Starting phenix.real_space_refine on Sat Oct 24 14:24:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uye_20947/10_2026/6uye_20947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uye_20947/10_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_20947/10_2026/6uye_20947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uye_20947/10_2026/6uye_20947.map" model { file = "/net/cci-nas-00/data/ceres_data/6uye_20947/10_2026/6uye_20947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uye_20947/10_2026/6uye_20947.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uye_20947/10_2026/6uye_20947.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uye_20947/10_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-2.3rc1-6221/lib/python3.11/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 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 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 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 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: 2.59, per 1000 atoms: 0.19 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 B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 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: 1.13 Conformation dependent library (CDL) restraints added in 509.9 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: 0.38 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: 2.49 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 - 16.82: 7660 16.82 - 33.65: 205 33.65 - 50.47: 52 50.47 - 67.29: 3 67.29 - 84.12: 9 Dihedral angle restraints: 7929 sinusoidal: 3111 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 7926 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: 0.04 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.020 Set scattering table: 0.020 Process input model: 12.340 Find NCS groups from input model: 0.140 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 9.519 84.119 4812 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/Z covalent geometry : bond 0.01025 / 0.46 (13998) covalent geometry : angle 1.11496 / 0.60 (18999) SS BOND : bond 0.00659 / 0.41 ( 15) SS BOND : angle 1.23633 / 0.81 ( 30) hydrogen bonds : bond 0.23518 / 16.18 ( 429) hydrogen bonds : angle 9.56156 / 6.84 ( 1143) link_ALPHA1-3 : bond 0.00629 / 0.31 ( 6) link_ALPHA1-3 : angle 1.94754 / 1.19 ( 18) link_ALPHA1-6 : bond 0.00177 / 0.09 ( 3) link_ALPHA1-6 : angle 1.52075 / 0.86 ( 9) link_BETA1-4 : bond 0.00833 / 0.48 ( 15) link_BETA1-4 : angle 2.93093 / 1.87 ( 45) link_NAG-ASN : bond 0.01111 / 0.71 ( 15) link_NAG-ASN : angle 5.47245 / 3.20 ( 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 : 0.491 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: 0.1334 time to fit residues: 97.0971 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 : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] 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... 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.119875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092655 restraints weight = 27374.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095725 restraints weight = 16045.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097787 restraints weight = 11298.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099150 restraints weight = 8934.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100063 restraints weight = 7649.617| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14052 Z= 0.169 Angle : 0.755 8.461 19146 Z= 0.379 Chirality : 0.047 0.196 2205 Planarity : 0.005 0.054 2370 Dihedral : 6.489 78.095 1833 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.55 % Allowed : 11.37 % Favored : 87.08 % 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: -2.08 (0.19), residues: 1644 helix: 0.08 (0.40), residues: 174 sheet: -1.44 (0.19), residues: 642 loop : -1.58 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.024 0.002 TYR H 115 PHE 0.018 0.002 PHE L 71 TRP 0.013 0.001 TRP I 108 HIS 0.002 0.001 HIS D 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (13998) covalent geometry : angle 0.73459 / 0.37 (18999) SS BOND : bond 0.00430 / 0.29 ( 15) SS BOND : angle 1.62517 / 1.08 ( 30) hydrogen bonds : bond 0.03727 / 2.60 ( 429) hydrogen bonds : angle 6.99520 / 4.94 ( 1143) link_ALPHA1-3 : bond 0.00647 / 0.39 ( 6) link_ALPHA1-3 : angle 1.36149 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00715 / 0.36 ( 3) link_ALPHA1-6 : angle 1.45190 / 0.82 ( 9) link_BETA1-4 : bond 0.00470 / 0.30 ( 15) link_BETA1-4 : angle 2.02708 / 1.28 ( 45) link_NAG-ASN : bond 0.00397 / 0.32 ( 15) link_NAG-ASN : angle 2.81233 / 1.61 ( 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 405 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 383 time to evaluate : 0.534 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: 0.7417 (mmmt) cc_final: 0.6893 (mptt) REVERT: A 117 ASP cc_start: 0.8321 (p0) cc_final: 0.7938 (p0) REVERT: A 235 GLU cc_start: 0.8067 (tt0) cc_final: 0.7491 (tm-30) REVERT: A 291 TRP cc_start: 0.5867 (p90) cc_final: 0.5297 (p90) REVERT: D 587 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8143 (ttm110) REVERT: G 34 MET cc_start: 0.8147 (mmm) cc_final: 0.7850 (mmm) REVERT: G 54 ASP cc_start: 0.8176 (p0) cc_final: 0.7767 (p0) REVERT: G 57 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8246 (mmmm) REVERT: G 119 ASP cc_start: 0.8234 (p0) cc_final: 0.7840 (t70) REVERT: J 4 MET cc_start: 0.6937 (ttm) cc_final: 0.6550 (ttm) REVERT: J 90 GLN cc_start: 0.8686 (pp30) cc_final: 0.8073 (pp30) REVERT: J 104 LEU cc_start: 0.8937 (tp) cc_final: 0.8530 (tt) REVERT: J 108 ARG cc_start: 0.3730 (mtt180) cc_final: 0.1554 (ptt90) REVERT: B 56 LYS cc_start: 0.7372 (mmmt) cc_final: 0.7007 (mptt) REVERT: B 117 ASP cc_start: 0.8302 (p0) cc_final: 0.7936 (p0) REVERT: B 235 GLU cc_start: 0.8199 (tt0) cc_final: 0.7608 (tm-30) REVERT: B 291 TRP cc_start: 0.6039 (p90) cc_final: 0.5556 (p90) REVERT: E 587 ARG cc_start: 0.8356 (mtp85) cc_final: 0.7850 (ttm-80) REVERT: H 36 TRP cc_start: 0.7627 (m100) cc_final: 0.6716 (m100) REVERT: H 54 ASP cc_start: 0.8264 (p0) cc_final: 0.7745 (p0) REVERT: H 57 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8186 (mmtp) REVERT: K 108 ARG cc_start: 0.3642 (mtt180) cc_final: 0.1207 (ptt90) REVERT: C 117 ASP cc_start: 0.8262 (p0) cc_final: 0.7943 (p0) REVERT: C 229 GLU cc_start: 0.7750 (pp20) cc_final: 0.7428 (pp20) REVERT: C 235 GLU cc_start: 0.8183 (tt0) cc_final: 0.7570 (tm-30) REVERT: C 291 TRP cc_start: 0.5986 (p90) cc_final: 0.5373 (p90) REVERT: F 527 ILE cc_start: 0.5718 (mm) cc_final: 0.5177 (mm) REVERT: F 587 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8087 (ttm-80) REVERT: I 36 TRP cc_start: 0.7652 (m100) cc_final: 0.6752 (m100) REVERT: I 46 GLU cc_start: 0.6966 (pt0) cc_final: 0.6573 (pt0) REVERT: I 48 MET cc_start: 0.6102 (mtp) cc_final: 0.5272 (mtp) REVERT: I 54 ASP cc_start: 0.8221 (p0) cc_final: 0.7713 (p0) REVERT: I 95 TYR cc_start: 0.7510 (m-80) cc_final: 0.7170 (m-10) REVERT: I 104 TYR cc_start: 0.8185 (m-10) cc_final: 0.7902 (m-10) REVERT: L 2 ILE cc_start: 0.6903 (pt) cc_final: 0.6694 (pt) REVERT: L 67 SER cc_start: 0.7950 (t) cc_final: 0.7698 (p) REVERT: L 104 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8114 (tt) REVERT: L 108 ARG cc_start: 0.3433 (mtt180) cc_final: 0.1017 (ptt90) outliers start: 22 outliers final: 14 residues processed: 396 average time/residue: 0.1313 time to fit residues: 72.2141 Evaluate side-chains 332 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 317 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 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 135 CYS Chi-restraints excluded: chain I residue 2 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: [140, 66, 162, 151, 156, 138, 126, 111, 125, 147, 44] chunk 140 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 595 GLN J 37 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 100 GLN ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.119004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091323 restraints weight = 27628.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094334 restraints weight = 16378.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096392 restraints weight = 11608.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.097774 restraints weight = 9220.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098677 restraints weight = 7886.484| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14052 Z= 0.172 Angle : 0.726 8.061 19146 Z= 0.357 Chirality : 0.046 0.177 2205 Planarity : 0.005 0.055 2370 Dihedral : 6.137 71.828 1833 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.54 % Allowed : 14.12 % 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: -1.73 (0.20), residues: 1644 helix: 0.56 (0.41), residues: 180 sheet: -1.30 (0.20), residues: 654 loop : -1.31 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 24 TYR 0.020 0.002 TYR G 115 PHE 0.019 0.002 PHE L 71 TRP 0.024 0.001 TRP D 597 HIS 0.004 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (13998) covalent geometry : angle 0.70817 / 0.35 (18999) SS BOND : bond 0.00374 / 0.30 ( 15) SS BOND : angle 1.43575 / 0.90 ( 30) hydrogen bonds : bond 0.03464 / 2.41 ( 429) hydrogen bonds : angle 6.40247 / 4.52 ( 1143) link_ALPHA1-3 : bond 0.00564 / 0.33 ( 6) link_ALPHA1-3 : angle 1.26560 / 0.75 ( 18) link_ALPHA1-6 : bond 0.00482 / 0.24 ( 3) link_ALPHA1-6 : angle 1.32277 / 0.75 ( 9) link_BETA1-4 : bond 0.00336 / 0.21 ( 15) link_BETA1-4 : angle 1.89215 / 1.19 ( 45) link_NAG-ASN : bond 0.00216 / 0.17 ( 15) link_NAG-ASN : angle 2.59506 / 1.45 ( 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 370 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 0.419 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: 0.7549 (mmmt) cc_final: 0.7139 (mptt) REVERT: A 117 ASP cc_start: 0.8359 (p0) cc_final: 0.7985 (p0) REVERT: A 235 GLU cc_start: 0.8062 (tt0) cc_final: 0.7564 (tm-30) REVERT: D 587 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8174 (ttm-80) REVERT: G 34 MET cc_start: 0.8295 (mmm) cc_final: 0.7970 (mmm) REVERT: G 54 ASP cc_start: 0.8183 (p0) cc_final: 0.7787 (p0) REVERT: G 95 TYR cc_start: 0.7305 (m-80) cc_final: 0.7052 (m-10) REVERT: G 119 ASP cc_start: 0.8253 (p0) cc_final: 0.7819 (t70) REVERT: J 67 SER cc_start: 0.8155 (t) cc_final: 0.7788 (p) REVERT: J 90 GLN cc_start: 0.8625 (pp30) cc_final: 0.8132 (pp30) REVERT: J 104 LEU cc_start: 0.8832 (tp) cc_final: 0.8390 (tt) REVERT: J 108 ARG cc_start: 0.3743 (mtt180) cc_final: 0.1478 (ptt90) REVERT: B 56 LYS cc_start: 0.7312 (mmmt) cc_final: 0.7046 (mptt) REVERT: B 117 ASP cc_start: 0.8287 (p0) cc_final: 0.7912 (p0) REVERT: B 235 GLU cc_start: 0.8213 (tt0) cc_final: 0.7687 (tm-30) REVERT: B 291 TRP cc_start: 0.6048 (p90) cc_final: 0.5508 (p90) REVERT: E 587 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7880 (ttm-80) REVERT: E 597 TRP cc_start: 0.5702 (m100) cc_final: 0.5456 (m100) REVERT: H 54 ASP cc_start: 0.8232 (p0) cc_final: 0.7808 (p0) REVERT: H 68 PHE cc_start: 0.5728 (m-80) cc_final: 0.5403 (m-80) REVERT: K 45 GLU cc_start: 0.8243 (tp30) cc_final: 0.8003 (tp30) REVERT: K 90 GLN cc_start: 0.8769 (pp30) cc_final: 0.8201 (pp30) REVERT: K 97 THR cc_start: 0.8564 (p) cc_final: 0.8268 (p) REVERT: K 108 ARG cc_start: 0.3602 (mtt180) cc_final: 0.1281 (ptt90) REVERT: C 56 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7008 (mptt) REVERT: C 117 ASP cc_start: 0.8224 (p0) cc_final: 0.7900 (p0) REVERT: C 229 GLU cc_start: 0.7831 (pp20) cc_final: 0.7398 (pp20) REVERT: C 235 GLU cc_start: 0.8177 (tt0) cc_final: 0.7577 (tm-30) REVERT: C 291 TRP cc_start: 0.6054 (p90) cc_final: 0.5419 (p90) REVERT: F 527 ILE cc_start: 0.5750 (mm) cc_final: 0.5243 (mm) REVERT: F 587 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8036 (ttm-80) REVERT: I 38 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6548 (ptp90) REVERT: I 54 ASP cc_start: 0.8187 (p0) cc_final: 0.7725 (p0) REVERT: I 95 TYR cc_start: 0.7530 (m-80) cc_final: 0.7067 (m-10) REVERT: I 104 TYR cc_start: 0.8347 (m-10) cc_final: 0.8079 (m-10) REVERT: L 2 ILE cc_start: 0.6883 (pt) cc_final: 0.6665 (pt) REVERT: L 31 ASN cc_start: 0.8278 (t0) cc_final: 0.7962 (t0) REVERT: L 67 SER cc_start: 0.8209 (t) cc_final: 0.7638 (p) REVERT: L 104 LEU cc_start: 0.8768 (tp) cc_final: 0.8019 (tt) REVERT: L 108 ARG cc_start: 0.3250 (mtt180) cc_final: 0.0976 (ptt90) outliers start: 36 outliers final: 20 residues processed: 353 average time/residue: 0.1298 time to fit residues: 64.1342 Evaluate side-chains 323 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 302 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 G residue 2 VAL Chi-restraints excluded: chain G residue 127 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 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 K residue 20 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 2 VAL 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 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [161, 116, 44, 115, 7, 118, 20, 35, 40, 30, 164] chunk 161 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.088073 restraints weight = 27972.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091052 restraints weight = 16467.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093005 restraints weight = 11670.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.094397 restraints weight = 9336.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095242 restraints weight = 8011.625| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14052 Z= 0.259 Angle : 0.785 9.755 19146 Z= 0.382 Chirality : 0.048 0.214 2205 Planarity : 0.005 0.045 2370 Dihedral : 6.039 66.208 1833 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.32 % Allowed : 14.55 % Favored : 82.13 % 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: -1.75 (0.21), residues: 1644 helix: 0.64 (0.40), residues: 180 sheet: -1.33 (0.20), residues: 648 loop : -1.35 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 67 TYR 0.021 0.002 TYR G 115 PHE 0.022 0.002 PHE G 68 TRP 0.029 0.002 TRP F 597 HIS 0.004 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (13998) covalent geometry : angle 0.76737 / 0.38 (18999) SS BOND : bond 0.00252 / 0.18 ( 15) SS BOND : angle 1.41965 / 0.92 ( 30) hydrogen bonds : bond 0.03759 / 2.65 ( 429) hydrogen bonds : angle 6.43227 / 4.54 ( 1143) link_ALPHA1-3 : bond 0.00507 / 0.29 ( 6) link_ALPHA1-3 : angle 1.34234 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00435 / 0.22 ( 3) link_ALPHA1-6 : angle 1.41122 / 0.80 ( 9) link_BETA1-4 : bond 0.00313 / 0.19 ( 15) link_BETA1-4 : angle 1.87715 / 1.19 ( 45) link_NAG-ASN : bond 0.00250 / 0.16 ( 15) link_NAG-ASN : angle 2.72632 / 1.52 ( 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 352 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 305 time to evaluate : 0.476 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: 0.7541 (mmmt) cc_final: 0.7179 (mptt) REVERT: A 89 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.6344 (tmt90) REVERT: A 117 ASP cc_start: 0.8357 (p0) cc_final: 0.8004 (p0) REVERT: A 229 GLU cc_start: 0.7820 (pp20) cc_final: 0.7506 (pp20) REVERT: A 235 GLU cc_start: 0.8088 (tt0) cc_final: 0.7626 (tm-30) REVERT: D 587 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8188 (ttm-80) REVERT: G 34 MET cc_start: 0.8299 (mmm) cc_final: 0.8014 (mmm) REVERT: G 54 ASP cc_start: 0.8218 (p0) cc_final: 0.7820 (p0) REVERT: G 119 ASP cc_start: 0.8256 (p0) cc_final: 0.7907 (t70) REVERT: J 37 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: J 67 SER cc_start: 0.8218 (t) cc_final: 0.7890 (p) REVERT: J 90 GLN cc_start: 0.8819 (pp30) cc_final: 0.8356 (pp30) REVERT: J 92 LYS cc_start: 0.8806 (tttm) cc_final: 0.8548 (tttp) REVERT: J 104 LEU cc_start: 0.8845 (tp) cc_final: 0.8342 (tt) REVERT: J 108 ARG cc_start: 0.3736 (mtt180) cc_final: 0.1559 (ptt90) REVERT: B 89 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.6344 (tmt90) REVERT: B 117 ASP cc_start: 0.8224 (p0) cc_final: 0.7824 (p0) REVERT: B 235 GLU cc_start: 0.8235 (tt0) cc_final: 0.7747 (tm-30) REVERT: E 587 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7856 (ttm-80) REVERT: E 591 ASP cc_start: 0.8244 (t0) cc_final: 0.8009 (t0) REVERT: E 597 TRP cc_start: 0.5720 (OUTLIER) cc_final: 0.5413 (m100) REVERT: H 54 ASP cc_start: 0.8177 (p0) cc_final: 0.7703 (p0) REVERT: K 45 GLU cc_start: 0.8373 (tp30) cc_final: 0.8144 (tp30) REVERT: K 67 SER cc_start: 0.8024 (t) cc_final: 0.7810 (p) REVERT: K 108 ARG cc_start: 0.3532 (mtt180) cc_final: 0.1243 (ptt90) REVERT: C 56 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7264 (mptt) REVERT: C 117 ASP cc_start: 0.8348 (p0) cc_final: 0.8040 (p0) REVERT: C 229 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7394 (pp20) REVERT: C 235 GLU cc_start: 0.8240 (tt0) cc_final: 0.7622 (tm-30) REVERT: F 587 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7977 (ttm-80) REVERT: I 38 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6991 (ptp-110) REVERT: I 46 GLU cc_start: 0.7246 (pt0) cc_final: 0.7028 (pt0) REVERT: I 54 ASP cc_start: 0.8175 (p0) cc_final: 0.7755 (p0) REVERT: I 104 TYR cc_start: 0.8432 (m-10) cc_final: 0.8078 (m-10) REVERT: L 31 ASN cc_start: 0.8408 (t0) cc_final: 0.7835 (t0) REVERT: L 37 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: L 67 SER cc_start: 0.8044 (t) cc_final: 0.7641 (p) REVERT: L 108 ARG cc_start: 0.3258 (mtt180) cc_final: 0.1101 (ptt90) outliers start: 47 outliers final: 31 residues processed: 335 average time/residue: 0.1296 time to fit residues: 60.7904 Evaluate side-chains 324 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 89 ARG 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 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 E residue 597 TRP 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 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 79 VAL 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 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR 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: [109, 49, 21, 146, 53, 112, 47, 10, 126, 147, 60] chunk 109 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3643 r_free = 0.3643 target = 0.118599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091000 restraints weight = 27541.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094013 restraints weight = 16407.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096054 restraints weight = 11646.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.097403 restraints weight = 9274.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098253 restraints weight = 7959.767| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14052 Z= 0.133 Angle : 0.692 8.503 19146 Z= 0.337 Chirality : 0.045 0.173 2205 Planarity : 0.004 0.065 2370 Dihedral : 5.661 61.128 1833 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.26 % Allowed : 16.60 % Favored : 81.14 % 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: -1.49 (0.21), residues: 1644 helix: 0.96 (0.40), residues: 183 sheet: -1.21 (0.20), residues: 645 loop : -1.16 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 24 TYR 0.020 0.001 TYR G 115 PHE 0.015 0.001 PHE G 68 TRP 0.034 0.002 TRP F 597 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13998) covalent geometry : angle 0.67532 / 0.33 (18999) SS BOND : bond 0.00326 / 0.25 ( 15) SS BOND : angle 1.08173 / 0.76 ( 30) hydrogen bonds : bond 0.03289 / 2.27 ( 429) hydrogen bonds : angle 6.11750 / 4.30 ( 1143) link_ALPHA1-3 : bond 0.00480 / 0.27 ( 6) link_ALPHA1-3 : angle 1.30797 / 0.77 ( 18) link_ALPHA1-6 : bond 0.00465 / 0.23 ( 3) link_ALPHA1-6 : angle 1.39427 / 0.79 ( 9) link_BETA1-4 : bond 0.00334 / 0.21 ( 15) link_BETA1-4 : angle 1.70825 / 1.10 ( 45) link_NAG-ASN : bond 0.00212 / 0.16 ( 15) link_NAG-ASN : angle 2.53594 / 1.35 ( 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 355 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 323 time to evaluate : 0.522 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: 0.7484 (mmmt) cc_final: 0.7237 (mptt) REVERT: A 117 ASP cc_start: 0.8366 (p0) cc_final: 0.8037 (p0) REVERT: A 229 GLU cc_start: 0.7797 (pp20) cc_final: 0.7451 (pp20) REVERT: A 235 GLU cc_start: 0.8053 (tt0) cc_final: 0.7552 (tm-30) REVERT: D 587 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8182 (ttm-80) REVERT: G 34 MET cc_start: 0.8310 (mmm) cc_final: 0.7974 (mmm) REVERT: G 43 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7410 (mmmt) REVERT: G 54 ASP cc_start: 0.8198 (p0) cc_final: 0.7812 (p0) REVERT: G 119 ASP cc_start: 0.8247 (p0) cc_final: 0.7827 (t70) REVERT: J 37 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: J 67 SER cc_start: 0.8051 (t) cc_final: 0.7746 (p) REVERT: J 90 GLN cc_start: 0.8848 (pp30) cc_final: 0.8318 (pp30) REVERT: J 92 LYS cc_start: 0.8815 (tttm) cc_final: 0.8540 (tttm) REVERT: J 104 LEU cc_start: 0.8812 (tp) cc_final: 0.8339 (tt) REVERT: J 108 ARG cc_start: 0.3537 (mtt180) cc_final: 0.1409 (ptt90) REVERT: B 117 ASP cc_start: 0.8192 (p0) cc_final: 0.7805 (p0) REVERT: B 235 GLU cc_start: 0.8208 (tt0) cc_final: 0.7731 (tm-30) REVERT: E 587 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7820 (ttm-80) REVERT: E 588 LYS cc_start: 0.8070 (mmmm) cc_final: 0.7656 (mmmm) REVERT: E 597 TRP cc_start: 0.5897 (OUTLIER) cc_final: 0.5676 (m100) REVERT: H 54 ASP cc_start: 0.8167 (p0) cc_final: 0.7707 (p0) REVERT: H 57 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8271 (mmtp) REVERT: K 67 SER cc_start: 0.7977 (t) cc_final: 0.7666 (p) REVERT: K 108 ARG cc_start: 0.3502 (mtt180) cc_final: 0.1256 (ptt90) REVERT: C 56 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7255 (mptt) REVERT: C 117 ASP cc_start: 0.8340 (p0) cc_final: 0.8033 (p0) REVERT: C 229 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7437 (pp20) REVERT: C 235 GLU cc_start: 0.8165 (tt0) cc_final: 0.7591 (tm-30) REVERT: C 291 TRP cc_start: 0.6071 (p90) cc_final: 0.5251 (p90) REVERT: F 545 GLU cc_start: 0.8037 (mp0) cc_final: 0.7802 (mp0) REVERT: F 587 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7995 (ttm-80) REVERT: I 34 MET cc_start: 0.8313 (mmm) cc_final: 0.8024 (mmm) REVERT: I 38 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7215 (ptp-110) REVERT: I 48 MET cc_start: 0.6214 (mmt) cc_final: 0.5999 (mmt) REVERT: I 54 ASP cc_start: 0.8195 (p0) cc_final: 0.7766 (p0) REVERT: I 104 TYR cc_start: 0.8413 (m-10) cc_final: 0.8076 (m-10) REVERT: L 31 ASN cc_start: 0.8379 (t0) cc_final: 0.7969 (t0) REVERT: L 37 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: L 67 SER cc_start: 0.7884 (t) cc_final: 0.7415 (p) REVERT: L 104 LEU cc_start: 0.8678 (tp) cc_final: 0.7914 (tt) REVERT: L 108 ARG cc_start: 0.3196 (mtt180) cc_final: 0.1116 (ptt90) outliers start: 32 outliers final: 18 residues processed: 341 average time/residue: 0.1267 time to fit residues: 60.4547 Evaluate side-chains 322 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 299 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 129 VAL 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 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 597 TRP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR 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 L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [13, 15, 4, 123, 138, 91, 164, 9, 46, 87, 1] chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 164 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 0.0370 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092038 restraints weight = 27661.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095076 restraints weight = 16560.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097162 restraints weight = 11735.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098545 restraints weight = 9311.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099455 restraints weight = 7979.901| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14052 Z= 0.123 Angle : 0.689 9.024 19146 Z= 0.335 Chirality : 0.044 0.179 2205 Planarity : 0.004 0.052 2370 Dihedral : 5.419 57.042 1833 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.47 % Allowed : 16.81 % Favored : 80.72 % 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: 1.27 (0.40), residues: 183 sheet: -1.01 (0.20), residues: 627 loop : -1.11 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.016 0.001 TYR G 115 PHE 0.025 0.002 PHE D 592 TRP 0.033 0.001 TRP F 597 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13998) covalent geometry : angle 0.67258 / 0.33 (18999) SS BOND : bond 0.00452 / 0.36 ( 15) SS BOND : angle 1.39449 / 0.90 ( 30) hydrogen bonds : bond 0.03109 / 2.12 ( 429) hydrogen bonds : angle 5.90831 / 4.15 ( 1143) link_ALPHA1-3 : bond 0.00435 / 0.25 ( 6) link_ALPHA1-3 : angle 1.32891 / 0.78 ( 18) link_ALPHA1-6 : bond 0.00436 / 0.22 ( 3) link_ALPHA1-6 : angle 1.38828 / 0.79 ( 9) link_BETA1-4 : bond 0.00379 / 0.25 ( 15) link_BETA1-4 : angle 1.62629 / 1.05 ( 45) link_NAG-ASN : bond 0.00203 / 0.16 ( 15) link_NAG-ASN : angle 2.45404 / 1.32 ( 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 361 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 0.506 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: 0.8371 (p0) cc_final: 0.8034 (p0) REVERT: A 229 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: A 235 GLU cc_start: 0.8005 (tt0) cc_final: 0.7562 (tm-30) REVERT: D 587 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8138 (ttm-80) REVERT: G 5 GLU cc_start: 0.7189 (tp30) cc_final: 0.6762 (pm20) REVERT: G 34 MET cc_start: 0.8401 (mmm) cc_final: 0.7972 (mmm) REVERT: G 36 TRP cc_start: 0.7908 (m100) cc_final: 0.7574 (m100) REVERT: G 54 ASP cc_start: 0.8245 (p0) cc_final: 0.7831 (p0) REVERT: G 119 ASP cc_start: 0.8233 (p0) cc_final: 0.7836 (t70) REVERT: J 37 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: J 67 SER cc_start: 0.8128 (t) cc_final: 0.7766 (p) REVERT: J 90 GLN cc_start: 0.8774 (pp30) cc_final: 0.8365 (pp30) REVERT: J 92 LYS cc_start: 0.8847 (tttm) cc_final: 0.8549 (tttm) REVERT: J 104 LEU cc_start: 0.8792 (tp) cc_final: 0.8255 (tt) REVERT: J 108 ARG cc_start: 0.3549 (mtt180) cc_final: 0.1492 (ptt90) REVERT: B 56 LYS cc_start: 0.6973 (mptt) cc_final: 0.6704 (mmtt) REVERT: B 117 ASP cc_start: 0.8214 (p0) cc_final: 0.7855 (p0) REVERT: B 235 GLU cc_start: 0.8213 (tt0) cc_final: 0.7751 (tm-30) REVERT: E 587 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7853 (ttm-80) REVERT: H 54 ASP cc_start: 0.8193 (p0) cc_final: 0.7750 (p0) REVERT: K 37 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: K 67 SER cc_start: 0.8028 (t) cc_final: 0.7708 (p) REVERT: K 90 GLN cc_start: 0.8694 (pp30) cc_final: 0.8336 (pp30) REVERT: K 108 ARG cc_start: 0.3249 (mtt180) cc_final: 0.1075 (ptt90) REVERT: C 56 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7277 (mptt) REVERT: C 117 ASP cc_start: 0.8283 (p0) cc_final: 0.7983 (p0) REVERT: C 229 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: C 235 GLU cc_start: 0.8144 (tt0) cc_final: 0.7586 (tm-30) REVERT: C 291 TRP cc_start: 0.6022 (p90) cc_final: 0.5205 (p90) REVERT: F 545 GLU cc_start: 0.8056 (mp0) cc_final: 0.7848 (mp0) REVERT: F 573 LEU cc_start: 0.8948 (mt) cc_final: 0.8666 (tp) REVERT: F 587 ARG cc_start: 0.8285 (mtp85) cc_final: 0.8015 (ttm-80) REVERT: I 34 MET cc_start: 0.8252 (mmm) cc_final: 0.7981 (mmm) REVERT: I 36 TRP cc_start: 0.7827 (m100) cc_final: 0.7569 (m100) REVERT: I 38 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7218 (ptp-110) REVERT: I 46 GLU cc_start: 0.7254 (pt0) cc_final: 0.7044 (pt0) REVERT: I 54 ASP cc_start: 0.8152 (p0) cc_final: 0.7747 (p0) REVERT: I 104 TYR cc_start: 0.8404 (m-10) cc_final: 0.8057 (m-10) REVERT: L 4 MET cc_start: 0.7863 (ttm) cc_final: 0.7630 (ttm) REVERT: L 31 ASN cc_start: 0.8383 (t0) cc_final: 0.8027 (t0) REVERT: L 37 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: L 67 SER cc_start: 0.7975 (t) cc_final: 0.7528 (p) REVERT: L 70 ASP cc_start: 0.8891 (m-30) cc_final: 0.8628 (t70) REVERT: L 94 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7312 (t80) REVERT: L 104 LEU cc_start: 0.8552 (tp) cc_final: 0.7779 (tt) REVERT: L 108 ARG cc_start: 0.3156 (mtt180) cc_final: 0.1029 (ptt90) outliers start: 35 outliers final: 20 residues processed: 345 average time/residue: 0.1215 time to fit residues: 59.4298 Evaluate side-chains 332 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 305 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 129 VAL 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 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 54 LEU 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 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 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: [85, 67, 5, 120, 35, 64, 48, 82, 149, 3, 11] chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091415 restraints weight = 27492.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094382 restraints weight = 16518.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096402 restraints weight = 11800.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097764 restraints weight = 9412.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098683 restraints weight = 8084.959| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4421 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= 0.172 Angle : 0.725 9.437 19146 Z= 0.352 Chirality : 0.046 0.169 2205 Planarity : 0.004 0.052 2370 Dihedral : 5.448 55.852 1833 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.12 % Allowed : 17.58 % 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: -1.22 (0.21), residues: 1644 helix: 1.26 (0.39), residues: 183 sheet: -0.97 (0.20), residues: 621 loop : -1.07 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 24 TYR 0.017 0.001 TYR G 115 PHE 0.024 0.002 PHE H 50 TRP 0.020 0.001 TRP F 597 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (13998) covalent geometry : angle 0.70955 / 0.35 (18999) SS BOND : bond 0.00334 / 0.27 ( 15) SS BOND : angle 1.19802 / 0.82 ( 30) hydrogen bonds : bond 0.03353 / 2.33 ( 429) hydrogen bonds : angle 5.89480 / 4.14 ( 1143) link_ALPHA1-3 : bond 0.00420 / 0.24 ( 6) link_ALPHA1-3 : angle 1.35249 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00414 / 0.21 ( 3) link_ALPHA1-6 : angle 1.43133 / 0.81 ( 9) link_BETA1-4 : bond 0.00272 / 0.17 ( 15) link_BETA1-4 : angle 1.63623 / 1.04 ( 45) link_NAG-ASN : bond 0.00159 / 0.10 ( 15) link_NAG-ASN : angle 2.47615 / 1.35 ( 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 329 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 0.639 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: 0.7043 (mptt) cc_final: 0.6809 (mmtt) REVERT: A 117 ASP cc_start: 0.8342 (p0) cc_final: 0.8022 (p0) REVERT: A 229 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7363 (pp20) REVERT: A 235 GLU cc_start: 0.8009 (tt0) cc_final: 0.7584 (tm-30) REVERT: D 587 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8140 (ttm-80) REVERT: G 54 ASP cc_start: 0.8221 (p0) cc_final: 0.7824 (p0) REVERT: G 119 ASP cc_start: 0.8241 (p0) cc_final: 0.7889 (t70) REVERT: J 37 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: J 58 VAL cc_start: 0.9040 (t) cc_final: 0.8830 (p) REVERT: J 67 SER cc_start: 0.8265 (t) cc_final: 0.7927 (p) REVERT: J 90 GLN cc_start: 0.8821 (pp30) cc_final: 0.8384 (pp30) REVERT: J 92 LYS cc_start: 0.8882 (tttm) cc_final: 0.8655 (tttp) REVERT: J 104 LEU cc_start: 0.8770 (tp) cc_final: 0.8211 (tt) REVERT: J 108 ARG cc_start: 0.3625 (mtt180) cc_final: 0.1586 (ptt90) REVERT: B 56 LYS cc_start: 0.7139 (mptt) cc_final: 0.6755 (mmtt) REVERT: B 117 ASP cc_start: 0.8216 (p0) cc_final: 0.7835 (p0) REVERT: B 235 GLU cc_start: 0.8120 (tt0) cc_final: 0.7716 (tm-30) REVERT: E 587 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7827 (ttm-80) REVERT: H 54 ASP cc_start: 0.8188 (p0) cc_final: 0.7744 (p0) REVERT: H 57 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8304 (mmtp) REVERT: K 37 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: K 67 SER cc_start: 0.8175 (t) cc_final: 0.7803 (p) REVERT: K 70 ASP cc_start: 0.8881 (m-30) cc_final: 0.8504 (t0) REVERT: K 90 GLN cc_start: 0.8672 (pp30) cc_final: 0.8312 (pp30) REVERT: K 108 ARG cc_start: 0.3025 (mtt180) cc_final: 0.0931 (ptt90) REVERT: C 56 LYS cc_start: 0.7626 (mmmt) cc_final: 0.7279 (mptt) REVERT: C 117 ASP cc_start: 0.8319 (p0) cc_final: 0.8015 (p0) REVERT: C 229 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: C 235 GLU cc_start: 0.8166 (tt0) cc_final: 0.7642 (tm-30) REVERT: F 545 GLU cc_start: 0.8046 (mp0) cc_final: 0.7843 (mp0) REVERT: F 587 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7976 (ttm-80) REVERT: I 34 MET cc_start: 0.8202 (mmm) cc_final: 0.7946 (mmm) REVERT: I 38 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7050 (ptp-110) REVERT: I 54 ASP cc_start: 0.8160 (p0) cc_final: 0.7753 (p0) REVERT: I 104 TYR cc_start: 0.8460 (m-10) cc_final: 0.8047 (m-10) REVERT: L 4 MET cc_start: 0.7877 (ttm) cc_final: 0.7464 (ttm) REVERT: L 31 ASN cc_start: 0.8404 (t0) cc_final: 0.8061 (t0) REVERT: L 37 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: L 67 SER cc_start: 0.7971 (t) cc_final: 0.7517 (p) REVERT: L 70 ASP cc_start: 0.8914 (m-30) cc_final: 0.8579 (t0) REVERT: L 94 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7477 (t80) REVERT: L 104 LEU cc_start: 0.8576 (tp) cc_final: 0.7745 (tt) REVERT: L 108 ARG cc_start: 0.3190 (mtt180) cc_final: 0.1126 (ptt90) outliers start: 30 outliers final: 19 residues processed: 314 average time/residue: 0.1287 time to fit residues: 57.0058 Evaluate side-chains 310 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 573 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 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 54 LEU 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: [54, 112, 108, 59, 60, 119, 123, 105, 9, 136, 76] chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 chunk 108 optimal weight: 5.9990 chunk 59 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094043 restraints weight = 27166.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097108 restraints weight = 16122.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099226 restraints weight = 11399.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100580 restraints weight = 9028.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101536 restraints weight = 7737.988| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14052 Z= 0.115 Angle : 0.707 10.957 19146 Z= 0.341 Chirality : 0.044 0.159 2205 Planarity : 0.004 0.054 2370 Dihedral : 5.173 53.261 1833 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.62 % Allowed : 17.87 % Favored : 80.51 % 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: -1.03 (0.21), residues: 1644 helix: 1.51 (0.40), residues: 183 sheet: -0.90 (0.20), residues: 645 loop : -0.91 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.023 0.001 TYR K 96 PHE 0.029 0.002 PHE D 592 TRP 0.019 0.001 TRP I 36 HIS 0.002 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (13998) covalent geometry : angle 0.69092 / 0.34 (18999) SS BOND : bond 0.00520 / 0.42 ( 15) SS BOND : angle 1.66854 / 1.12 ( 30) hydrogen bonds : bond 0.03098 / 2.09 ( 429) hydrogen bonds : angle 5.74755 / 4.02 ( 1143) link_ALPHA1-3 : bond 0.00425 / 0.24 ( 6) link_ALPHA1-3 : angle 1.34680 / 0.79 ( 18) link_ALPHA1-6 : bond 0.00476 / 0.24 ( 3) link_ALPHA1-6 : angle 1.42090 / 0.80 ( 9) link_BETA1-4 : bond 0.00396 / 0.26 ( 15) link_BETA1-4 : angle 1.56125 / 1.02 ( 45) link_NAG-ASN : bond 0.00250 / 0.19 ( 15) link_NAG-ASN : angle 2.41981 / 1.28 ( 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 336 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 313 time to evaluate : 0.415 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: 0.7182 (mptt) cc_final: 0.6940 (mmtt) REVERT: A 117 ASP cc_start: 0.8345 (p0) cc_final: 0.8034 (p0) REVERT: A 229 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7422 (pp20) REVERT: A 235 GLU cc_start: 0.7981 (tt0) cc_final: 0.7489 (tm-30) REVERT: D 587 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8074 (ttm-80) REVERT: D 588 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7767 (mmmt) REVERT: G 36 TRP cc_start: 0.7849 (m100) cc_final: 0.7486 (m100) REVERT: G 54 ASP cc_start: 0.8175 (p0) cc_final: 0.7755 (p0) REVERT: G 119 ASP cc_start: 0.8201 (p0) cc_final: 0.7892 (t70) REVERT: J 18 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8148 (tmm160) REVERT: J 37 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: J 58 VAL cc_start: 0.8949 (t) cc_final: 0.8742 (p) REVERT: J 67 SER cc_start: 0.8194 (t) cc_final: 0.7833 (p) REVERT: J 90 GLN cc_start: 0.8680 (pp30) cc_final: 0.8294 (pp30) REVERT: J 92 LYS cc_start: 0.8939 (tttm) cc_final: 0.8670 (tttm) REVERT: J 104 LEU cc_start: 0.8737 (tp) cc_final: 0.8159 (tt) REVERT: J 108 ARG cc_start: 0.3674 (mtt180) cc_final: 0.1719 (ptt90) REVERT: B 56 LYS cc_start: 0.7235 (mptt) cc_final: 0.6844 (mmtt) REVERT: B 117 ASP cc_start: 0.8201 (p0) cc_final: 0.7817 (p0) REVERT: B 235 GLU cc_start: 0.8046 (tt0) cc_final: 0.7655 (tm-30) REVERT: E 587 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7852 (ttm-80) REVERT: H 36 TRP cc_start: 0.7629 (m100) cc_final: 0.7375 (m100) REVERT: H 54 ASP cc_start: 0.8189 (p0) cc_final: 0.7752 (p0) REVERT: H 57 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8264 (mmmm) REVERT: K 37 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: K 67 SER cc_start: 0.8159 (t) cc_final: 0.7752 (p) REVERT: K 70 ASP cc_start: 0.8816 (m-30) cc_final: 0.8596 (t0) REVERT: K 108 ARG cc_start: 0.3054 (mtt180) cc_final: 0.0959 (ptt90) REVERT: C 56 LYS cc_start: 0.7613 (mmmt) cc_final: 0.7313 (mptt) REVERT: C 117 ASP cc_start: 0.8280 (p0) cc_final: 0.7969 (p0) REVERT: C 229 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7459 (pp20) REVERT: C 235 GLU cc_start: 0.8126 (tt0) cc_final: 0.7627 (tm-30) REVERT: C 291 TRP cc_start: 0.5931 (p90) cc_final: 0.5191 (p90) REVERT: F 545 GLU cc_start: 0.8066 (mp0) cc_final: 0.7863 (mp0) REVERT: F 573 LEU cc_start: 0.8945 (mt) cc_final: 0.8667 (tp) REVERT: F 587 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7718 (ttm-80) REVERT: I 34 MET cc_start: 0.8145 (mmm) cc_final: 0.7853 (mmm) REVERT: I 36 TRP cc_start: 0.7652 (m100) cc_final: 0.7328 (m100) REVERT: I 38 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6985 (ptp-110) REVERT: I 54 ASP cc_start: 0.8181 (p0) cc_final: 0.7742 (p0) REVERT: I 104 TYR cc_start: 0.8415 (m-10) cc_final: 0.8073 (m-10) REVERT: I 119 ASP cc_start: 0.8089 (p0) cc_final: 0.7836 (p0) REVERT: L 31 ASN cc_start: 0.8330 (t0) cc_final: 0.8108 (t0) REVERT: L 37 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: L 67 SER cc_start: 0.7982 (t) cc_final: 0.7504 (p) REVERT: L 70 ASP cc_start: 0.8847 (m-30) cc_final: 0.8597 (t0) REVERT: L 94 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7386 (t80) REVERT: L 104 LEU cc_start: 0.8533 (tp) cc_final: 0.7677 (tt) REVERT: L 108 ARG cc_start: 0.3153 (mtt180) cc_final: 0.1043 (ptt90) outliers start: 23 outliers final: 14 residues processed: 325 average time/residue: 0.1296 time to fit residues: 59.5211 Evaluate side-chains 313 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 292 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 82 VAL 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 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain I residue 2 VAL 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: [28, 96, 97, 142, 25, 27, 114, 100, 48, 103, 115] chunk 28 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 114 optimal weight: 0.0770 chunk 100 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.122241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094527 restraints weight = 27391.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097622 restraints weight = 16253.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099749 restraints weight = 11456.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101189 restraints weight = 9070.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102065 restraints weight = 7738.395| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14052 Z= 0.117 Angle : 0.722 11.631 19146 Z= 0.346 Chirality : 0.044 0.167 2205 Planarity : 0.004 0.056 2370 Dihedral : 5.066 51.983 1833 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.98 % Allowed : 18.08 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1644 helix: 1.60 (0.40), residues: 183 sheet: -0.91 (0.20), residues: 651 loop : -0.79 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.014 0.001 TYR J 96 PHE 0.016 0.001 PHE J 94 TRP 0.034 0.001 TRP D 597 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13998) covalent geometry : angle 0.70536 / 0.34 (18999) SS BOND : bond 0.00574 / 0.47 ( 15) SS BOND : angle 1.89140 / 1.23 ( 30) hydrogen bonds : bond 0.03085 / 2.06 ( 429) hydrogen bonds : angle 5.65157 / 3.97 ( 1143) link_ALPHA1-3 : bond 0.00407 / 0.23 ( 6) link_ALPHA1-3 : angle 1.37606 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00458 / 0.23 ( 3) link_ALPHA1-6 : angle 1.40670 / 0.80 ( 9) link_BETA1-4 : bond 0.00373 / 0.25 ( 15) link_BETA1-4 : angle 1.52351 / 0.98 ( 45) link_NAG-ASN : bond 0.00231 / 0.17 ( 15) link_NAG-ASN : angle 2.45709 / 1.30 ( 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: 28 poor density : 314 time to evaluate : 0.720 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: 0.7149 (mptt) cc_final: 0.6901 (mmtt) REVERT: A 117 ASP cc_start: 0.8249 (p0) cc_final: 0.7975 (p0) REVERT: A 229 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7403 (pp20) REVERT: A 235 GLU cc_start: 0.7990 (tt0) cc_final: 0.7564 (tm-30) REVERT: D 587 ARG cc_start: 0.8307 (mtp85) cc_final: 0.8066 (ttm-80) REVERT: D 588 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7763 (mmmt) REVERT: G 34 MET cc_start: 0.8394 (mmm) cc_final: 0.8183 (mmm) REVERT: G 36 TRP cc_start: 0.7823 (m100) cc_final: 0.7466 (m100) REVERT: G 54 ASP cc_start: 0.8147 (p0) cc_final: 0.7740 (p0) REVERT: G 119 ASP cc_start: 0.8244 (p0) cc_final: 0.7876 (t70) REVERT: J 18 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8163 (tmm160) REVERT: J 37 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: J 67 SER cc_start: 0.8188 (t) cc_final: 0.7833 (p) REVERT: J 90 GLN cc_start: 0.8739 (pp30) cc_final: 0.8382 (pp30) REVERT: J 92 LYS cc_start: 0.8912 (tttm) cc_final: 0.8685 (tttp) REVERT: J 104 LEU cc_start: 0.8680 (tp) cc_final: 0.8052 (tt) REVERT: J 108 ARG cc_start: 0.3532 (mtt180) cc_final: 0.1693 (ptt90) REVERT: B 56 LYS cc_start: 0.7218 (mptt) cc_final: 0.6807 (mmtt) REVERT: B 117 ASP cc_start: 0.8228 (p0) cc_final: 0.7858 (p0) REVERT: B 235 GLU cc_start: 0.8011 (tt0) cc_final: 0.7644 (tm-30) REVERT: E 573 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8742 (tp) REVERT: E 587 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7874 (ttm-80) REVERT: H 34 MET cc_start: 0.8396 (mmm) cc_final: 0.7599 (mmm) REVERT: H 54 ASP cc_start: 0.8171 (p0) cc_final: 0.7796 (p0) REVERT: H 57 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8312 (mmtp) REVERT: K 37 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: K 67 SER cc_start: 0.8073 (t) cc_final: 0.7662 (p) REVERT: K 70 ASP cc_start: 0.8813 (m-30) cc_final: 0.8530 (t0) REVERT: K 90 GLN cc_start: 0.8503 (pp30) cc_final: 0.8270 (pp30) REVERT: K 108 ARG cc_start: 0.3068 (mtt180) cc_final: 0.0981 (ptt90) REVERT: C 56 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7289 (mptt) REVERT: C 117 ASP cc_start: 0.8290 (p0) cc_final: 0.7980 (p0) REVERT: C 229 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: C 235 GLU cc_start: 0.8181 (tt0) cc_final: 0.7637 (tm-30) REVERT: C 291 TRP cc_start: 0.5911 (p90) cc_final: 0.5159 (p90) REVERT: F 545 GLU cc_start: 0.8066 (mp0) cc_final: 0.7810 (mp0) REVERT: F 573 LEU cc_start: 0.8943 (mt) cc_final: 0.8676 (tp) REVERT: F 587 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7672 (ttm-80) REVERT: I 36 TRP cc_start: 0.7630 (m100) cc_final: 0.7374 (m100) REVERT: I 38 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7028 (ptp-110) REVERT: I 54 ASP cc_start: 0.8193 (p0) cc_final: 0.7751 (p0) REVERT: I 104 TYR cc_start: 0.8438 (m-10) cc_final: 0.8086 (m-10) REVERT: I 119 ASP cc_start: 0.7988 (p0) cc_final: 0.7743 (p0) REVERT: L 37 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: L 67 SER cc_start: 0.7999 (t) cc_final: 0.7532 (p) REVERT: L 70 ASP cc_start: 0.8882 (m-30) cc_final: 0.8610 (t0) REVERT: L 94 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7409 (t80) REVERT: L 104 LEU cc_start: 0.8464 (tp) cc_final: 0.7620 (tt) REVERT: L 108 ARG cc_start: 0.3159 (mtt180) cc_final: 0.1123 (ptt90) outliers start: 28 outliers final: 15 residues processed: 330 average time/residue: 0.1288 time to fit residues: 60.1893 Evaluate side-chains 316 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 293 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain H residue 69 THR 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 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain I residue 38 ARG 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: [31, 23, 157, 32, 128, 55, 27, 17, 151, 83, 20] chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 13 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092432 restraints weight = 27669.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.095468 restraints weight = 16470.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.097547 restraints weight = 11691.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098976 restraints weight = 9288.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.099775 restraints weight = 7945.277| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14052 Z= 0.147 Angle : 0.767 18.426 19146 Z= 0.365 Chirality : 0.045 0.177 2205 Planarity : 0.005 0.058 2370 Dihedral : 5.200 52.876 1833 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.41 % Allowed : 18.50 % Favored : 80.08 % 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: -0.94 (0.21), residues: 1644 helix: 1.62 (0.39), residues: 183 sheet: -0.84 (0.20), residues: 627 loop : -0.88 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 24 TYR 0.013 0.001 TYR G 115 PHE 0.029 0.002 PHE E 592 TRP 0.036 0.002 TRP D 597 HIS 0.002 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13998) covalent geometry : angle 0.75050 / 0.36 (18999) SS BOND : bond 0.00495 / 0.41 ( 15) SS BOND : angle 2.20869 / 1.56 ( 30) hydrogen bonds : bond 0.03271 / 2.24 ( 429) hydrogen bonds : angle 5.64440 / 3.98 ( 1143) link_ALPHA1-3 : bond 0.00407 / 0.23 ( 6) link_ALPHA1-3 : angle 1.37649 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00441 / 0.22 ( 3) link_ALPHA1-6 : angle 1.44373 / 0.82 ( 9) link_BETA1-4 : bond 0.00295 / 0.19 ( 15) link_BETA1-4 : angle 1.54133 / 0.98 ( 45) link_NAG-ASN : bond 0.00195 / 0.14 ( 15) link_NAG-ASN : angle 2.41304 / 1.30 ( 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 314 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 294 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: A 56 LYS cc_start: 0.7204 (mptt) cc_final: 0.6930 (mmtt) REVERT: A 117 ASP cc_start: 0.8295 (p0) cc_final: 0.8034 (p0) REVERT: A 229 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: A 235 GLU cc_start: 0.8020 (tt0) cc_final: 0.7582 (tm-30) REVERT: D 587 ARG cc_start: 0.8329 (mtp85) cc_final: 0.8102 (ttm-80) REVERT: D 588 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7778 (mmmt) REVERT: G 34 MET cc_start: 0.8411 (mmm) cc_final: 0.8193 (mmm) REVERT: G 36 TRP cc_start: 0.7788 (m100) cc_final: 0.7445 (m100) REVERT: G 43 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7697 (mmmt) REVERT: G 54 ASP cc_start: 0.8164 (p0) cc_final: 0.7763 (p0) REVERT: G 119 ASP cc_start: 0.8235 (p0) cc_final: 0.7851 (t70) REVERT: J 18 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8337 (tmm160) REVERT: J 37 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: J 67 SER cc_start: 0.8143 (t) cc_final: 0.7735 (p) REVERT: J 90 GLN cc_start: 0.8644 (pp30) cc_final: 0.8330 (pp30) REVERT: J 92 LYS cc_start: 0.8981 (tttm) cc_final: 0.8760 (tttm) REVERT: J 104 LEU cc_start: 0.8606 (tp) cc_final: 0.7968 (tt) REVERT: J 108 ARG cc_start: 0.3577 (mtt180) cc_final: 0.1672 (ptt90) REVERT: B 56 LYS cc_start: 0.7264 (mptt) cc_final: 0.6847 (mmtt) REVERT: B 117 ASP cc_start: 0.8266 (p0) cc_final: 0.7897 (p0) REVERT: B 235 GLU cc_start: 0.8022 (tt0) cc_final: 0.7653 (tm-30) REVERT: E 573 LEU cc_start: 0.8989 (tp) cc_final: 0.8783 (tp) REVERT: E 587 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7820 (ttm-80) REVERT: H 34 MET cc_start: 0.8368 (mmm) cc_final: 0.7518 (mmm) REVERT: H 54 ASP cc_start: 0.8193 (p0) cc_final: 0.7767 (p0) REVERT: H 57 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8363 (mmtp) REVERT: K 18 ARG cc_start: 0.8536 (ttp80) cc_final: 0.7190 (tmm160) REVERT: K 37 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: K 67 SER cc_start: 0.8112 (t) cc_final: 0.7756 (p) REVERT: K 70 ASP cc_start: 0.8855 (m-30) cc_final: 0.8571 (t70) REVERT: K 90 GLN cc_start: 0.8726 (pp30) cc_final: 0.8501 (pp30) REVERT: K 108 ARG cc_start: 0.2936 (mtt180) cc_final: 0.0915 (ptt90) REVERT: C 56 LYS cc_start: 0.7693 (mmmt) cc_final: 0.7309 (mptt) REVERT: C 117 ASP cc_start: 0.8264 (p0) cc_final: 0.7974 (p0) REVERT: C 130 ARG cc_start: 0.8730 (mmm160) cc_final: 0.8465 (mmm160) REVERT: C 229 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: C 235 GLU cc_start: 0.8175 (tt0) cc_final: 0.7669 (tm-30) REVERT: F 545 GLU cc_start: 0.8000 (mp0) cc_final: 0.7765 (mp0) REVERT: F 573 LEU cc_start: 0.8989 (mt) cc_final: 0.8696 (tp) REVERT: F 587 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7695 (ttm-80) REVERT: I 36 TRP cc_start: 0.7652 (m100) cc_final: 0.7383 (m100) REVERT: I 38 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7023 (ptp-110) REVERT: I 43 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7886 (mmmt) REVERT: I 54 ASP cc_start: 0.8181 (p0) cc_final: 0.7774 (p0) REVERT: I 104 TYR cc_start: 0.8460 (m-10) cc_final: 0.8033 (m-10) REVERT: I 119 ASP cc_start: 0.8040 (p0) cc_final: 0.7783 (p0) REVERT: L 37 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: L 67 SER cc_start: 0.8087 (t) cc_final: 0.7656 (p) REVERT: L 70 ASP cc_start: 0.8879 (m-30) cc_final: 0.8665 (t0) REVERT: L 94 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7547 (t80) REVERT: L 104 LEU cc_start: 0.8390 (tp) cc_final: 0.7585 (tt) REVERT: L 108 ARG cc_start: 0.3112 (mtt180) cc_final: 0.1111 (ptt90) outliers start: 20 outliers final: 13 residues processed: 307 average time/residue: 0.1325 time to fit residues: 56.9167 Evaluate side-chains 310 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 290 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 69 THR 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 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain I residue 38 ARG 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: [139, 49, 132, 32, 38, 93, 44, 152, 19, 101, 63] chunk 139 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092469 restraints weight = 27786.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095546 restraints weight = 16516.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097628 restraints weight = 11707.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099032 restraints weight = 9282.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099884 restraints weight = 7949.725| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14052 Z= 0.145 Angle : 0.759 15.560 19146 Z= 0.363 Chirality : 0.046 0.210 2205 Planarity : 0.004 0.058 2370 Dihedral : 5.177 53.385 1833 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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: -1.04 (0.21), residues: 1644 helix: 1.02 (0.39), residues: 201 sheet: -0.77 (0.21), residues: 609 loop : -0.98 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.017 0.001 TYR K 96 PHE 0.018 0.002 PHE L 94 TRP 0.021 0.001 TRP H 36 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13998) covalent geometry : angle 0.74066 / 0.36 (18999) SS BOND : bond 0.00494 / 0.41 ( 15) SS BOND : angle 2.51295 / 1.80 ( 30) hydrogen bonds : bond 0.03230 / 2.22 ( 429) hydrogen bonds : angle 5.59533 / 3.95 ( 1143) link_ALPHA1-3 : bond 0.00415 / 0.23 ( 6) link_ALPHA1-3 : angle 1.36759 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00442 / 0.22 ( 3) link_ALPHA1-6 : angle 1.45771 / 0.83 ( 9) link_BETA1-4 : bond 0.00304 / 0.20 ( 15) link_BETA1-4 : angle 1.52016 / 0.97 ( 45) link_NAG-ASN : bond 0.00205 / 0.14 ( 15) link_NAG-ASN : angle 2.37306 / 1.27 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.25 seconds wall clock time: 41 minutes 32.60 seconds (2492.60 seconds total)