8071 (ttm110) REVERT: G 34 MET cc_start: 0.8263 (mmm) cc_final: 0.7938 (mmm) REVERT: G 54 ASP cc_start: 0.8264 (p0) cc_final: 0.7880 (p0) REVERT: G 57 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8553 (mmtp) REVERT: G 95 TYR cc_start: 0.7290 (m-80) cc_final: 0.7018 (m-10) REVERT: G 119 ASP cc_start: 0.8273 (p0) cc_final: 0.7844 (t70) REVERT: J 24 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.6790 (mmm-85) REVERT: J 70 ASP cc_start: 0.8358 (t0) cc_final: 0.7717 (t70) REVERT: J 90 GLN cc_start: 0.8642 (pp30) cc_final: 0.8141 (pp30) REVERT: J 104 LEU cc_start: 0.8859 (tp) cc_final: 0.8346 (tt) REVERT: J 108 ARG cc_start: 0.3753 (mtt180) cc_final: 0.1580 (ptt90) REVERT: B 56 LYS cc_start: 0.7350 (mmmt) cc_final: 0.7085 (mptt) REVERT: B 117 ASP cc_start: 0.8297 (p0) cc_final: 0.7929 (p0) REVERT: B 235 GLU cc_start: 0.8197 (tt0) cc_final: 0.7682 (tm-30) REVERT: B 291 TRP cc_start: 0.6058 (p90) cc_final: 0.5514 (p90) REVERT: E 587 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7815 (ttm-80) REVERT: H 36 TRP cc_start: 0.7672 (m100) cc_final: 0.6458 (m100) REVERT: H 54 ASP cc_start: 0.8239 (p0) cc_final: 0.7810 (p0) REVERT: H 68 PHE cc_start: 0.5770 (m-80) cc_final: 0.5275 (m-80) REVERT: H 86 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7160 (mt) REVERT: K 45 GLU cc_start: 0.8243 (tp30) cc_final: 0.8007 (tp30) REVERT: K 70 ASP cc_start: 0.8321 (t70) cc_final: 0.7914 (t70) REVERT: K 90 GLN cc_start: 0.8757 (pp30) cc_final: 0.8215 (pp30) REVERT: K 97 THR cc_start: 0.8542 (p) cc_final: 0.8240 (p) REVERT: K 108 ARG cc_start: 0.3556 (mtt180) cc_final: 0.1253 (ptt90) REVERT: C 56 LYS cc_start: 0.7576 (mmmt) cc_final: 0.6902 (mptt) REVERT: C 117 ASP cc_start: 0.8215 (p0) cc_final: 0.7898 (p0) REVERT: C 229 GLU cc_start: 0.7845 (pp20) cc_final: 0.7419 (pp20) REVERT: C 235 GLU cc_start: 0.8162 (tt0) cc_final: 0.7573 (tm-30) REVERT: C 291 TRP cc_start: 0.6049 (p90) cc_final: 0.5347 (p90) REVERT: F 527 ILE cc_start: 0.5757 (mm) cc_final: 0.5245 (mm) REVERT: F 587 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8031 (ttm-80) REVERT: I 38 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6747 (ptp-110) REVERT: I 54 ASP cc_start: 0.8211 (p0) cc_final: 0.7762 (p0) REVERT: I 95 TYR cc_start: 0.7376 (m-10) cc_final: 0.7127 (m-10) REVERT: I 104 TYR cc_start: 0.8323 (m-10) cc_final: 0.7919 (m-10) REVERT: L 2 ILE cc_start: 0.6902 (pt) cc_final: 0.6627 (pt) REVERT: L 37 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: L 67 SER cc_start: 0.8086 (t) cc_final: 0.7612 (p) REVERT: L 104 LEU cc_start: 0.8760 (tp) cc_final: 0.7989 (tt) REVERT: L 108 ARG cc_start: 0.3220 (mtt180) cc_final: 0.0959 (ptt90) outliers start: 35 outliers final: 21 residues processed: 352 average time/residue: 0.1314 time to fit residues: 64.4595 Evaluate side-chains 331 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 307 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN K 37 GLN K 38 GLN F 508 GLN ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088160 restraints weight = 27840.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091050 restraints weight = 16764.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092973 restraints weight = 11993.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094239 restraints weight = 9657.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095013 restraints weight = 8359.338| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14052 Z= 0.272 Angle : 0.801 9.835 19146 Z= 0.390 Chirality : 0.050 0.207 2205 Planarity : 0.005 0.045 2370 Dihedral : 9.109 65.672 2622 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.46 % Allowed : 15.04 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.21), residues: 1644 helix: 0.62 (0.40), residues: 180 sheet: -1.23 (0.20), residues: 630 loop : -1.36 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.023 0.002 TYR I 115 PHE 0.014 0.002 PHE I 68 TRP 0.027 0.002 TRP D 597 HIS 0.005 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00634 (13998) covalent geometry : angle 0.78219 (18999) SS BOND : bond 0.00266 ( 15) SS BOND : angle 1.45854 ( 30) hydrogen bonds : bond 0.03771 ( 429) hydrogen bonds : angle 6.39673 ( 1143) link_ALPHA1-3 : bond 0.01021 ( 6) link_ALPHA1-3 : angle 1.87110 ( 18) link_ALPHA1-6 : bond 0.00975 ( 3) link_ALPHA1-6 : angle 1.30433 ( 9) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.95420 ( 45) link_NAG-ASN : bond 0.00271 ( 15) link_NAG-ASN : angle 2.81607 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7535 (mmmt) cc_final: 0.7174 (mptt) REVERT: A 117 ASP cc_start: 0.8425 (p0) cc_final: 0.8123 (p0) REVERT: A 140 LYS cc_start: 0.8937 (tttt) cc_final: 0.8703 (ttmm) REVERT: A 229 GLU cc_start: 0.7822 (pp20) cc_final: 0.7519 (pp20) REVERT: A 235 GLU cc_start: 0.8143 (tt0) cc_final: 0.7594 (tm-30) REVERT: D 587 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8255 (ttm-80) REVERT: D 597 TRP cc_start: 0.5976 (m-10) cc_final: 0.5738 (m-10) REVERT: G 34 MET cc_start: 0.8349 (mmm) cc_final: 0.8022 (mmm) REVERT: G 54 ASP cc_start: 0.8247 (p0) cc_final: 0.7904 (p0) REVERT: G 119 ASP cc_start: 0.8283 (p0) cc_final: 0.7942 (t70) REVERT: J 37 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: J 70 ASP cc_start: 0.8521 (t0) cc_final: 0.8058 (t0) REVERT: J 90 GLN cc_start: 0.8717 (pp30) cc_final: 0.8225 (pp30) REVERT: J 92 LYS cc_start: 0.8853 (tttm) cc_final: 0.8584 (tttp) REVERT: J 104 LEU cc_start: 0.8930 (tp) cc_final: 0.8379 (tt) REVERT: J 108 ARG cc_start: 0.3500 (mtt180) cc_final: 0.1356 (ptt90) REVERT: B 56 LYS cc_start: 0.7399 (mmmt) cc_final: 0.7163 (mptt) REVERT: B 89 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.6278 (tmt90) REVERT: B 117 ASP cc_start: 0.8337 (p0) cc_final: 0.7991 (p0) REVERT: B 235 GLU cc_start: 0.8278 (tt0) cc_final: 0.7723 (tm-30) REVERT: E 587 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7888 (ttm-80) REVERT: E 591 ASP cc_start: 0.8360 (t0) cc_final: 0.8118 (t0) REVERT: H 54 ASP cc_start: 0.8225 (p0) cc_final: 0.7780 (p0) REVERT: H 68 PHE cc_start: 0.6198 (m-80) cc_final: 0.5776 (m-80) REVERT: K 67 SER cc_start: 0.8094 (t) cc_final: 0.7852 (p) REVERT: K 90 GLN cc_start: 0.8814 (pp30) cc_final: 0.8166 (pp30) REVERT: K 97 THR cc_start: 0.8620 (p) cc_final: 0.8356 (p) REVERT: K 108 ARG cc_start: 0.3366 (mtt180) cc_final: 0.1119 (ptt90) REVERT: C 56 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7271 (mptt) REVERT: C 117 ASP cc_start: 0.8401 (p0) cc_final: 0.8120 (p0) REVERT: C 229 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: C 235 GLU cc_start: 0.8269 (tt0) cc_final: 0.7593 (tm-30) REVERT: F 587 ARG cc_start: 0.8421 (mtp85) cc_final: 0.8054 (ttm-80) REVERT: I 38 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7148 (ptp-110) REVERT: I 54 ASP cc_start: 0.8210 (p0) cc_final: 0.7843 (p0) REVERT: I 86 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7721 (mt) REVERT: I 104 TYR cc_start: 0.8499 (m-10) cc_final: 0.8156 (m-10) REVERT: L 37 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: L 67 SER cc_start: 0.7907 (t) cc_final: 0.7596 (p) REVERT: L 104 LEU cc_start: 0.8739 (tp) cc_final: 0.7974 (tt) REVERT: L 108 ARG cc_start: 0.3185 (mtt180) cc_final: 0.1075 (ptt90) outliers start: 49 outliers final: 35 residues processed: 330 average time/residue: 0.1343 time to fit residues: 61.0285 Evaluate side-chains 325 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 109 optimal weight: 0.0270 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN I 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.117013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.089229 restraints weight = 28073.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092154 restraints weight = 16924.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094142 restraints weight = 12158.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095490 restraints weight = 9763.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096354 restraints weight = 8411.249| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14052 Z= 0.168 Angle : 0.715 8.133 19146 Z= 0.347 Chirality : 0.047 0.202 2205 Planarity : 0.004 0.061 2370 Dihedral : 8.320 60.961 2622 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.40 % Allowed : 16.74 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.21), residues: 1644 helix: 0.93 (0.40), residues: 183 sheet: -1.27 (0.20), residues: 648 loop : -1.21 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 61 TYR 0.022 0.001 TYR G 115 PHE 0.020 0.002 PHE I 68 TRP 0.031 0.002 TRP F 597 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00387 (13998) covalent geometry : angle 0.69629 (18999) SS BOND : bond 0.00503 ( 15) SS BOND : angle 1.27731 ( 30) hydrogen bonds : bond 0.03304 ( 429) hydrogen bonds : angle 6.07197 ( 1143) link_ALPHA1-3 : bond 0.01029 ( 6) link_ALPHA1-3 : angle 1.88401 ( 18) link_ALPHA1-6 : bond 0.01064 ( 3) link_ALPHA1-6 : angle 1.22760 ( 9) link_BETA1-4 : bond 0.00362 ( 15) link_BETA1-4 : angle 1.79654 ( 45) link_NAG-ASN : bond 0.00202 ( 15) link_NAG-ASN : angle 2.65840 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 307 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7266 (mptt) REVERT: A 117 ASP cc_start: 0.8362 (p0) cc_final: 0.8073 (p0) REVERT: A 229 GLU cc_start: 0.7841 (pp20) cc_final: 0.7459 (pp20) REVERT: A 235 GLU cc_start: 0.8057 (tt0) cc_final: 0.7581 (tm-30) REVERT: D 587 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8187 (ttm-80) REVERT: G 46 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7825 (mm-30) REVERT: G 54 ASP cc_start: 0.8214 (p0) cc_final: 0.7831 (p0) REVERT: G 119 ASP cc_start: 0.8259 (p0) cc_final: 0.7845 (t70) REVERT: J 37 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: J 90 GLN cc_start: 0.8845 (pp30) cc_final: 0.8358 (pp30) REVERT: J 92 LYS cc_start: 0.8820 (tttm) cc_final: 0.8550 (tttp) REVERT: J 104 LEU cc_start: 0.8829 (tp) cc_final: 0.8317 (tt) REVERT: J 108 ARG cc_start: 0.3553 (mtt180) cc_final: 0.1389 (ptt90) REVERT: B 89 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.6205 (tmt90) REVERT: B 112 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7869 (tt0) REVERT: B 117 ASP cc_start: 0.8260 (p0) cc_final: 0.7845 (p0) REVERT: B 235 GLU cc_start: 0.8175 (tt0) cc_final: 0.7726 (tm-30) REVERT: E 587 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7843 (ttm-80) REVERT: H 54 ASP cc_start: 0.8193 (p0) cc_final: 0.7745 (p0) REVERT: H 68 PHE cc_start: 0.6217 (m-80) cc_final: 0.5896 (m-80) REVERT: K 37 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: K 67 SER cc_start: 0.8050 (t) cc_final: 0.7727 (p) REVERT: K 108 ARG cc_start: 0.3500 (mtt180) cc_final: 0.1242 (ptt90) REVERT: C 56 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7274 (mptt) REVERT: C 117 ASP cc_start: 0.8330 (p0) cc_final: 0.8030 (p0) REVERT: C 229 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7377 (pp20) REVERT: C 235 GLU cc_start: 0.8175 (tt0) cc_final: 0.7615 (tm-30) REVERT: F 587 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7994 (ttm-80) REVERT: I 34 MET cc_start: 0.8313 (mmm) cc_final: 0.8043 (mmm) REVERT: I 38 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7198 (ptp-110) REVERT: I 54 ASP cc_start: 0.8175 (p0) cc_final: 0.7771 (p0) REVERT: I 104 TYR cc_start: 0.8441 (m-10) cc_final: 0.8096 (m-10) REVERT: L 37 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: L 67 SER cc_start: 0.7764 (t) cc_final: 0.7407 (p) REVERT: L 104 LEU cc_start: 0.8674 (tp) cc_final: 0.7944 (tt) REVERT: L 108 ARG cc_start: 0.3166 (mtt180) cc_final: 0.1073 (ptt90) outliers start: 34 outliers final: 21 residues processed: 328 average time/residue: 0.1314 time to fit residues: 59.8492 Evaluate side-chains 312 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 123 optimal weight: 0.0870 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN C 39 HIS L 6 GLN L 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088593 restraints weight = 28298.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.091612 restraints weight = 16773.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093688 restraints weight = 11921.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095078 restraints weight = 9474.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095988 restraints weight = 8127.010| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14052 Z= 0.170 Angle : 0.712 8.876 19146 Z= 0.346 Chirality : 0.047 0.200 2205 Planarity : 0.004 0.050 2370 Dihedral : 7.826 58.353 2622 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.18 % Allowed : 16.60 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1644 helix: 1.11 (0.40), residues: 183 sheet: -1.05 (0.20), residues: 624 loop : -1.24 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.020 0.001 TYR G 115 PHE 0.024 0.002 PHE I 50 TRP 0.036 0.002 TRP D 597 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00390 (13998) covalent geometry : angle 0.69348 (18999) SS BOND : bond 0.00511 ( 15) SS BOND : angle 1.41649 ( 30) hydrogen bonds : bond 0.03290 ( 429) hydrogen bonds : angle 5.97223 ( 1143) link_ALPHA1-3 : bond 0.00995 ( 6) link_ALPHA1-3 : angle 1.74159 ( 18) link_ALPHA1-6 : bond 0.01068 ( 3) link_ALPHA1-6 : angle 1.18673 ( 9) link_BETA1-4 : bond 0.00332 ( 15) link_BETA1-4 : angle 1.69995 ( 45) link_NAG-ASN : bond 0.00186 ( 15) link_NAG-ASN : angle 2.62593 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7507 (mmmt) cc_final: 0.7303 (mptt) REVERT: A 117 ASP cc_start: 0.8309 (p0) cc_final: 0.8046 (p0) REVERT: A 229 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7384 (pp20) REVERT: A 235 GLU cc_start: 0.8020 (tt0) cc_final: 0.7586 (tm-30) REVERT: D 587 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8160 (ttm-80) REVERT: G 34 MET cc_start: 0.8293 (mmm) cc_final: 0.7960 (mmm) REVERT: G 43 LYS cc_start: 0.7834 (mtpp) cc_final: 0.7619 (mmmt) REVERT: G 46 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7767 (mm-30) REVERT: G 54 ASP cc_start: 0.8250 (p0) cc_final: 0.7873 (p0) REVERT: G 119 ASP cc_start: 0.8267 (p0) cc_final: 0.7867 (t70) REVERT: J 37 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: J 90 GLN cc_start: 0.8796 (pp30) cc_final: 0.8318 (pp30) REVERT: J 92 LYS cc_start: 0.8870 (tttm) cc_final: 0.8579 (tttm) REVERT: J 104 LEU cc_start: 0.8814 (tp) cc_final: 0.8267 (tt) REVERT: J 108 ARG cc_start: 0.3554 (mtt180) cc_final: 0.1456 (ptt90) REVERT: B 89 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.6241 (tmt90) REVERT: B 112 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7858 (tt0) REVERT: B 117 ASP cc_start: 0.8232 (p0) cc_final: 0.7841 (p0) REVERT: B 235 GLU cc_start: 0.8161 (tt0) cc_final: 0.7753 (tm-30) REVERT: E 587 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7707 (ttm-80) REVERT: H 48 MET cc_start: 0.6213 (mmt) cc_final: 0.5910 (tpp) REVERT: H 54 ASP cc_start: 0.8205 (p0) cc_final: 0.7765 (p0) REVERT: H 68 PHE cc_start: 0.6483 (m-80) cc_final: 0.5604 (m-10) REVERT: K 4 MET cc_start: 0.6744 (ttm) cc_final: 0.5824 (ttm) REVERT: K 67 SER cc_start: 0.8189 (t) cc_final: 0.7840 (p) REVERT: K 90 GLN cc_start: 0.8839 (pp30) cc_final: 0.8244 (pp30) REVERT: K 94 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7577 (t80) REVERT: K 108 ARG cc_start: 0.3137 (mtt180) cc_final: 0.0990 (ptt90) REVERT: C 56 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7287 (mptt) REVERT: C 117 ASP cc_start: 0.8338 (p0) cc_final: 0.8028 (p0) REVERT: C 229 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7345 (pp20) REVERT: C 235 GLU cc_start: 0.8163 (tt0) cc_final: 0.7620 (tm-30) REVERT: F 587 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7975 (ttm-80) REVERT: I 34 MET cc_start: 0.8248 (mmm) cc_final: 0.7982 (mmm) REVERT: I 43 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7881 (mmmt) REVERT: I 54 ASP cc_start: 0.8146 (p0) cc_final: 0.7773 (p0) REVERT: I 104 TYR cc_start: 0.8450 (m-10) cc_final: 0.8114 (m-10) REVERT: I 119 ASP cc_start: 0.8345 (p0) cc_final: 0.7990 (p0) REVERT: L 6 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6419 (pt0) REVERT: L 55 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8419 (tp40) REVERT: L 67 SER cc_start: 0.7962 (t) cc_final: 0.7609 (p) REVERT: L 94 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7683 (t80) REVERT: L 104 LEU cc_start: 0.8694 (tp) cc_final: 0.7928 (tt) REVERT: L 108 ARG cc_start: 0.3166 (mtt180) cc_final: 0.1169 (ptt90) outliers start: 45 outliers final: 27 residues processed: 325 average time/residue: 0.1362 time to fit residues: 61.5540 Evaluate side-chains 320 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 3 optimal weight: 0.0270 chunk 11 optimal weight: 6.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 39 GLN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 38 GLN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.090206 restraints weight = 27813.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093170 restraints weight = 16652.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095160 restraints weight = 11854.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096486 restraints weight = 9471.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097277 restraints weight = 8153.668| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14052 Z= 0.167 Angle : 0.722 9.985 19146 Z= 0.350 Chirality : 0.047 0.194 2205 Planarity : 0.004 0.051 2370 Dihedral : 7.588 57.778 2622 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.97 % Allowed : 16.74 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.21), residues: 1644 helix: 1.24 (0.39), residues: 183 sheet: -1.05 (0.21), residues: 630 loop : -1.16 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 38 TYR 0.020 0.001 TYR G 115 PHE 0.017 0.002 PHE L 94 TRP 0.033 0.002 TRP D 597 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00386 (13998) covalent geometry : angle 0.70372 (18999) SS BOND : bond 0.00323 ( 15) SS BOND : angle 1.68428 ( 30) hydrogen bonds : bond 0.03221 ( 429) hydrogen bonds : angle 5.90334 ( 1143) link_ALPHA1-3 : bond 0.00949 ( 6) link_ALPHA1-3 : angle 1.70868 ( 18) link_ALPHA1-6 : bond 0.01056 ( 3) link_ALPHA1-6 : angle 1.17303 ( 9) link_BETA1-4 : bond 0.00338 ( 15) link_BETA1-4 : angle 1.64253 ( 45) link_NAG-ASN : bond 0.00181 ( 15) link_NAG-ASN : angle 2.61155 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8247 (p0) cc_final: 0.7973 (p0) REVERT: A 229 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7375 (pp20) REVERT: A 235 GLU cc_start: 0.7925 (tt0) cc_final: 0.7596 (tm-30) REVERT: D 587 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8108 (ttm-80) REVERT: G 46 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7738 (mm-30) REVERT: G 54 ASP cc_start: 0.8196 (p0) cc_final: 0.7773 (p0) REVERT: G 119 ASP cc_start: 0.8256 (p0) cc_final: 0.7900 (t70) REVERT: J 37 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: J 90 GLN cc_start: 0.8838 (pp30) cc_final: 0.8391 (pp30) REVERT: J 92 LYS cc_start: 0.8904 (tttm) cc_final: 0.8694 (tttp) REVERT: J 104 LEU cc_start: 0.8749 (tp) cc_final: 0.8195 (tt) REVERT: J 108 ARG cc_start: 0.3615 (mtt180) cc_final: 0.1606 (ptt90) REVERT: B 56 LYS cc_start: 0.7107 (mptt) cc_final: 0.6818 (mmtt) REVERT: B 69 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7719 (t0) REVERT: B 89 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.6385 (tmt90) REVERT: B 112 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7795 (tt0) REVERT: B 117 ASP cc_start: 0.8171 (p0) cc_final: 0.7771 (p0) REVERT: B 235 GLU cc_start: 0.8124 (tt0) cc_final: 0.7784 (tm-30) REVERT: E 552 ASP cc_start: 0.6602 (t0) cc_final: 0.6381 (t0) REVERT: E 587 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7715 (ttm-80) REVERT: H 54 ASP cc_start: 0.8174 (p0) cc_final: 0.7715 (p0) REVERT: H 57 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8283 (mmtp) REVERT: K 67 SER cc_start: 0.8080 (t) cc_final: 0.7660 (p) REVERT: K 70 ASP cc_start: 0.8799 (t0) cc_final: 0.8403 (t0) REVERT: K 90 GLN cc_start: 0.8787 (pp30) cc_final: 0.8196 (pp30) REVERT: K 94 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7642 (t80) REVERT: K 108 ARG cc_start: 0.3051 (mtt180) cc_final: 0.0963 (ptt90) REVERT: C 56 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7343 (mptt) REVERT: C 117 ASP cc_start: 0.8310 (p0) cc_final: 0.7987 (p0) REVERT: C 229 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: C 235 GLU cc_start: 0.8150 (tt0) cc_final: 0.7685 (tm-30) REVERT: F 587 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7920 (ttm-80) REVERT: I 34 MET cc_start: 0.8138 (mmm) cc_final: 0.7906 (mmm) REVERT: I 38 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6757 (ptp-110) REVERT: I 54 ASP cc_start: 0.8084 (p0) cc_final: 0.7708 (p0) REVERT: I 104 TYR cc_start: 0.8432 (m-10) cc_final: 0.8065 (m-10) REVERT: I 119 ASP cc_start: 0.8244 (p0) cc_final: 0.7997 (p0) REVERT: L 37 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: L 55 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8395 (tp40) REVERT: L 67 SER cc_start: 0.7962 (t) cc_final: 0.7556 (p) REVERT: L 94 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7765 (t80) REVERT: L 104 LEU cc_start: 0.8634 (tp) cc_final: 0.7793 (tt) REVERT: L 108 ARG cc_start: 0.3192 (mtt180) cc_final: 0.1211 (ptt90) outliers start: 42 outliers final: 29 residues processed: 317 average time/residue: 0.1285 time to fit residues: 56.8689 Evaluate side-chains 312 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 54 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 59 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 0.0570 chunk 123 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.118108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.090736 restraints weight = 27549.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.093677 restraints weight = 16611.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095672 restraints weight = 11855.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097020 restraints weight = 9448.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097850 restraints weight = 8120.325| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14052 Z= 0.159 Angle : 0.738 14.236 19146 Z= 0.356 Chirality : 0.047 0.197 2205 Planarity : 0.004 0.054 2370 Dihedral : 7.414 57.116 2622 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.82 % Allowed : 17.16 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.21), residues: 1644 helix: 1.44 (0.39), residues: 183 sheet: -1.05 (0.20), residues: 630 loop : -1.13 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 67 TYR 0.018 0.001 TYR G 115 PHE 0.022 0.002 PHE D 592 TRP 0.034 0.002 TRP D 597 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00366 (13998) covalent geometry : angle 0.72117 (18999) SS BOND : bond 0.00696 ( 15) SS BOND : angle 1.47281 ( 30) hydrogen bonds : bond 0.03241 ( 429) hydrogen bonds : angle 5.89445 ( 1143) link_ALPHA1-3 : bond 0.00958 ( 6) link_ALPHA1-3 : angle 1.64392 ( 18) link_ALPHA1-6 : bond 0.01027 ( 3) link_ALPHA1-6 : angle 1.15323 ( 9) link_BETA1-4 : bond 0.00363 ( 15) link_BETA1-4 : angle 1.59062 ( 45) link_NAG-ASN : bond 0.00190 ( 15) link_NAG-ASN : angle 2.58735 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8223 (p0) cc_final: 0.7957 (p0) REVERT: A 229 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: A 235 GLU cc_start: 0.7981 (tt0) cc_final: 0.7511 (tm-30) REVERT: D 587 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8074 (ttm-80) REVERT: D 588 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7854 (mmmt) REVERT: G 34 MET cc_start: 0.8198 (mmm) cc_final: 0.7855 (mmm) REVERT: G 36 TRP cc_start: 0.7881 (m100) cc_final: 0.7539 (m100) REVERT: G 46 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7869 (mm-30) REVERT: G 54 ASP cc_start: 0.8195 (p0) cc_final: 0.7803 (p0) REVERT: G 119 ASP cc_start: 0.8306 (p0) cc_final: 0.7875 (t70) REVERT: J 18 ARG cc_start: 0.8727 (ttp80) cc_final: 0.8154 (tmm160) REVERT: J 37 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: J 90 GLN cc_start: 0.8754 (pp30) cc_final: 0.8310 (pp30) REVERT: J 92 LYS cc_start: 0.8907 (tttm) cc_final: 0.8640 (tttm) REVERT: J 104 LEU cc_start: 0.8774 (tp) cc_final: 0.8173 (tt) REVERT: J 108 ARG cc_start: 0.3419 (mtt180) cc_final: 0.1475 (ptt90) REVERT: B 56 LYS cc_start: 0.7187 (mptt) cc_final: 0.6913 (mmtt) REVERT: B 89 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6324 (tmt90) REVERT: B 112 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7835 (tt0) REVERT: B 117 ASP cc_start: 0.8240 (p0) cc_final: 0.7846 (p0) REVERT: B 235 GLU cc_start: 0.8190 (tt0) cc_final: 0.7791 (tm-30) REVERT: E 587 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7736 (ttm-80) REVERT: H 36 TRP cc_start: 0.7672 (m100) cc_final: 0.7411 (m100) REVERT: H 54 ASP cc_start: 0.8118 (p0) cc_final: 0.7740 (p0) REVERT: H 57 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8253 (mmmm) REVERT: H 69 THR cc_start: 0.9147 (m) cc_final: 0.8944 (p) REVERT: K 67 SER cc_start: 0.8102 (t) cc_final: 0.7711 (p) REVERT: K 90 GLN cc_start: 0.8752 (pp30) cc_final: 0.8230 (pp30) REVERT: K 94 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7512 (t80) REVERT: K 108 ARG cc_start: 0.2971 (mtt180) cc_final: 0.0919 (ptt90) REVERT: C 56 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7368 (mptt) REVERT: C 117 ASP cc_start: 0.8329 (p0) cc_final: 0.8029 (p0) REVERT: C 229 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7306 (pp20) REVERT: C 235 GLU cc_start: 0.8179 (tt0) cc_final: 0.7656 (tm-30) REVERT: F 587 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7951 (ttm-80) REVERT: I 38 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7009 (ptp-110) REVERT: I 54 ASP cc_start: 0.8116 (p0) cc_final: 0.7751 (p0) REVERT: I 104 TYR cc_start: 0.8467 (m-10) cc_final: 0.8123 (m-10) REVERT: I 119 ASP cc_start: 0.8215 (p0) cc_final: 0.7948 (p0) REVERT: L 37 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: L 67 SER cc_start: 0.8056 (t) cc_final: 0.7663 (p) REVERT: L 70 ASP cc_start: 0.8979 (m-30) cc_final: 0.8507 (t0) REVERT: L 94 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7651 (t80) REVERT: L 104 LEU cc_start: 0.8627 (tp) cc_final: 0.7768 (tt) REVERT: L 108 ARG cc_start: 0.3007 (mtt180) cc_final: 0.1083 (ptt90) outliers start: 40 outliers final: 26 residues processed: 316 average time/residue: 0.1286 time to fit residues: 56.6538 Evaluate side-chains 317 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 283 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 114 optimal weight: 0.0670 chunk 100 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 1.0118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.091836 restraints weight = 27708.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094845 restraints weight = 16471.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096892 restraints weight = 11666.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098261 restraints weight = 9258.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099118 restraints weight = 7930.763| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14052 Z= 0.137 Angle : 0.735 13.396 19146 Z= 0.353 Chirality : 0.046 0.183 2205 Planarity : 0.004 0.055 2370 Dihedral : 7.286 58.502 2622 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.75 % Allowed : 17.09 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1644 helix: 1.58 (0.40), residues: 183 sheet: -1.06 (0.20), residues: 636 loop : -1.09 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.016 0.001 TYR G 115 PHE 0.020 0.002 PHE J 94 TRP 0.020 0.001 TRP D 597 HIS 0.002 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00312 (13998) covalent geometry : angle 0.71926 (18999) SS BOND : bond 0.00577 ( 15) SS BOND : angle 1.53542 ( 30) hydrogen bonds : bond 0.03118 ( 429) hydrogen bonds : angle 5.79773 ( 1143) link_ALPHA1-3 : bond 0.00890 ( 6) link_ALPHA1-3 : angle 1.57595 ( 18) link_ALPHA1-6 : bond 0.00994 ( 3) link_ALPHA1-6 : angle 1.13871 ( 9) link_BETA1-4 : bond 0.00394 ( 15) link_BETA1-4 : angle 1.52529 ( 45) link_NAG-ASN : bond 0.00208 ( 15) link_NAG-ASN : angle 2.54434 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8233 (p0) cc_final: 0.7972 (p0) REVERT: A 229 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7388 (pp20) REVERT: A 235 GLU cc_start: 0.7962 (tt0) cc_final: 0.7497 (tm-30) REVERT: D 587 ARG cc_start: 0.8299 (mtp85) cc_final: 0.8050 (ttm-80) REVERT: G 36 TRP cc_start: 0.7776 (m100) cc_final: 0.7322 (m100) REVERT: G 43 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7701 (mmmt) REVERT: G 46 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7860 (mm-30) REVERT: G 54 ASP cc_start: 0.8180 (p0) cc_final: 0.7765 (p0) REVERT: G 57 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8413 (mmmm) REVERT: G 119 ASP cc_start: 0.8287 (p0) cc_final: 0.7886 (t70) REVERT: J 18 ARG cc_start: 0.8748 (ttp80) cc_final: 0.8388 (ttp80) REVERT: J 37 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: J 90 GLN cc_start: 0.8724 (pp30) cc_final: 0.8380 (pp30) REVERT: J 92 LYS cc_start: 0.8912 (tttm) cc_final: 0.8676 (tttp) REVERT: J 104 LEU cc_start: 0.8674 (tp) cc_final: 0.8084 (tt) REVERT: J 108 ARG cc_start: 0.3460 (mtt180) cc_final: 0.1544 (ptt90) REVERT: B 56 LYS cc_start: 0.7168 (mptt) cc_final: 0.6876 (mmtt) REVERT: B 69 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7757 (t0) REVERT: B 89 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.6333 (tmt90) REVERT: B 112 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7810 (tt0) REVERT: B 117 ASP cc_start: 0.8244 (p0) cc_final: 0.7855 (p0) REVERT: B 235 GLU cc_start: 0.8153 (tt0) cc_final: 0.7754 (tm-30) REVERT: E 552 ASP cc_start: 0.6517 (t0) cc_final: 0.6314 (t0) REVERT: E 587 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7743 (ttm-80) REVERT: H 34 MET cc_start: 0.8321 (mmm) cc_final: 0.7451 (mmm) REVERT: H 36 TRP cc_start: 0.7636 (m100) cc_final: 0.7408 (m100) REVERT: H 54 ASP cc_start: 0.8101 (p0) cc_final: 0.7730 (p0) REVERT: H 57 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8271 (mmmm) REVERT: K 67 SER cc_start: 0.8087 (t) cc_final: 0.7655 (p) REVERT: K 90 GLN cc_start: 0.8615 (pp30) cc_final: 0.8300 (pp30) REVERT: K 94 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7530 (t80) REVERT: K 108 ARG cc_start: 0.2988 (mtt180) cc_final: 0.0956 (ptt90) REVERT: C 56 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7381 (mptt) REVERT: C 117 ASP cc_start: 0.8313 (p0) cc_final: 0.8019 (p0) REVERT: C 130 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8405 (mmm160) REVERT: C 229 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: C 235 GLU cc_start: 0.8159 (tt0) cc_final: 0.7645 (tm-30) REVERT: F 587 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7935 (ttm-80) REVERT: I 34 MET cc_start: 0.8082 (mmm) cc_final: 0.7861 (mmm) REVERT: I 43 LYS cc_start: 0.8207 (mtpp) cc_final: 0.8002 (mmmt) REVERT: I 54 ASP cc_start: 0.8146 (p0) cc_final: 0.7781 (p0) REVERT: I 104 TYR cc_start: 0.8421 (m-10) cc_final: 0.8105 (m-10) REVERT: I 119 ASP cc_start: 0.8137 (p0) cc_final: 0.7929 (p0) REVERT: L 37 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: L 67 SER cc_start: 0.8139 (t) cc_final: 0.7752 (p) REVERT: L 70 ASP cc_start: 0.8935 (m-30) cc_final: 0.8579 (t0) REVERT: L 94 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7578 (t80) REVERT: L 104 LEU cc_start: 0.8573 (tp) cc_final: 0.7731 (tt) REVERT: L 108 ARG cc_start: 0.3047 (mtt180) cc_final: 0.1088 (ptt90) outliers start: 39 outliers final: 23 residues processed: 326 average time/residue: 0.1330 time to fit residues: 60.2452 Evaluate side-chains 314 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.119730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092269 restraints weight = 27915.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095314 restraints weight = 16590.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097356 restraints weight = 11740.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098757 restraints weight = 9349.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099666 restraints weight = 7992.695| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14052 Z= 0.128 Angle : 0.739 13.668 19146 Z= 0.353 Chirality : 0.046 0.193 2205 Planarity : 0.004 0.055 2370 Dihedral : 7.113 59.777 2622 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.33 % Allowed : 17.80 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.21), residues: 1644 helix: 1.71 (0.40), residues: 183 sheet: -0.96 (0.20), residues: 627 loop : -1.06 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 87 TYR 0.014 0.001 TYR G 115 PHE 0.032 0.002 PHE E 592 TRP 0.022 0.001 TRP I 36 HIS 0.002 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00289 (13998) covalent geometry : angle 0.72387 (18999) SS BOND : bond 0.00587 ( 15) SS BOND : angle 1.43757 ( 30) hydrogen bonds : bond 0.03071 ( 429) hydrogen bonds : angle 5.71672 ( 1143) link_ALPHA1-3 : bond 0.00811 ( 6) link_ALPHA1-3 : angle 1.52398 ( 18) link_ALPHA1-6 : bond 0.00934 ( 3) link_ALPHA1-6 : angle 1.11764 ( 9) link_BETA1-4 : bond 0.00409 ( 15) link_BETA1-4 : angle 1.47927 ( 45) link_NAG-ASN : bond 0.00225 ( 15) link_NAG-ASN : angle 2.53739 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 302 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8203 (p0) cc_final: 0.7980 (p0) REVERT: A 229 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7406 (pp20) REVERT: A 235 GLU cc_start: 0.7989 (tt0) cc_final: 0.7511 (tm-30) REVERT: D 529 LEU cc_start: 0.8455 (mt) cc_final: 0.8247 (tt) REVERT: D 587 ARG cc_start: 0.8262 (mtp85) cc_final: 0.8004 (ttm-80) REVERT: D 588 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7763 (mmmt) REVERT: G 34 MET cc_start: 0.8132 (mmm) cc_final: 0.7806 (mmm) REVERT: G 36 TRP cc_start: 0.7709 (m100) cc_final: 0.7439 (m100) REVERT: G 43 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7638 (mmmt) REVERT: G 54 ASP cc_start: 0.8164 (p0) cc_final: 0.7783 (p0) REVERT: G 57 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8412 (mmmm) REVERT: G 119 ASP cc_start: 0.8277 (p0) cc_final: 0.7839 (t70) REVERT: J 18 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8427 (ttp80) REVERT: J 37 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: J 90 GLN cc_start: 0.8642 (pp30) cc_final: 0.8338 (pp30) REVERT: J 92 LYS cc_start: 0.8950 (tttm) cc_final: 0.8746 (tttm) REVERT: J 104 LEU cc_start: 0.8627 (tp) cc_final: 0.7989 (tt) REVERT: J 108 ARG cc_start: 0.3422 (mtt180) cc_final: 0.1520 (ptt90) REVERT: B 56 LYS cc_start: 0.7193 (mptt) cc_final: 0.6897 (mmtt) REVERT: B 69 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7758 (t0) REVERT: B 89 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.6278 (tmt90) REVERT: B 117 ASP cc_start: 0.8234 (p0) cc_final: 0.7841 (p0) REVERT: B 235 GLU cc_start: 0.8029 (tt0) cc_final: 0.7676 (tm-30) REVERT: E 587 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7753 (ttm-80) REVERT: H 34 MET cc_start: 0.8300 (mmm) cc_final: 0.7489 (mmm) REVERT: H 36 TRP cc_start: 0.7581 (m100) cc_final: 0.7349 (m100) REVERT: H 54 ASP cc_start: 0.8092 (p0) cc_final: 0.7717 (p0) REVERT: H 57 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8305 (mmmm) REVERT: K 67 SER cc_start: 0.8028 (t) cc_final: 0.7567 (p) REVERT: K 90 GLN cc_start: 0.8527 (pp30) cc_final: 0.8294 (pp30) REVERT: K 108 ARG cc_start: 0.2966 (mtt180) cc_final: 0.0925 (ptt90) REVERT: C 56 LYS cc_start: 0.7754 (mmmt) cc_final: 0.7386 (mptt) REVERT: C 117 ASP cc_start: 0.8292 (p0) cc_final: 0.7987 (p0) REVERT: C 130 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8382 (mmm160) REVERT: C 229 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7481 (pp20) REVERT: C 235 GLU cc_start: 0.8142 (tt0) cc_final: 0.7632 (tm-30) REVERT: F 587 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7919 (ttm-80) REVERT: I 36 TRP cc_start: 0.7678 (m100) cc_final: 0.7347 (m100) REVERT: I 38 ARG cc_start: 0.7486 (ptp-110) cc_final: 0.7044 (ptp-110) REVERT: I 54 ASP cc_start: 0.8200 (p0) cc_final: 0.7818 (p0) REVERT: I 104 TYR cc_start: 0.8439 (m-10) cc_final: 0.8140 (m-10) REVERT: I 119 ASP cc_start: 0.8116 (p0) cc_final: 0.7833 (p0) REVERT: L 37 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: L 67 SER cc_start: 0.8210 (t) cc_final: 0.7824 (p) REVERT: L 70 ASP cc_start: 0.8895 (m-30) cc_final: 0.8531 (t0) REVERT: L 104 LEU cc_start: 0.8477 (tp) cc_final: 0.7626 (tt) REVERT: L 108 ARG cc_start: 0.3093 (mtt180) cc_final: 0.1125 (ptt90) outliers start: 33 outliers final: 21 residues processed: 322 average time/residue: 0.1385 time to fit residues: 61.5615 Evaluate side-chains 313 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 152 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092702 restraints weight = 27897.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095709 restraints weight = 16712.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097784 restraints weight = 11925.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099157 restraints weight = 9469.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099882 restraints weight = 8124.733| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14052 Z= 0.133 Angle : 0.754 13.918 19146 Z= 0.360 Chirality : 0.046 0.179 2205 Planarity : 0.004 0.059 2370 Dihedral : 6.881 54.481 2622 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.91 % Allowed : 18.43 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.21), residues: 1644 helix: 1.71 (0.40), residues: 183 sheet: -0.89 (0.20), residues: 627 loop : -1.02 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 24 TYR 0.014 0.001 TYR L 96 PHE 0.024 0.002 PHE K 94 TRP 0.019 0.001 TRP D 597 HIS 0.008 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00301 (13998) covalent geometry : angle 0.73923 (18999) SS BOND : bond 0.00627 ( 15) SS BOND : angle 1.45679 ( 30) hydrogen bonds : bond 0.03071 ( 429) hydrogen bonds : angle 5.65050 ( 1143) link_ALPHA1-3 : bond 0.00778 ( 6) link_ALPHA1-3 : angle 1.50746 ( 18) link_ALPHA1-6 : bond 0.00959 ( 3) link_ALPHA1-6 : angle 1.14527 ( 9) link_BETA1-4 : bond 0.00417 ( 15) link_BETA1-4 : angle 1.46490 ( 45) link_NAG-ASN : bond 0.00237 ( 15) link_NAG-ASN : angle 2.58927 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.96 seconds wall clock time: 40 minutes 21.95 seconds (2421.95 seconds total)