Starting phenix.real_space_refine on Sat Sep 12 04:55:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uye_20947/09_2026/6uye_20947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uye_20947/09_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_20947/09_2026/6uye_20947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uye_20947/09_2026/6uye_20947.map" model { file = "/net/cci-nas-00/data/ceres_data/6uye_20947/09_2026/6uye_20947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uye_20947/09_2026/6uye_20947.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uye_20947/09_2026/6uye_20947.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uye_20947/09_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-2.2.1-6174/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: 2.62, 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 C 108 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA P 3 " - " MAN P 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 301 " - " ASN A 228 " " NAG A 309 " - " ASN A 238 " " NAG B 301 " - " ASN B 228 " " NAG B 309 " - " ASN B 238 " " NAG C 301 " - " ASN C 228 " " NAG C 309 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN A 268 " " NAG O 1 " - " ASN D 563 " " NAG P 1 " - " ASN B 257 " " NAG Q 1 " - " ASN B 268 " " NAG R 1 " - " ASN E 563 " " NAG S 1 " - " ASN C 257 " " NAG T 1 " - " ASN C 268 " " NAG U 1 " - " ASN F 563 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 549.6 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: 0.46 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: 2.17 Time building geometry restraints manager: 1.55 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.190 Find NCS groups from input model: 0.120 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- 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 / 0.85 ( 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 : 0.592 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: 0.1487 time to fit residues: 108.0572 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 : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.092657 restraints weight = 27374.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095723 restraints weight = 16045.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097785 restraints weight = 11302.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099150 restraints weight = 8937.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100073 restraints weight = 7648.743| |-----------------------------------------------------------------------------| 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 0.195 2205 Planarity : 0.005 0.054 2370 Dihedral : 6.489 78.093 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 0.73461 / 0.37 (18999) SS BOND : bond 0.00430 / 0.29 ( 15) SS BOND : angle 1.62421 / 0.97 ( 30) hydrogen bonds : bond 0.03727 / 2.60 ( 429) hydrogen bonds : angle 6.99506 / 4.94 ( 1143) link_ALPHA1-3 : bond 0.00647 / 0.39 ( 6) link_ALPHA1-3 : angle 1.36152 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00715 / 0.36 ( 3) link_ALPHA1-6 : angle 1.45192 / 0.82 ( 9) link_BETA1-4 : bond 0.00470 / 0.30 ( 15) link_BETA1-4 : angle 2.02694 / 1.28 ( 45) link_NAG-ASN : bond 0.00397 / 0.32 ( 15) link_NAG-ASN : angle 2.81221 / 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 : 0.550 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: 0.7415 (mmmt) cc_final: 0.6891 (mptt) REVERT: A 117 ASP cc_start: 0.8321 (p0) cc_final: 0.7937 (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: 0.8522 (mtp85) cc_final: 0.8144 (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: 0.8245 (mmmm) REVERT: G 119 ASP cc_start: 0.8235 (p0) cc_final: 0.7841 (t70) REVERT: J 4 MET cc_start: 0.6935 (ttm) cc_final: 0.6548 (ttm) REVERT: J 90 GLN cc_start: 0.8685 (pp30) cc_final: 0.8072 (pp30) REVERT: J 104 LEU cc_start: 0.8939 (tp) cc_final: 0.8532 (tt) REVERT: J 108 ARG cc_start: 0.3724 (mtt180) cc_final: 0.1549 (ptt90) REVERT: B 56 LYS cc_start: 0.7372 (mmmt) cc_final: 0.7007 (mptt) REVERT: B 117 ASP cc_start: 0.8301 (p0) cc_final: 0.7937 (p0) REVERT: B 235 GLU cc_start: 0.8198 (tt0) cc_final: 0.7607 (tm-30) REVERT: B 291 TRP cc_start: 0.6037 (p90) cc_final: 0.5555 (p90) REVERT: E 587 ARG cc_start: 0.8356 (mtp85) cc_final: 0.7851 (ttm-80) REVERT: H 36 TRP cc_start: 0.7628 (m100) cc_final: 0.6717 (m100) REVERT: H 54 ASP cc_start: 0.8264 (p0) cc_final: 0.7745 (p0) REVERT: H 57 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8187 (mmtp) REVERT: K 108 ARG cc_start: 0.3636 (mtt180) cc_final: 0.1202 (ptt90) REVERT: C 117 ASP cc_start: 0.8261 (p0) cc_final: 0.7942 (p0) REVERT: C 229 GLU cc_start: 0.7749 (pp20) cc_final: 0.7428 (pp20) REVERT: C 235 GLU cc_start: 0.8182 (tt0) cc_final: 0.7570 (tm-30) REVERT: C 291 TRP cc_start: 0.5984 (p90) cc_final: 0.5373 (p90) REVERT: F 527 ILE cc_start: 0.5718 (mm) cc_final: 0.5178 (mm) REVERT: F 587 ARG cc_start: 0.8395 (mtp85) cc_final: 0.8090 (ttm-80) REVERT: I 36 TRP cc_start: 0.7652 (m100) cc_final: 0.6752 (m100) REVERT: I 46 GLU cc_start: 0.6967 (pt0) cc_final: 0.6573 (pt0) REVERT: I 48 MET cc_start: 0.6103 (mtp) cc_final: 0.5273 (mtp) REVERT: I 54 ASP cc_start: 0.8221 (p0) cc_final: 0.7714 (p0) REVERT: I 95 TYR cc_start: 0.7511 (m-80) cc_final: 0.7171 (m-10) REVERT: I 104 TYR cc_start: 0.8186 (m-10) cc_final: 0.7902 (m-10) REVERT: L 2 ILE cc_start: 0.6902 (pt) cc_final: 0.6692 (pt) REVERT: L 67 SER cc_start: 0.7950 (t) cc_final: 0.7697 (p) REVERT: L 104 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8115 (tt) REVERT: L 108 ARG cc_start: 0.3430 (mtt180) cc_final: 0.1014 (ptt90) outliers start: 22 outliers final: 14 residues processed: 396 average time/residue: 0.1441 time to fit residues: 78.6994 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 : 0.522 ------------------------------------------------------------------------------- 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: chunk 140 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.090909 restraints weight = 27627.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093933 restraints weight = 16480.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095976 restraints weight = 11661.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097296 restraints weight = 9250.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098223 restraints weight = 7933.776| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14052 Z= 0.187 Angle : 0.736 8.105 19146 Z= 0.362 Chirality : 0.046 0.181 2205 Planarity : 0.005 0.056 2370 Dihedral : 6.182 72.116 1833 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.68 % Allowed : 14.12 % Favored : 83.19 % 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 (0.20), residues: 1644 helix: 0.53 (0.41), residues: 180 sheet: -1.31 (0.20), residues: 654 loop : -1.34 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 24 TYR 0.021 0.002 TYR G 115 PHE 0.019 0.002 PHE L 71 TRP 0.022 0.001 TRP D 597 HIS 0.005 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (13998) covalent geometry : angle 0.71754 / 0.36 (18999) SS BOND : bond 0.00393 / 0.31 ( 15) SS BOND : angle 1.44955 / 0.90 ( 30) hydrogen bonds : bond 0.03531 / 2.46 ( 429) hydrogen bonds : angle 6.44163 / 4.55 ( 1143) link_ALPHA1-3 : bond 0.00552 / 0.32 ( 6) link_ALPHA1-3 : angle 1.26419 / 0.75 ( 18) link_ALPHA1-6 : bond 0.00482 / 0.24 ( 3) link_ALPHA1-6 : angle 1.33224 / 0.76 ( 9) link_BETA1-4 : bond 0.00338 / 0.23 ( 15) link_BETA1-4 : angle 1.91376 / 1.20 ( 45) link_NAG-ASN : bond 0.00209 / 0.16 ( 15) link_NAG-ASN : angle 2.62789 / 1.47 ( 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: 38 poor density : 332 time to evaluate : 0.576 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: 0.7555 (mmmt) cc_final: 0.7141 (mptt) REVERT: A 117 ASP cc_start: 0.8364 (p0) cc_final: 0.7997 (p0) REVERT: A 235 GLU cc_start: 0.8073 (tt0) cc_final: 0.7570 (tm-30) REVERT: D 587 ARG cc_start: 0.8495 (mtp85) cc_final: 0.8070 (ttm110) REVERT: G 34 MET cc_start: 0.8281 (mmm) cc_final: 0.7926 (mmm) REVERT: G 54 ASP cc_start: 0.8171 (p0) cc_final: 0.7757 (p0) REVERT: G 95 TYR cc_start: 0.7232 (m-80) cc_final: 0.6986 (m-10) REVERT: G 119 ASP cc_start: 0.8231 (p0) cc_final: 0.7837 (t70) REVERT: J 67 SER cc_start: 0.8161 (t) cc_final: 0.7803 (p) REVERT: J 90 GLN cc_start: 0.8641 (pp30) cc_final: 0.8139 (pp30) REVERT: J 104 LEU cc_start: 0.8844 (tp) cc_final: 0.8405 (tt) REVERT: J 108 ARG cc_start: 0.3753 (mtt180) cc_final: 0.1480 (ptt90) REVERT: B 56 LYS cc_start: 0.7317 (mmmt) cc_final: 0.7049 (mptt) REVERT: B 117 ASP cc_start: 0.8293 (p0) cc_final: 0.7920 (p0) REVERT: B 235 GLU cc_start: 0.8218 (tt0) cc_final: 0.7687 (tm-30) REVERT: E 587 ARG cc_start: 0.8373 (mtp85) cc_final: 0.7896 (ttm-80) REVERT: E 597 TRP cc_start: 0.5736 (m100) cc_final: 0.5470 (m100) REVERT: H 36 TRP cc_start: 0.7667 (m100) cc_final: 0.6483 (m100) REVERT: H 54 ASP cc_start: 0.8238 (p0) cc_final: 0.7823 (p0) REVERT: H 68 PHE cc_start: 0.5815 (m-80) cc_final: 0.5331 (m-80) REVERT: H 86 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7024 (mt) REVERT: K 45 GLU cc_start: 0.8255 (tp30) cc_final: 0.8008 (tp30) REVERT: K 90 GLN cc_start: 0.8786 (pp30) cc_final: 0.8214 (pp30) REVERT: K 97 THR cc_start: 0.8579 (p) cc_final: 0.8271 (p) REVERT: K 108 ARG cc_start: 0.3613 (mtt180) cc_final: 0.1286 (ptt90) REVERT: C 56 LYS cc_start: 0.7624 (mmmt) cc_final: 0.6978 (mptt) REVERT: C 117 ASP cc_start: 0.8230 (p0) cc_final: 0.7902 (p0) REVERT: C 229 GLU cc_start: 0.7831 (pp20) cc_final: 0.7397 (pp20) REVERT: C 235 GLU cc_start: 0.8183 (tt0) cc_final: 0.7566 (tm-30) REVERT: C 291 TRP cc_start: 0.6079 (p90) cc_final: 0.5432 (p90) REVERT: F 527 ILE cc_start: 0.5771 (mm) cc_final: 0.5254 (mm) REVERT: F 587 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8035 (ttm-80) REVERT: I 38 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.5531 (ptp-110) REVERT: I 54 ASP cc_start: 0.8189 (p0) cc_final: 0.7731 (p0) REVERT: I 95 TYR cc_start: 0.7484 (m-80) cc_final: 0.7026 (m-10) REVERT: I 104 TYR cc_start: 0.8356 (m-10) cc_final: 0.8097 (m-10) REVERT: L 2 ILE cc_start: 0.6906 (pt) cc_final: 0.6681 (pt) REVERT: L 31 ASN cc_start: 0.8260 (t0) cc_final: 0.7952 (t0) REVERT: L 37 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: L 67 SER cc_start: 0.8192 (t) cc_final: 0.7613 (p) REVERT: L 108 ARG cc_start: 0.3263 (mtt180) cc_final: 0.0980 (ptt90) outliers start: 38 outliers final: 24 residues processed: 353 average time/residue: 0.1374 time to fit residues: 68.0037 Evaluate side-chains 331 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain 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 H residue 86 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 C residue 69 ASN 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 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 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 = 0.116196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.088460 restraints weight = 27908.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.091368 restraints weight = 16820.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093309 restraints weight = 12012.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094618 restraints weight = 9659.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095360 restraints weight = 8334.642| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14052 Z= 0.238 Angle : 0.767 9.190 19146 Z= 0.374 Chirality : 0.047 0.203 2205 Planarity : 0.005 0.045 2370 Dihedral : 6.012 66.155 1833 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.25 % Allowed : 14.48 % Favored : 82.27 % 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: -1.72 (0.21), residues: 1644 helix: 0.66 (0.40), residues: 180 sheet: -1.30 (0.20), residues: 651 loop : -1.32 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.021 0.002 TYR G 115 PHE 0.018 0.002 PHE G 68 TRP 0.030 0.002 TRP F 597 HIS 0.004 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (13998) covalent geometry : angle 0.74994 / 0.37 (18999) SS BOND : bond 0.00298 / 0.22 ( 15) SS BOND : angle 1.40215 / 0.87 ( 30) hydrogen bonds : bond 0.03695 / 2.59 ( 429) hydrogen bonds : angle 6.41271 / 4.55 ( 1143) link_ALPHA1-3 : bond 0.00507 / 0.29 ( 6) link_ALPHA1-3 : angle 1.32445 / 0.79 ( 18) link_ALPHA1-6 : bond 0.00469 / 0.24 ( 3) link_ALPHA1-6 : angle 1.42726 / 0.81 ( 9) link_BETA1-4 : bond 0.00302 / 0.18 ( 15) link_BETA1-4 : angle 1.86942 / 1.19 ( 45) link_NAG-ASN : bond 0.00210 / 0.14 ( 15) link_NAG-ASN : angle 2.67847 / 1.48 ( 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 351 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 305 time to evaluate : 0.516 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: 0.7575 (mmmt) cc_final: 0.7194 (mptt) REVERT: A 117 ASP cc_start: 0.8389 (p0) cc_final: 0.8027 (p0) REVERT: A 229 GLU cc_start: 0.7831 (pp20) cc_final: 0.7517 (pp20) REVERT: A 235 GLU cc_start: 0.8102 (tt0) cc_final: 0.7611 (tm-30) REVERT: D 587 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8204 (ttm-80) REVERT: D 596 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7804 (ttm-80) REVERT: G 34 MET cc_start: 0.8313 (mmm) cc_final: 0.8007 (mmm) REVERT: G 54 ASP cc_start: 0.8227 (p0) cc_final: 0.7833 (p0) REVERT: G 119 ASP cc_start: 0.8249 (p0) cc_final: 0.7904 (t70) REVERT: J 37 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: J 67 SER cc_start: 0.8237 (t) cc_final: 0.7891 (p) REVERT: J 90 GLN cc_start: 0.8798 (pp30) cc_final: 0.8305 (pp30) REVERT: J 92 LYS cc_start: 0.8803 (tttm) cc_final: 0.8545 (tttp) REVERT: J 104 LEU cc_start: 0.8899 (tp) cc_final: 0.8359 (tt) REVERT: J 108 ARG cc_start: 0.3718 (mtt180) cc_final: 0.1523 (ptt90) REVERT: B 56 LYS cc_start: 0.7389 (mmmt) cc_final: 0.7176 (mptt) REVERT: B 89 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.6194 (tmt90) REVERT: B 117 ASP cc_start: 0.8254 (p0) cc_final: 0.7863 (p0) REVERT: B 235 GLU cc_start: 0.8238 (tt0) cc_final: 0.7748 (tm-30) REVERT: E 587 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7849 (ttm-80) REVERT: E 591 ASP cc_start: 0.8265 (t0) cc_final: 0.8018 (t0) REVERT: E 597 TRP cc_start: 0.5759 (OUTLIER) cc_final: 0.5443 (m100) REVERT: H 36 TRP cc_start: 0.7670 (m100) cc_final: 0.6228 (m100) REVERT: H 54 ASP cc_start: 0.8197 (p0) cc_final: 0.7721 (p0) REVERT: H 68 PHE cc_start: 0.6088 (m-80) cc_final: 0.5677 (m-80) REVERT: K 45 GLU cc_start: 0.8359 (tp30) cc_final: 0.8106 (tp30) REVERT: K 67 SER cc_start: 0.8019 (t) cc_final: 0.7795 (p) REVERT: K 108 ARG cc_start: 0.3483 (mtt180) cc_final: 0.1209 (ptt90) REVERT: C 56 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7263 (mptt) REVERT: C 117 ASP cc_start: 0.8351 (p0) cc_final: 0.8050 (p0) REVERT: C 229 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: C 235 GLU cc_start: 0.8230 (tt0) cc_final: 0.7648 (tm-30) REVERT: F 587 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7987 (ttm-80) REVERT: I 46 GLU cc_start: 0.7242 (pt0) cc_final: 0.7012 (pt0) REVERT: I 48 MET cc_start: 0.7141 (mmm) cc_final: 0.6898 (tpt) REVERT: I 54 ASP cc_start: 0.8183 (p0) cc_final: 0.7773 (p0) REVERT: I 68 PHE cc_start: 0.5832 (m-80) cc_final: 0.5470 (m-80) REVERT: I 104 TYR cc_start: 0.8422 (m-10) cc_final: 0.8076 (m-10) REVERT: L 31 ASN cc_start: 0.8410 (t0) cc_final: 0.7842 (t0) REVERT: L 37 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: L 67 SER cc_start: 0.8036 (t) cc_final: 0.7635 (p) REVERT: L 104 LEU cc_start: 0.8693 (tp) cc_final: 0.7907 (tt) REVERT: L 108 ARG cc_start: 0.3206 (mtt180) cc_final: 0.1005 (ptt90) outliers start: 46 outliers final: 31 residues processed: 333 average time/residue: 0.1455 time to fit residues: 67.1399 Evaluate side-chains 324 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 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 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 109 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 112 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087828 restraints weight = 28284.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.090710 restraints weight = 17227.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092691 restraints weight = 12360.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094010 restraints weight = 9943.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094875 restraints weight = 8590.004| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14052 Z= 0.210 Angle : 0.735 9.139 19146 Z= 0.359 Chirality : 0.046 0.188 2205 Planarity : 0.005 0.061 2370 Dihedral : 5.844 61.398 1833 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.82 % Allowed : 16.10 % Favored : 81.07 % 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: -1.64 (0.21), residues: 1644 helix: 0.86 (0.40), residues: 180 sheet: -1.25 (0.20), residues: 630 loop : -1.33 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 61 TYR 0.023 0.002 TYR G 115 PHE 0.028 0.002 PHE D 592 TRP 0.028 0.002 TRP F 597 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (13998) covalent geometry : angle 0.71786 / 0.35 (18999) SS BOND : bond 0.00599 / 0.45 ( 15) SS BOND : angle 1.23518 / 0.78 ( 30) hydrogen bonds : bond 0.03561 / 2.53 ( 429) hydrogen bonds : angle 6.19658 / 4.37 ( 1143) link_ALPHA1-3 : bond 0.00481 / 0.27 ( 6) link_ALPHA1-3 : angle 1.32512 / 0.79 ( 18) link_ALPHA1-6 : bond 0.00414 / 0.21 ( 3) link_ALPHA1-6 : angle 1.44419 / 0.82 ( 9) link_BETA1-4 : bond 0.00267 / 0.16 ( 15) link_BETA1-4 : angle 1.78317 / 1.14 ( 45) link_NAG-ASN : bond 0.00199 / 0.13 ( 15) link_NAG-ASN : angle 2.64828 / 1.44 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 0.565 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: A 56 LYS cc_start: 0.7574 (mmmt) cc_final: 0.7288 (mptt) REVERT: A 117 ASP cc_start: 0.8449 (p0) cc_final: 0.8122 (p0) REVERT: A 229 GLU cc_start: 0.7867 (pp20) cc_final: 0.7516 (pp20) REVERT: A 235 GLU cc_start: 0.8115 (tt0) cc_final: 0.7567 (tm-30) REVERT: D 587 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8265 (ttm-80) REVERT: G 34 MET cc_start: 0.8407 (mmm) cc_final: 0.8002 (mmm) REVERT: G 54 ASP cc_start: 0.8234 (p0) cc_final: 0.7871 (p0) REVERT: G 119 ASP cc_start: 0.8285 (p0) cc_final: 0.7929 (t70) REVERT: J 37 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: J 67 SER cc_start: 0.8175 (t) cc_final: 0.7891 (p) REVERT: J 70 ASP cc_start: 0.8730 (t0) cc_final: 0.8492 (t0) REVERT: J 90 GLN cc_start: 0.8824 (pp30) cc_final: 0.8311 (pp30) REVERT: J 92 LYS cc_start: 0.8883 (tttm) cc_final: 0.8584 (tttm) REVERT: J 104 LEU cc_start: 0.8910 (tp) cc_final: 0.8370 (tt) REVERT: J 108 ARG cc_start: 0.3428 (mtt180) cc_final: 0.1352 (ptt90) REVERT: B 89 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.6345 (tmt90) REVERT: B 117 ASP cc_start: 0.8323 (p0) cc_final: 0.7946 (p0) REVERT: B 235 GLU cc_start: 0.8262 (tt0) cc_final: 0.7720 (tm-30) REVERT: E 587 ARG cc_start: 0.8332 (mtp85) cc_final: 0.7835 (ttm-80) REVERT: E 588 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7509 (mmmm) REVERT: E 597 TRP cc_start: 0.5867 (OUTLIER) cc_final: 0.5664 (m100) REVERT: H 36 TRP cc_start: 0.7784 (m100) cc_final: 0.6233 (m100) REVERT: H 54 ASP cc_start: 0.8228 (p0) cc_final: 0.7809 (p0) REVERT: H 57 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8267 (mmtp) REVERT: H 68 PHE cc_start: 0.6393 (m-80) cc_final: 0.5802 (m-10) REVERT: K 67 SER cc_start: 0.8100 (t) cc_final: 0.7793 (p) REVERT: K 108 ARG cc_start: 0.3312 (mtt180) cc_final: 0.1109 (ptt90) REVERT: C 56 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7306 (mptt) REVERT: C 117 ASP cc_start: 0.8384 (p0) cc_final: 0.8099 (p0) REVERT: C 229 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7434 (pp20) REVERT: C 235 GLU cc_start: 0.8248 (tt0) cc_final: 0.7606 (tm-30) REVERT: F 587 ARG cc_start: 0.8378 (mtp85) cc_final: 0.8054 (ttm-80) REVERT: I 38 ARG cc_start: 0.7206 (ptp-110) cc_final: 0.6816 (ptp-110) REVERT: I 54 ASP cc_start: 0.8225 (p0) cc_final: 0.7855 (p0) REVERT: I 104 TYR cc_start: 0.8481 (m-10) cc_final: 0.8080 (m-10) REVERT: L 31 ASN cc_start: 0.8434 (t0) cc_final: 0.7992 (t0) REVERT: L 67 SER cc_start: 0.7890 (t) cc_final: 0.7441 (p) REVERT: L 104 LEU cc_start: 0.8745 (tp) cc_final: 0.7948 (tt) REVERT: L 108 ARG cc_start: 0.3108 (mtt180) cc_final: 0.1033 (ptt90) outliers start: 40 outliers final: 26 residues processed: 323 average time/residue: 0.1383 time to fit residues: 62.2430 Evaluate side-chains 318 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 A residue 261 TYR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 597 TRP Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 129 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 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 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 ILE 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: chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.0030 chunk 123 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 13 GLN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS F 567 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.117042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.089303 restraints weight = 28195.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092255 restraints weight = 16999.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094276 restraints weight = 12159.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.095620 restraints weight = 9774.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096393 restraints weight = 8416.096| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14052 Z= 0.164 Angle : 0.707 8.547 19146 Z= 0.344 Chirality : 0.045 0.181 2205 Planarity : 0.004 0.052 2370 Dihedral : 5.639 57.674 1833 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.90 % Allowed : 17.09 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1644 helix: 1.06 (0.40), residues: 183 sheet: -1.06 (0.20), residues: 624 loop : -1.26 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.021 0.001 TYR G 115 PHE 0.026 0.002 PHE D 592 TRP 0.032 0.002 TRP F 597 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (13998) covalent geometry : angle 0.69048 / 0.34 (18999) SS BOND : bond 0.00491 / 0.39 ( 15) SS BOND : angle 1.29259 / 0.86 ( 30) hydrogen bonds : bond 0.03360 / 2.34 ( 429) hydrogen bonds : angle 6.05108 / 4.28 ( 1143) link_ALPHA1-3 : bond 0.00460 / 0.25 ( 6) link_ALPHA1-3 : angle 1.33560 / 0.79 ( 18) link_ALPHA1-6 : bond 0.00422 / 0.21 ( 3) link_ALPHA1-6 : angle 1.44004 / 0.82 ( 9) link_BETA1-4 : bond 0.00271 / 0.17 ( 15) link_BETA1-4 : angle 1.67483 / 1.08 ( 45) link_NAG-ASN : bond 0.00180 / 0.13 ( 15) link_NAG-ASN : angle 2.56755 / 1.39 ( 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 349 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 0.539 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: 0.7579 (mmmt) cc_final: 0.7367 (mptt) REVERT: A 117 ASP cc_start: 0.8438 (p0) cc_final: 0.8138 (p0) REVERT: A 229 GLU cc_start: 0.7879 (pp20) cc_final: 0.7483 (pp20) REVERT: A 235 GLU cc_start: 0.8077 (tt0) cc_final: 0.7596 (tm-30) REVERT: D 587 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8201 (ttm-80) REVERT: G 34 MET cc_start: 0.8326 (mmm) cc_final: 0.7926 (mmm) REVERT: G 54 ASP cc_start: 0.8205 (p0) cc_final: 0.7836 (p0) REVERT: G 119 ASP cc_start: 0.8225 (p0) cc_final: 0.7886 (t70) REVERT: J 37 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: J 58 VAL cc_start: 0.9092 (t) cc_final: 0.8873 (p) REVERT: J 67 SER cc_start: 0.8261 (t) cc_final: 0.7889 (p) REVERT: J 90 GLN cc_start: 0.8788 (pp30) cc_final: 0.8299 (pp30) REVERT: J 92 LYS cc_start: 0.8907 (tttm) cc_final: 0.8649 (tttm) REVERT: J 104 LEU cc_start: 0.8856 (tp) cc_final: 0.8325 (tt) REVERT: J 108 ARG cc_start: 0.3538 (mtt180) cc_final: 0.1398 (ptt90) REVERT: B 89 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.6307 (tmt90) REVERT: B 117 ASP cc_start: 0.8284 (p0) cc_final: 0.7920 (p0) REVERT: B 235 GLU cc_start: 0.8243 (tt0) cc_final: 0.7778 (tm-30) REVERT: E 587 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7733 (ttm-80) REVERT: H 6 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6171 (mt-10) REVERT: H 36 TRP cc_start: 0.7806 (m100) cc_final: 0.6241 (m100) REVERT: H 48 MET cc_start: 0.6290 (mmt) cc_final: 0.6031 (tpp) REVERT: H 54 ASP cc_start: 0.8246 (p0) cc_final: 0.7807 (p0) REVERT: H 68 PHE cc_start: 0.6682 (m-80) cc_final: 0.6392 (m-80) REVERT: H 95 TYR cc_start: 0.7425 (m-80) cc_final: 0.7090 (m-10) REVERT: K 37 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: K 55 GLN cc_start: 0.9054 (tp40) cc_final: 0.8835 (tp40) REVERT: K 67 SER cc_start: 0.8136 (t) cc_final: 0.7766 (p) REVERT: K 90 GLN cc_start: 0.8737 (pp30) cc_final: 0.8185 (pp30) REVERT: K 94 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7597 (t80) REVERT: K 108 ARG cc_start: 0.3081 (mtt180) cc_final: 0.0950 (ptt90) REVERT: C 56 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7293 (mptt) REVERT: C 117 ASP cc_start: 0.8388 (p0) cc_final: 0.8084 (p0) REVERT: C 229 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: C 235 GLU cc_start: 0.8212 (tt0) cc_final: 0.7612 (tm-30) REVERT: F 587 ARG cc_start: 0.8342 (mtp85) cc_final: 0.8030 (ttm-80) REVERT: I 38 ARG cc_start: 0.7288 (ptp-110) cc_final: 0.6773 (ptm160) REVERT: I 46 GLU cc_start: 0.7392 (pt0) cc_final: 0.7188 (pt0) REVERT: I 54 ASP cc_start: 0.8162 (p0) cc_final: 0.7804 (p0) REVERT: I 104 TYR cc_start: 0.8440 (m-10) cc_final: 0.8010 (m-10) REVERT: I 119 ASP cc_start: 0.8312 (p0) cc_final: 0.7972 (p0) REVERT: L 4 MET cc_start: 0.7972 (ttm) cc_final: 0.7631 (ttm) REVERT: L 31 ASN cc_start: 0.8405 (t0) cc_final: 0.8001 (t0) REVERT: L 37 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: L 67 SER cc_start: 0.8019 (t) cc_final: 0.7557 (p) REVERT: L 94 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7335 (t80) REVERT: L 104 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.7883 (tt) REVERT: L 108 ARG cc_start: 0.3069 (mtt180) cc_final: 0.1033 (ptt90) outliers start: 41 outliers final: 24 residues processed: 330 average time/residue: 0.1393 time to fit residues: 64.2133 Evaluate side-chains 317 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 A residue 261 TYR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 29 ILE 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 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 13 GLN ** H 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 = 0.3597 r_free = 0.3597 target = 0.115237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087608 restraints weight = 28081.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.090450 restraints weight = 17042.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092383 restraints weight = 12233.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093698 restraints weight = 9857.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094365 restraints weight = 8518.418| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14052 Z= 0.238 Angle : 0.772 10.549 19146 Z= 0.375 Chirality : 0.047 0.203 2205 Planarity : 0.005 0.049 2370 Dihedral : 5.742 57.301 1833 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.97 % Allowed : 17.44 % Favored : 79.59 % 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: -1.53 (0.21), residues: 1644 helix: 0.98 (0.39), residues: 183 sheet: -1.17 (0.20), residues: 630 loop : -1.27 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 24 TYR 0.023 0.002 TYR G 115 PHE 0.023 0.002 PHE H 68 TRP 0.033 0.002 TRP F 597 HIS 0.004 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (13998) covalent geometry : angle 0.75479 / 0.37 (18999) SS BOND : bond 0.00367 / 0.29 ( 15) SS BOND : angle 1.76836 / 1.16 ( 30) hydrogen bonds : bond 0.03695 / 2.63 ( 429) hydrogen bonds : angle 6.13145 / 4.33 ( 1143) link_ALPHA1-3 : bond 0.00436 / 0.24 ( 6) link_ALPHA1-3 : angle 1.35711 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00344 / 0.17 ( 3) link_ALPHA1-6 : angle 1.45565 / 0.83 ( 9) link_BETA1-4 : bond 0.00258 / 0.15 ( 15) link_BETA1-4 : angle 1.72990 / 1.09 ( 45) link_NAG-ASN : bond 0.00268 / 0.16 ( 15) link_NAG-ASN : angle 2.63342 / 1.45 ( 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 332 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 0.527 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: A 117 ASP cc_start: 0.8469 (p0) cc_final: 0.8166 (p0) REVERT: A 229 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: A 235 GLU cc_start: 0.8042 (tt0) cc_final: 0.7589 (tm-30) REVERT: D 587 ARG cc_start: 0.8429 (mtp85) cc_final: 0.8162 (ttm-80) REVERT: G 34 MET cc_start: 0.8336 (mmm) cc_final: 0.7989 (mmm) REVERT: G 54 ASP cc_start: 0.8216 (p0) cc_final: 0.7859 (p0) REVERT: G 95 TYR cc_start: 0.7193 (m-80) cc_final: 0.6959 (m-10) REVERT: G 119 ASP cc_start: 0.8288 (p0) cc_final: 0.7952 (t70) REVERT: J 37 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: J 58 VAL cc_start: 0.9095 (t) cc_final: 0.8894 (p) REVERT: J 67 SER cc_start: 0.8216 (t) cc_final: 0.7785 (p) REVERT: J 90 GLN cc_start: 0.8821 (pp30) cc_final: 0.8326 (pp30) REVERT: J 92 LYS cc_start: 0.9013 (tttm) cc_final: 0.8709 (tttp) REVERT: J 104 LEU cc_start: 0.8857 (tp) cc_final: 0.8277 (tt) REVERT: J 108 ARG cc_start: 0.3467 (mtt180) cc_final: 0.1416 (ptt90) REVERT: B 56 LYS cc_start: 0.7204 (mptt) cc_final: 0.6908 (mmtt) REVERT: B 69 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7676 (t0) REVERT: B 89 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.6328 (tmt90) REVERT: B 117 ASP cc_start: 0.8296 (p0) cc_final: 0.7940 (p0) REVERT: B 235 GLU cc_start: 0.8286 (tt0) cc_final: 0.7829 (tm-30) REVERT: E 587 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7755 (ttm-80) REVERT: E 591 ASP cc_start: 0.8226 (t0) cc_final: 0.7954 (t0) REVERT: H 6 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6359 (mt-10) REVERT: H 36 TRP cc_start: 0.7783 (m100) cc_final: 0.6179 (m100) REVERT: H 48 MET cc_start: 0.6260 (mmt) cc_final: 0.6001 (tpp) REVERT: H 54 ASP cc_start: 0.8204 (p0) cc_final: 0.7788 (p0) REVERT: H 57 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8374 (mmtp) REVERT: H 68 PHE cc_start: 0.7257 (m-80) cc_final: 0.6901 (m-80) REVERT: K 37 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: K 67 SER cc_start: 0.8116 (t) cc_final: 0.7712 (p) REVERT: K 94 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7704 (t80) REVERT: K 108 ARG cc_start: 0.2873 (mtt180) cc_final: 0.0823 (ptt90) REVERT: C 56 LYS cc_start: 0.7763 (mmmt) cc_final: 0.7369 (mptt) REVERT: C 117 ASP cc_start: 0.8384 (p0) cc_final: 0.8086 (p0) REVERT: C 229 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7377 (pp20) REVERT: C 235 GLU cc_start: 0.8261 (tt0) cc_final: 0.7631 (tm-30) REVERT: F 587 ARG cc_start: 0.8367 (mtp85) cc_final: 0.8038 (ttm-80) REVERT: I 43 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7902 (mmmt) REVERT: I 54 ASP cc_start: 0.8171 (p0) cc_final: 0.7835 (p0) REVERT: I 104 TYR cc_start: 0.8513 (m-10) cc_final: 0.8070 (m-10) REVERT: I 119 ASP cc_start: 0.8256 (p0) cc_final: 0.8000 (p0) REVERT: L 31 ASN cc_start: 0.8437 (t0) cc_final: 0.8081 (t0) REVERT: L 37 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: L 67 SER cc_start: 0.8172 (t) cc_final: 0.7701 (p) REVERT: L 94 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7567 (t80) REVERT: L 104 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.7948 (tt) REVERT: L 108 ARG cc_start: 0.2996 (mtt180) cc_final: 0.1062 (ptt90) outliers start: 42 outliers final: 24 residues processed: 314 average time/residue: 0.1385 time to fit residues: 60.8876 Evaluate side-chains 309 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 54 optimal weight: 0.3980 chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 59 optimal weight: 0.0570 chunk 60 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.119181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091778 restraints weight = 27462.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094773 restraints weight = 16406.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096802 restraints weight = 11692.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098178 restraints weight = 9334.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099104 restraints weight = 8000.172| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14052 Z= 0.126 Angle : 0.713 9.675 19146 Z= 0.346 Chirality : 0.045 0.173 2205 Planarity : 0.004 0.047 2370 Dihedral : 5.416 54.587 1833 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.61 % Allowed : 17.80 % Favored : 79.59 % 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: 1.36 (0.40), residues: 183 sheet: -1.02 (0.20), residues: 630 loop : -1.14 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 24 TYR 0.018 0.001 TYR G 115 PHE 0.030 0.002 PHE D 592 TRP 0.033 0.001 TRP F 597 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13998) covalent geometry : angle 0.69645 / 0.34 (18999) SS BOND : bond 0.00611 / 0.50 ( 15) SS BOND : angle 1.60404 / 1.10 ( 30) hydrogen bonds : bond 0.03214 / 2.21 ( 429) hydrogen bonds : angle 5.92098 / 4.17 ( 1143) link_ALPHA1-3 : bond 0.00413 / 0.23 ( 6) link_ALPHA1-3 : angle 1.33651 / 0.79 ( 18) link_ALPHA1-6 : bond 0.00466 / 0.23 ( 3) link_ALPHA1-6 : angle 1.44152 / 0.82 ( 9) link_BETA1-4 : bond 0.00331 / 0.21 ( 15) link_BETA1-4 : angle 1.57367 / 1.03 ( 45) link_NAG-ASN : bond 0.00252 / 0.19 ( 15) link_NAG-ASN : angle 2.51818 / 1.34 ( 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 349 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 312 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8303 (p0) cc_final: 0.8076 (p0) REVERT: A 229 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7467 (pp20) REVERT: A 235 GLU cc_start: 0.8011 (tt0) cc_final: 0.7518 (tm-30) REVERT: D 587 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8099 (ttm-80) REVERT: D 588 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7819 (mmmt) REVERT: G 34 MET cc_start: 0.8295 (mmm) cc_final: 0.7950 (mmm) REVERT: G 36 TRP cc_start: 0.7925 (m100) cc_final: 0.7638 (m100) REVERT: G 43 LYS cc_start: 0.7810 (mtpp) cc_final: 0.7455 (mmmt) REVERT: G 46 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7800 (mm-30) REVERT: G 54 ASP cc_start: 0.8209 (p0) cc_final: 0.7830 (p0) REVERT: G 57 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8456 (mmmm) REVERT: G 119 ASP cc_start: 0.8249 (p0) cc_final: 0.7826 (t70) REVERT: J 18 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8070 (tmm160) REVERT: J 37 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: J 67 SER cc_start: 0.8246 (t) cc_final: 0.7811 (p) REVERT: J 90 GLN cc_start: 0.8712 (pp30) cc_final: 0.8254 (pp30) REVERT: J 92 LYS cc_start: 0.8912 (tttm) cc_final: 0.8637 (tttm) REVERT: J 104 LEU cc_start: 0.8780 (tp) cc_final: 0.8199 (tt) REVERT: J 108 ARG cc_start: 0.3224 (mtt180) cc_final: 0.1272 (ptt90) REVERT: B 56 LYS cc_start: 0.7191 (mptt) cc_final: 0.6908 (mmtt) REVERT: B 89 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.6327 (tmt90) REVERT: B 117 ASP cc_start: 0.8301 (p0) cc_final: 0.7924 (p0) REVERT: B 235 GLU cc_start: 0.8204 (tt0) cc_final: 0.7756 (tm-30) REVERT: E 552 ASP cc_start: 0.6675 (t0) cc_final: 0.6461 (t0) REVERT: E 587 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7813 (ttm-80) REVERT: H 6 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6166 (mt-10) REVERT: H 36 TRP cc_start: 0.7743 (m100) cc_final: 0.6271 (m100) REVERT: H 54 ASP cc_start: 0.8178 (p0) cc_final: 0.7812 (p0) REVERT: H 57 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8261 (mmmm) REVERT: K 37 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: K 67 SER cc_start: 0.8137 (t) cc_final: 0.7696 (p) REVERT: K 70 ASP cc_start: 0.8880 (m-30) cc_final: 0.8669 (t0) REVERT: K 90 GLN cc_start: 0.8593 (pp30) cc_final: 0.8182 (pp30) REVERT: K 94 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7677 (t80) REVERT: K 108 ARG cc_start: 0.2960 (mtt180) cc_final: 0.0881 (ptt90) REVERT: C 56 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7369 (mptt) REVERT: C 117 ASP cc_start: 0.8242 (p0) cc_final: 0.8022 (p0) REVERT: C 130 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8372 (mmm160) REVERT: C 229 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: C 235 GLU cc_start: 0.8217 (tt0) cc_final: 0.7594 (tm-30) REVERT: F 545 GLU cc_start: 0.8129 (mp0) cc_final: 0.7811 (mp0) REVERT: F 587 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7992 (ttm-80) REVERT: I 43 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7936 (mmmt) REVERT: I 54 ASP cc_start: 0.8177 (p0) cc_final: 0.7832 (p0) REVERT: I 104 TYR cc_start: 0.8470 (m-10) cc_final: 0.8052 (m-10) REVERT: I 119 ASP cc_start: 0.8155 (p0) cc_final: 0.7930 (p0) REVERT: L 31 ASN cc_start: 0.8409 (t0) cc_final: 0.8144 (t0) REVERT: L 37 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: L 67 SER cc_start: 0.8200 (t) cc_final: 0.7708 (p) REVERT: L 94 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7467 (t80) REVERT: L 104 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7812 (tt) REVERT: L 108 ARG cc_start: 0.2958 (mtt180) cc_final: 0.1052 (ptt90) outliers start: 37 outliers final: 20 residues processed: 334 average time/residue: 0.1361 time to fit residues: 64.0220 Evaluate side-chains 316 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 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 Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.118776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091050 restraints weight = 27784.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094039 restraints weight = 16672.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096075 restraints weight = 11907.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097422 restraints weight = 9496.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098364 restraints weight = 8173.706| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4688 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= 0.144 Angle : 0.725 9.457 19146 Z= 0.350 Chirality : 0.045 0.176 2205 Planarity : 0.005 0.055 2370 Dihedral : 5.331 53.686 1833 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.33 % Allowed : 18.29 % Favored : 79.38 % 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: -1.15 (0.21), residues: 1644 helix: 1.52 (0.39), residues: 183 sheet: -1.01 (0.21), residues: 633 loop : -1.00 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 24 TYR 0.016 0.001 TYR J 96 PHE 0.019 0.002 PHE I 68 TRP 0.024 0.001 TRP F 597 HIS 0.002 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13998) covalent geometry : angle 0.70931 / 0.35 (18999) SS BOND : bond 0.00508 / 0.42 ( 15) SS BOND : angle 1.51173 / 1.07 ( 30) hydrogen bonds : bond 0.03279 / 2.24 ( 429) hydrogen bonds : angle 5.83889 / 4.12 ( 1143) link_ALPHA1-3 : bond 0.00403 / 0.22 ( 6) link_ALPHA1-3 : angle 1.36028 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00445 / 0.22 ( 3) link_ALPHA1-6 : angle 1.44864 / 0.82 ( 9) link_BETA1-4 : bond 0.00276 / 0.18 ( 15) link_BETA1-4 : angle 1.55615 / 1.00 ( 45) link_NAG-ASN : bond 0.00180 / 0.11 ( 15) link_NAG-ASN : angle 2.45658 / 1.34 ( 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 328 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 0.510 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: A 117 ASP cc_start: 0.8276 (p0) cc_final: 0.8050 (p0) REVERT: A 229 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: A 235 GLU cc_start: 0.7973 (tt0) cc_final: 0.7539 (tm-30) REVERT: D 587 ARG cc_start: 0.8289 (mtp85) cc_final: 0.8041 (ttm-80) REVERT: G 43 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7554 (mmmt) REVERT: G 46 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7753 (mm-30) REVERT: G 54 ASP cc_start: 0.8160 (p0) cc_final: 0.7781 (p0) REVERT: G 57 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8429 (mmmm) REVERT: G 119 ASP cc_start: 0.8232 (p0) cc_final: 0.7815 (t70) REVERT: J 18 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8355 (ttp80) REVERT: J 37 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: J 67 SER cc_start: 0.8243 (t) cc_final: 0.7830 (p) REVERT: J 90 GLN cc_start: 0.8752 (pp30) cc_final: 0.8394 (pp30) REVERT: J 92 LYS cc_start: 0.8953 (tttm) cc_final: 0.8706 (tttm) REVERT: J 104 LEU cc_start: 0.8699 (tp) cc_final: 0.8095 (tt) REVERT: J 108 ARG cc_start: 0.3412 (mtt180) cc_final: 0.1523 (ptt90) REVERT: B 56 LYS cc_start: 0.7132 (mptt) cc_final: 0.6845 (mmtt) REVERT: B 89 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.6343 (tmt90) REVERT: B 117 ASP cc_start: 0.8226 (p0) cc_final: 0.7840 (p0) REVERT: B 235 GLU cc_start: 0.8168 (tt0) cc_final: 0.7766 (tm-30) REVERT: E 573 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8837 (tp) REVERT: E 587 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7767 (ttm-80) REVERT: H 36 TRP cc_start: 0.7644 (m100) cc_final: 0.6256 (m100) REVERT: H 46 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7979 (mm-30) REVERT: H 54 ASP cc_start: 0.8165 (p0) cc_final: 0.7789 (p0) REVERT: H 57 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8294 (mmmm) REVERT: H 86 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7288 (mt) REVERT: K 37 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: K 67 SER cc_start: 0.8211 (t) cc_final: 0.7760 (p) REVERT: K 90 GLN cc_start: 0.8456 (pp30) cc_final: 0.8100 (pp30) REVERT: K 94 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7670 (t80) REVERT: K 108 ARG cc_start: 0.2970 (mtt180) cc_final: 0.0895 (ptt90) REVERT: C 56 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7374 (mptt) REVERT: C 117 ASP cc_start: 0.8168 (p0) cc_final: 0.7942 (p0) REVERT: C 130 ARG cc_start: 0.8654 (mmm160) cc_final: 0.8370 (mmm160) REVERT: C 229 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7364 (pp20) REVERT: C 235 GLU cc_start: 0.8193 (tt0) cc_final: 0.7623 (tm-30) REVERT: F 545 GLU cc_start: 0.8021 (mp0) cc_final: 0.7683 (mp0) REVERT: F 587 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7944 (ttm-80) REVERT: I 43 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7971 (mmmt) REVERT: I 54 ASP cc_start: 0.8160 (p0) cc_final: 0.7799 (p0) REVERT: I 104 TYR cc_start: 0.8461 (m-10) cc_final: 0.8049 (m-10) REVERT: L 37 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: L 94 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7615 (t80) REVERT: L 104 LEU cc_start: 0.8528 (tp) cc_final: 0.7709 (tt) REVERT: L 108 ARG cc_start: 0.2989 (mtt180) cc_final: 0.1108 (ptt90) outliers start: 33 outliers final: 19 residues processed: 314 average time/residue: 0.1383 time to fit residues: 60.2557 Evaluate side-chains 307 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 A residue 261 TYR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 157 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092293 restraints weight = 27819.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095332 restraints weight = 16664.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097421 restraints weight = 11880.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098812 restraints weight = 9473.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099594 restraints weight = 8133.436| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14052 Z= 0.126 Angle : 0.735 9.684 19146 Z= 0.354 Chirality : 0.045 0.172 2205 Planarity : 0.005 0.059 2370 Dihedral : 5.266 52.790 1833 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.84 % Allowed : 19.14 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.21), residues: 1644 helix: 1.62 (0.40), residues: 183 sheet: -0.91 (0.21), residues: 627 loop : -0.97 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 24 TYR 0.015 0.001 TYR G 115 PHE 0.029 0.002 PHE D 592 TRP 0.022 0.001 TRP F 597 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13998) covalent geometry : angle 0.71829 / 0.35 (18999) SS BOND : bond 0.00470 / 0.39 ( 15) SS BOND : angle 1.88823 / 1.10 ( 30) hydrogen bonds : bond 0.03171 / 2.17 ( 429) hydrogen bonds : angle 5.72492 / 4.04 ( 1143) link_ALPHA1-3 : bond 0.00413 / 0.23 ( 6) link_ALPHA1-3 : angle 1.36670 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00471 / 0.24 ( 3) link_ALPHA1-6 : angle 1.44285 / 0.82 ( 9) link_BETA1-4 : bond 0.00365 / 0.24 ( 15) link_BETA1-4 : angle 1.52040 / 0.99 ( 45) link_NAG-ASN : bond 0.00217 / 0.16 ( 15) link_NAG-ASN : angle 2.43801 / 1.31 ( 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 320 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.541 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: 0.8279 (p0) cc_final: 0.8052 (p0) REVERT: A 229 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7412 (pp20) REVERT: A 235 GLU cc_start: 0.7952 (tt0) cc_final: 0.7521 (tm-30) REVERT: D 587 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7936 (ttm-80) REVERT: D 588 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7794 (mmmt) REVERT: G 36 TRP cc_start: 0.7822 (m100) cc_final: 0.7341 (m100) REVERT: G 43 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7491 (mmmt) REVERT: G 54 ASP cc_start: 0.8153 (p0) cc_final: 0.7808 (p0) REVERT: G 57 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8411 (mmmm) REVERT: G 119 ASP cc_start: 0.8239 (p0) cc_final: 0.7890 (t70) REVERT: J 18 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8342 (tmm160) REVERT: J 37 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: J 67 SER cc_start: 0.8195 (t) cc_final: 0.7726 (p) REVERT: J 90 GLN cc_start: 0.8676 (pp30) cc_final: 0.8329 (pp30) REVERT: J 92 LYS cc_start: 0.8956 (tttm) cc_final: 0.8750 (tttp) REVERT: J 104 LEU cc_start: 0.8683 (tp) cc_final: 0.8078 (tt) REVERT: J 108 ARG cc_start: 0.3309 (mtt180) cc_final: 0.1549 (ptt90) REVERT: B 56 LYS cc_start: 0.7139 (mptt) cc_final: 0.6832 (mmtt) REVERT: B 89 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.6282 (tmt90) REVERT: B 117 ASP cc_start: 0.8232 (p0) cc_final: 0.7839 (p0) REVERT: B 162 TYR cc_start: 0.8713 (m-80) cc_final: 0.8510 (m-10) REVERT: B 235 GLU cc_start: 0.8029 (tt0) cc_final: 0.7693 (tm-30) REVERT: E 587 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7751 (ttm-80) REVERT: H 34 MET cc_start: 0.8360 (mmm) cc_final: 0.7489 (mmm) REVERT: H 36 TRP cc_start: 0.7585 (m100) cc_final: 0.6218 (m100) REVERT: H 54 ASP cc_start: 0.8146 (p0) cc_final: 0.7747 (p0) REVERT: H 57 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8332 (mmmm) REVERT: K 37 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: K 67 SER cc_start: 0.8220 (t) cc_final: 0.7732 (p) REVERT: K 90 GLN cc_start: 0.8462 (pp30) cc_final: 0.8176 (pp30) REVERT: K 108 ARG cc_start: 0.3002 (mtt180) cc_final: 0.0912 (ptt90) REVERT: C 56 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7396 (mptt) REVERT: C 229 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7479 (pp20) REVERT: C 235 GLU cc_start: 0.8168 (tt0) cc_final: 0.7679 (tm-30) REVERT: F 545 GLU cc_start: 0.8019 (mp0) cc_final: 0.7730 (mp0) REVERT: F 573 LEU cc_start: 0.8956 (mt) cc_final: 0.8697 (tp) REVERT: F 587 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7927 (ttm-80) REVERT: I 54 ASP cc_start: 0.8197 (p0) cc_final: 0.7817 (p0) REVERT: I 104 TYR cc_start: 0.8422 (m-10) cc_final: 0.8014 (m-10) REVERT: L 37 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: L 94 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7665 (t80) REVERT: L 104 LEU cc_start: 0.8473 (tp) cc_final: 0.7721 (tt) REVERT: L 108 ARG cc_start: 0.3050 (mtt180) cc_final: 0.1101 (ptt90) outliers start: 26 outliers final: 16 residues processed: 308 average time/residue: 0.1361 time to fit residues: 58.5689 Evaluate side-chains 310 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 132 optimal weight: 0.1980 chunk 32 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094290 restraints weight = 27586.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097432 restraints weight = 16356.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099554 restraints weight = 11515.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100971 restraints weight = 9106.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101922 restraints weight = 7779.077| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14052 Z= 0.123 Angle : 0.742 13.485 19146 Z= 0.358 Chirality : 0.045 0.165 2205 Planarity : 0.005 0.057 2370 Dihedral : 5.173 51.637 1833 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.69 % Allowed : 19.35 % Favored : 78.95 % 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: -0.95 (0.21), residues: 1644 helix: 1.62 (0.40), residues: 183 sheet: -0.84 (0.21), residues: 627 loop : -0.89 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.012 0.001 TYR J 96 PHE 0.030 0.002 PHE E 592 TRP 0.019 0.001 TRP F 597 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13998) covalent geometry : angle 0.72348 / 0.35 (18999) SS BOND : bond 0.00593 / 0.47 ( 15) SS BOND : angle 2.30880 / 1.29 ( 30) hydrogen bonds : bond 0.03078 / 2.11 ( 429) hydrogen bonds : angle 5.54878 / 3.92 ( 1143) link_ALPHA1-3 : bond 0.00399 / 0.22 ( 6) link_ALPHA1-3 : angle 1.37639 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00469 / 0.24 ( 3) link_ALPHA1-6 : angle 1.42655 / 0.81 ( 9) link_BETA1-4 : bond 0.00356 / 0.24 ( 15) link_BETA1-4 : angle 1.48994 / 0.96 ( 45) link_NAG-ASN : bond 0.00229 / 0.17 ( 15) link_NAG-ASN : angle 2.45764 / 1.32 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.78 seconds wall clock time: 43 minutes 2.47 seconds (2582.47 seconds total)