Starting phenix.real_space_refine on Thu Jul 31 21:19:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uye_20947/07_2025/6uye_20947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uye_20947/07_2025/6uye_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_20947/07_2025/6uye_20947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uye_20947/07_2025/6uye_20947.map" model { file = "/net/cci-nas-00/data/ceres_data/6uye_20947/07_2025/6uye_20947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uye_20947/07_2025/6uye_20947.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.074 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: "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: "E" 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: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: I, H, C, B, R, U, J, L, D, F, Q, T, P, S Time building chain proxies: 6.28, per 1000 atoms: 0.46 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=7, 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 J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 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: 3.78 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.95 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: 4.13 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2433 1.32 - 1.44: 3874 1.44 - 1.56: 7622 1.56 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 13998 Sorted by residual: bond pdb=" CA HIS H 35 " pdb=" CB HIS H 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.14e+00 bond pdb=" CA HIS G 35 " pdb=" CB HIS G 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.09e+00 bond pdb=" CA HIS I 35 " pdb=" CB HIS I 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.07e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 13993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 17946 2.22 - 4.45: 904 4.45 - 6.67: 117 6.67 - 8.89: 26 8.89 - 11.12: 6 Bond angle restraints: 18999 Sorted by residual: angle pdb=" C ASP A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 120.43 125.49 -5.06 9.60e-01 1.09e+00 2.78e+01 angle pdb=" C ASP B 78 " pdb=" N VAL B 79 " pdb=" CA VAL B 79 " ideal model delta sigma weight residual 120.43 125.48 -5.05 9.60e-01 1.09e+00 2.77e+01 angle pdb=" C ASP C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta sigma weight residual 120.43 125.44 -5.01 9.60e-01 1.09e+00 2.73e+01 angle pdb=" C SER G 113 " pdb=" N TYR G 114 " pdb=" CA TYR G 114 " ideal model delta sigma weight residual 122.17 114.35 7.82 1.54e+00 4.22e-01 2.58e+01 angle pdb=" C SER H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta sigma weight residual 122.17 114.40 7.77 1.54e+00 4.22e-01 2.55e+01 ... (remaining 18994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 8410 21.54 - 43.07: 179 43.07 - 64.61: 36 64.61 - 86.14: 45 86.14 - 107.68: 24 Dihedral angle restraints: 8694 sinusoidal: 3876 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 8691 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: 2.02 - 2.60: 143 2.60 - 3.17: 10986 3.17 - 3.75: 20131 3.75 - 4.32: 27340 4.32 - 4.90: 45775 Nonbonded interactions: 104375 Sorted by model distance: nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS D 511 " pdb=" SG CYS D 556 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS F 511 " pdb=" SG CYS F 556 " model vdw 2.029 3.760 ... (remaining 104370 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: 0.09 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } 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: 1.720 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.980 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.069 14044 Z= 0.460 Angle : 1.154 16.482 19130 Z= 0.607 Chirality : 0.063 0.296 2205 Planarity : 0.007 0.092 2370 Dihedral : 13.382 107.679 5601 Min Nonbonded Distance : 2.019 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.004 TRP C 104 HIS 0.013 0.002 HIS I 35 PHE 0.027 0.004 PHE C 176 TYR 0.030 0.004 TYR B 109 ARG 0.014 0.001 ARG F 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01111 ( 15) link_NAG-ASN : angle 5.47245 ( 45) link_ALPHA1-6 : bond 0.00177 ( 3) link_ALPHA1-6 : angle 1.52075 ( 9) link_BETA1-4 : bond 0.00833 ( 15) link_BETA1-4 : angle 2.93093 ( 45) link_ALPHA1-3 : bond 0.00629 ( 6) link_ALPHA1-3 : angle 1.94754 ( 18) hydrogen bonds : bond 0.23518 ( 429) hydrogen bonds : angle 9.56156 ( 1143) SS BOND : bond 0.00457 ( 7) SS BOND : angle 1.07826 ( 14) covalent geometry : bond 0.01025 (13998) covalent geometry : angle 1.11496 (18999) *********************** 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 : 1.400 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: 0.7976 (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: 0.7912 (mmm) REVERT: G 54 ASP cc_start: 0.8402 (p0) cc_final: 0.8104 (p0) REVERT: G 68 PHE cc_start: 0.6834 (m-10) cc_final: 0.6295 (m-80) REVERT: G 119 ASP cc_start: 0.8208 (p0) cc_final: 0.7945 (p0) REVERT: J 28 ASP cc_start: 0.8110 (t0) cc_final: 0.7885 (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: 0.8055 (p0) REVERT: B 229 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7500 (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: 0.5466 (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: 0.7919 (p0) REVERT: H 57 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8409 (tptt) REVERT: H 68 PHE cc_start: 0.6897 (m-10) cc_final: 0.6268 (m-80) REVERT: H 119 ASP cc_start: 0.8366 (p0) cc_final: 0.8152 (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: 0.7667 (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: 0.8087 (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: 0.5114 (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: 0.6711 (m100) REVERT: I 38 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7728 (ttm-80) REVERT: I 54 ASP cc_start: 0.8389 (p0) cc_final: 0.7895 (p0) REVERT: I 94 TYR cc_start: 0.6507 (m-10) cc_final: 0.6283 (m-10) REVERT: I 104 TYR cc_start: 0.8253 (m-10) cc_final: 0.7954 (m-10) REVERT: L 49 TYR cc_start: 0.8000 (p90) cc_final: 0.7555 (p90) REVERT: L 67 SER cc_start: 0.7996 (t) cc_final: 0.7448 (p) REVERT: L 71 PHE cc_start: 0.7798 (m-10) cc_final: 0.7208 (m-10) REVERT: L 108 ARG cc_start: 0.3197 (mtt180) cc_final: 0.0520 (ptt90) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.3218 time to fit residues: 230.4302 Evaluate side-chains 324 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN D 516 HIS D 595 GLN J 6 GLN J 38 GLN E 516 HIS E 595 GLN K 38 GLN C 251 GLN F 508 GLN F 516 HIS ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093472 restraints weight = 27094.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096482 restraints weight = 16093.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098532 restraints weight = 11403.497| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14044 Z= 0.154 Angle : 0.767 8.582 19130 Z= 0.379 Chirality : 0.048 0.186 2205 Planarity : 0.005 0.049 2370 Dihedral : 11.890 77.547 2622 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.91 % Allowed : 11.44 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1644 helix: 0.15 (0.41), residues: 174 sheet: -1.48 (0.19), residues: 648 loop : -1.49 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 121 HIS 0.004 0.001 HIS D 516 PHE 0.022 0.002 PHE L 71 TYR 0.024 0.002 TYR I 115 ARG 0.008 0.001 ARG C 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 15) link_NAG-ASN : angle 2.79459 ( 45) link_ALPHA1-6 : bond 0.00901 ( 3) link_ALPHA1-6 : angle 1.35841 ( 9) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 2.30299 ( 45) link_ALPHA1-3 : bond 0.00873 ( 6) link_ALPHA1-3 : angle 2.29807 ( 18) hydrogen bonds : bond 0.03708 ( 429) hydrogen bonds : angle 6.89099 ( 1143) SS BOND : bond 0.00582 ( 7) SS BOND : angle 2.34579 ( 14) covalent geometry : bond 0.00349 (13998) covalent geometry : angle 0.74231 (18999) *********************** 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 414 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 387 time to evaluate : 1.447 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: 0.7460 (mmmt) cc_final: 0.6966 (mptt) REVERT: A 117 ASP cc_start: 0.8309 (p0) cc_final: 0.7931 (p0) REVERT: A 235 GLU cc_start: 0.7986 (tt0) cc_final: 0.7441 (tm-30) REVERT: A 291 TRP cc_start: 0.5758 (p90) cc_final: 0.5252 (p90) REVERT: D 587 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8073 (ttm110) REVERT: G 34 MET cc_start: 0.8036 (mmm) cc_final: 0.7791 (mmm) REVERT: G 43 LYS cc_start: 0.7606 (mmmm) cc_final: 0.7400 (mmmt) REVERT: G 54 ASP cc_start: 0.8152 (p0) cc_final: 0.7688 (p0) REVERT: J 4 MET cc_start: 0.6982 (ttm) cc_final: 0.6575 (ttm) REVERT: J 70 ASP cc_start: 0.8275 (t70) cc_final: 0.7992 (t70) REVERT: J 90 GLN cc_start: 0.8686 (pp30) cc_final: 0.8129 (pp30) REVERT: J 104 LEU cc_start: 0.8917 (tp) cc_final: 0.8480 (tt) REVERT: J 108 ARG cc_start: 0.3729 (mtt180) cc_final: 0.1559 (ptt90) REVERT: B 56 LYS cc_start: 0.7424 (mmmt) cc_final: 0.7071 (mptt) REVERT: B 117 ASP cc_start: 0.8275 (p0) cc_final: 0.7916 (p0) REVERT: B 235 GLU cc_start: 0.8120 (tt0) cc_final: 0.7595 (tm-30) REVERT: B 291 TRP cc_start: 0.5954 (p90) cc_final: 0.5458 (p90) REVERT: E 587 ARG cc_start: 0.8295 (mtp85) cc_final: 0.7840 (ttm-80) REVERT: H 54 ASP cc_start: 0.8248 (p0) cc_final: 0.7718 (p0) REVERT: H 57 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8161 (mmtp) REVERT: K 4 MET cc_start: 0.7109 (ttm) cc_final: 0.6790 (ttm) REVERT: K 23 CYS cc_start: 0.7106 (t) cc_final: 0.6022 (t) REVERT: K 90 GLN cc_start: 0.8831 (pp30) cc_final: 0.8227 (pp30) REVERT: K 92 LYS cc_start: 0.8554 (tttm) cc_final: 0.8335 (tttm) REVERT: K 108 ARG cc_start: 0.3604 (mtt180) cc_final: 0.1198 (ptt90) REVERT: C 117 ASP cc_start: 0.8232 (p0) cc_final: 0.7928 (p0) REVERT: C 229 GLU cc_start: 0.7739 (pp20) cc_final: 0.7405 (pp20) REVERT: C 235 GLU cc_start: 0.8120 (tt0) cc_final: 0.7581 (tm-30) REVERT: C 291 TRP cc_start: 0.5882 (p90) cc_final: 0.5288 (p90) REVERT: F 527 ILE cc_start: 0.5714 (mm) cc_final: 0.5191 (mm) REVERT: F 587 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7992 (ttm-80) REVERT: I 48 MET cc_start: 0.5826 (mtp) cc_final: 0.5328 (mtp) REVERT: I 54 ASP cc_start: 0.8195 (p0) cc_final: 0.7670 (p0) REVERT: I 104 TYR cc_start: 0.8142 (m-10) cc_final: 0.7851 (m-10) REVERT: L 6 GLN cc_start: 0.6811 (mt0) cc_final: 0.6512 (mt0) REVERT: L 67 SER cc_start: 0.7922 (t) cc_final: 0.7632 (p) REVERT: L 104 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8069 (tt) REVERT: L 108 ARG cc_start: 0.3358 (mtt180) cc_final: 0.0977 (ptt90) outliers start: 27 outliers final: 17 residues processed: 402 average time/residue: 0.3062 time to fit residues: 169.0507 Evaluate side-chains 328 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 B residue 82 VAL 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 82 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 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 43 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 139 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 114 optimal weight: 0.0000 chunk 54 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 595 GLN J 37 GLN E 508 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN F 567 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093001 restraints weight = 27599.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096232 restraints weight = 15635.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098455 restraints weight = 10842.114| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14044 Z= 0.132 Angle : 0.722 9.184 19130 Z= 0.349 Chirality : 0.047 0.193 2205 Planarity : 0.005 0.054 2370 Dihedral : 10.449 72.098 2622 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.68 % Allowed : 13.98 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1644 helix: 0.55 (0.41), residues: 180 sheet: -1.24 (0.20), residues: 654 loop : -1.25 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.004 0.001 HIS C 154 PHE 0.020 0.002 PHE L 71 TYR 0.018 0.001 TYR I 115 ARG 0.005 0.001 ARG B 136 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 15) link_NAG-ASN : angle 2.55512 ( 45) link_ALPHA1-6 : bond 0.00882 ( 3) link_ALPHA1-6 : angle 1.26025 ( 9) link_BETA1-4 : bond 0.00425 ( 15) link_BETA1-4 : angle 2.04129 ( 45) link_ALPHA1-3 : bond 0.01022 ( 6) link_ALPHA1-3 : angle 1.73577 ( 18) hydrogen bonds : bond 0.03320 ( 429) hydrogen bonds : angle 6.44658 ( 1143) SS BOND : bond 0.00349 ( 7) SS BOND : angle 1.48286 ( 14) covalent geometry : bond 0.00296 (13998) covalent geometry : angle 0.70270 (18999) *********************** 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 388 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 350 time to evaluate : 2.387 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: 0.7601 (mmmt) cc_final: 0.7157 (mptt) REVERT: A 117 ASP cc_start: 0.8422 (p0) cc_final: 0.8104 (p0) REVERT: A 235 GLU cc_start: 0.8034 (tt0) cc_final: 0.7516 (tm-30) REVERT: A 291 TRP cc_start: 0.5673 (p90) cc_final: 0.5185 (p90) REVERT: D 587 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8174 (ttm-80) REVERT: G 34 MET cc_start: 0.8225 (mmm) cc_final: 0.7947 (mmm) REVERT: G 43 LYS cc_start: 0.7671 (mmmm) cc_final: 0.7406 (mmmt) REVERT: G 54 ASP cc_start: 0.8277 (p0) cc_final: 0.7905 (p0) REVERT: G 57 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8487 (mmtp) REVERT: G 95 TYR cc_start: 0.7028 (m-80) cc_final: 0.6774 (m-10) REVERT: J 67 SER cc_start: 0.8176 (t) cc_final: 0.7755 (p) REVERT: J 70 ASP cc_start: 0.8524 (t70) cc_final: 0.8301 (t70) REVERT: J 90 GLN cc_start: 0.8614 (pp30) cc_final: 0.8173 (pp30) REVERT: J 104 LEU cc_start: 0.8801 (tp) cc_final: 0.8387 (tt) REVERT: J 108 ARG cc_start: 0.3664 (mtt180) cc_final: 0.1450 (ptt90) REVERT: B 56 LYS cc_start: 0.7465 (mmmt) cc_final: 0.7154 (mptt) REVERT: B 117 ASP cc_start: 0.8301 (p0) cc_final: 0.7965 (p0) REVERT: B 235 GLU cc_start: 0.8164 (tt0) cc_final: 0.7594 (tm-30) REVERT: B 291 TRP cc_start: 0.5884 (p90) cc_final: 0.5360 (p90) REVERT: E 587 ARG cc_start: 0.8337 (mtp85) cc_final: 0.7914 (ttm-80) REVERT: H 54 ASP cc_start: 0.8245 (p0) cc_final: 0.7833 (p0) REVERT: K 4 MET cc_start: 0.7055 (ttm) cc_final: 0.6456 (ttm) REVERT: K 23 CYS cc_start: 0.7170 (t) cc_final: 0.5395 (t) REVERT: K 70 ASP cc_start: 0.8429 (t70) cc_final: 0.8029 (t70) REVERT: K 90 GLN cc_start: 0.8756 (pp30) cc_final: 0.8319 (pp30) REVERT: K 97 THR cc_start: 0.8508 (p) cc_final: 0.8213 (p) REVERT: K 108 ARG cc_start: 0.3448 (mtt180) cc_final: 0.1179 (ptt90) REVERT: C 56 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7024 (mptt) REVERT: C 117 ASP cc_start: 0.8281 (p0) cc_final: 0.8004 (p0) REVERT: C 229 GLU cc_start: 0.7881 (pp20) cc_final: 0.7466 (pp20) REVERT: C 235 GLU cc_start: 0.8130 (tt0) cc_final: 0.7544 (tm-30) REVERT: C 282 ASP cc_start: 0.7675 (t0) cc_final: 0.7421 (t0) REVERT: C 291 TRP cc_start: 0.5839 (p90) cc_final: 0.5311 (p90) REVERT: F 527 ILE cc_start: 0.5549 (mm) cc_final: 0.4932 (mm) REVERT: F 587 ARG cc_start: 0.8336 (mtp85) cc_final: 0.8062 (ttm-80) REVERT: I 38 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7071 (ptp-110) REVERT: I 54 ASP cc_start: 0.8198 (p0) cc_final: 0.7740 (p0) REVERT: I 95 TYR cc_start: 0.7374 (m-10) cc_final: 0.7079 (m-10) REVERT: I 104 TYR cc_start: 0.8292 (m-10) cc_final: 0.7907 (m-10) REVERT: L 67 SER cc_start: 0.8009 (t) cc_final: 0.7482 (p) REVERT: L 104 LEU cc_start: 0.8718 (tp) cc_final: 0.7956 (tt) REVERT: L 108 ARG cc_start: 0.3183 (mtt180) cc_final: 0.0877 (ptt90) outliers start: 38 outliers final: 24 residues processed: 372 average time/residue: 0.3591 time to fit residues: 188.6228 Evaluate side-chains 329 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 304 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain 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 53 CYS 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 L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 150 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN F 508 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.115157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.087430 restraints weight = 27856.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.090252 restraints weight = 17041.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092146 restraints weight = 12303.461| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 14044 Z= 0.319 Angle : 0.844 11.402 19130 Z= 0.408 Chirality : 0.051 0.204 2205 Planarity : 0.005 0.049 2370 Dihedral : 9.136 66.651 2622 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.67 % Allowed : 14.97 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1644 helix: 0.41 (0.38), residues: 180 sheet: -1.38 (0.20), residues: 654 loop : -1.28 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 597 HIS 0.006 0.001 HIS C 154 PHE 0.015 0.002 PHE J 71 TYR 0.022 0.002 TYR I 115 ARG 0.006 0.001 ARG I 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 15) link_NAG-ASN : angle 2.91069 ( 45) link_ALPHA1-6 : bond 0.00938 ( 3) link_ALPHA1-6 : angle 1.33208 ( 9) link_BETA1-4 : bond 0.00374 ( 15) link_BETA1-4 : angle 1.97801 ( 45) link_ALPHA1-3 : bond 0.00992 ( 6) link_ALPHA1-3 : angle 1.86190 ( 18) hydrogen bonds : bond 0.04017 ( 429) hydrogen bonds : angle 6.45767 ( 1143) SS BOND : bond 0.00416 ( 7) SS BOND : angle 2.02403 ( 14) covalent geometry : bond 0.00739 (13998) covalent geometry : angle 0.82531 (18999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 1.436 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: 0.7599 (mmmt) cc_final: 0.7220 (mptt) REVERT: A 89 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.6341 (tmt90) REVERT: A 117 ASP cc_start: 0.8439 (p0) cc_final: 0.8101 (p0) REVERT: A 229 GLU cc_start: 0.7820 (pp20) cc_final: 0.7518 (pp20) REVERT: A 235 GLU cc_start: 0.8173 (tt0) cc_final: 0.7607 (tm-30) REVERT: D 587 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8227 (ttm-80) REVERT: G 43 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7548 (mmmt) REVERT: G 54 ASP cc_start: 0.8232 (p0) cc_final: 0.7851 (p0) REVERT: G 119 ASP cc_start: 0.7960 (p0) cc_final: 0.7606 (t70) REVERT: J 37 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: J 67 SER cc_start: 0.8336 (t) cc_final: 0.7966 (p) REVERT: J 70 ASP cc_start: 0.8548 (t70) cc_final: 0.8237 (t70) REVERT: J 90 GLN cc_start: 0.8780 (pp30) cc_final: 0.8327 (pp30) REVERT: J 92 LYS cc_start: 0.8831 (tttm) cc_final: 0.8576 (tttp) REVERT: J 108 ARG cc_start: 0.3646 (mtt180) cc_final: 0.1453 (ptt90) REVERT: B 56 LYS cc_start: 0.7498 (mmmt) cc_final: 0.7251 (mptt) REVERT: B 89 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6257 (tmt90) REVERT: B 117 ASP cc_start: 0.8274 (p0) cc_final: 0.7930 (p0) REVERT: B 235 GLU cc_start: 0.8223 (tt0) cc_final: 0.7737 (tm-30) REVERT: E 587 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7870 (ttm-80) REVERT: E 591 ASP cc_start: 0.8278 (t0) cc_final: 0.8030 (t0) REVERT: H 43 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7532 (mmmt) REVERT: H 54 ASP cc_start: 0.8216 (p0) cc_final: 0.7758 (p0) REVERT: K 24 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7009 (mmm-85) REVERT: K 67 SER cc_start: 0.8067 (t) cc_final: 0.7803 (p) REVERT: K 90 GLN cc_start: 0.8830 (pp30) cc_final: 0.8316 (pp30) REVERT: K 97 THR cc_start: 0.8596 (p) cc_final: 0.8328 (p) REVERT: K 108 ARG cc_start: 0.3416 (mtt180) cc_final: 0.1161 (ptt90) REVERT: C 56 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7290 (mptt) REVERT: C 117 ASP cc_start: 0.8408 (p0) cc_final: 0.8131 (p0) REVERT: C 229 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7515 (pp20) REVERT: C 235 GLU cc_start: 0.8215 (tt0) cc_final: 0.7698 (tm-30) REVERT: F 587 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8008 (ttm-80) REVERT: I 38 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.5555 (ptp-110) REVERT: I 54 ASP cc_start: 0.8169 (p0) cc_final: 0.7780 (p0) REVERT: I 104 TYR cc_start: 0.8451 (m-10) cc_final: 0.8102 (m-10) REVERT: L 67 SER cc_start: 0.7926 (t) cc_final: 0.7630 (p) REVERT: L 108 ARG cc_start: 0.3155 (mtt180) cc_final: 0.0977 (ptt90) outliers start: 52 outliers final: 35 residues processed: 328 average time/residue: 0.3562 time to fit residues: 160.0791 Evaluate side-chains 319 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 103 LYS 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 261 TYR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 20 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.0470 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN J 6 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS I 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.091923 restraints weight = 27525.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094983 restraints weight = 16268.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097072 restraints weight = 11481.883| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14044 Z= 0.127 Angle : 0.698 8.643 19130 Z= 0.336 Chirality : 0.046 0.198 2205 Planarity : 0.004 0.065 2370 Dihedral : 8.211 61.196 2622 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.54 % Allowed : 16.95 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1644 helix: 0.91 (0.40), residues: 183 sheet: -1.12 (0.20), residues: 645 loop : -1.11 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 597 HIS 0.003 0.001 HIS G 35 PHE 0.017 0.002 PHE F 582 TYR 0.019 0.001 TYR I 115 ARG 0.011 0.001 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 15) link_NAG-ASN : angle 2.57233 ( 45) link_ALPHA1-6 : bond 0.01070 ( 3) link_ALPHA1-6 : angle 1.20416 ( 9) link_BETA1-4 : bond 0.00393 ( 15) link_BETA1-4 : angle 1.75056 ( 45) link_ALPHA1-3 : bond 0.01044 ( 6) link_ALPHA1-3 : angle 1.89341 ( 18) hydrogen bonds : bond 0.03093 ( 429) hydrogen bonds : angle 6.10842 ( 1143) SS BOND : bond 0.00477 ( 7) SS BOND : angle 1.18918 ( 14) covalent geometry : bond 0.00281 (13998) covalent geometry : angle 0.68035 (18999) *********************** 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 356 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 2.100 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 56 LYS cc_start: 0.7531 (mmmt) cc_final: 0.7275 (mptt) REVERT: A 117 ASP cc_start: 0.8443 (p0) cc_final: 0.8142 (p0) REVERT: A 229 GLU cc_start: 0.7848 (pp20) cc_final: 0.7503 (pp20) REVERT: A 235 GLU cc_start: 0.7997 (tt0) cc_final: 0.7564 (tm-30) REVERT: D 587 ARG cc_start: 0.8427 (mtp85) cc_final: 0.8163 (ttm-80) REVERT: G 43 LYS cc_start: 0.7690 (mmmm) cc_final: 0.7484 (mmmt) REVERT: G 54 ASP cc_start: 0.8192 (p0) cc_final: 0.7806 (p0) REVERT: J 37 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: J 67 SER cc_start: 0.8297 (t) cc_final: 0.7927 (p) REVERT: J 70 ASP cc_start: 0.8559 (t70) cc_final: 0.8247 (t70) REVERT: J 90 GLN cc_start: 0.8861 (pp30) cc_final: 0.8344 (pp30) REVERT: J 92 LYS cc_start: 0.8795 (tttm) cc_final: 0.8513 (tttp) REVERT: J 108 ARG cc_start: 0.3576 (mtt180) cc_final: 0.1417 (ptt90) REVERT: B 117 ASP cc_start: 0.8271 (p0) cc_final: 0.7904 (p0) REVERT: B 235 GLU cc_start: 0.8172 (tt0) cc_final: 0.7685 (tm-30) REVERT: E 587 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7780 (ttm-80) REVERT: E 588 LYS cc_start: 0.8036 (mmmm) cc_final: 0.7611 (mmmm) REVERT: H 6 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5839 (mt-10) REVERT: H 43 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7419 (mmmt) REVERT: H 54 ASP cc_start: 0.8162 (p0) cc_final: 0.7699 (p0) REVERT: H 57 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8240 (mmtp) REVERT: K 37 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: K 67 SER cc_start: 0.7961 (t) cc_final: 0.7622 (p) REVERT: K 90 GLN cc_start: 0.8742 (pp30) cc_final: 0.8331 (pp30) REVERT: K 97 THR cc_start: 0.8499 (p) cc_final: 0.8226 (p) REVERT: K 108 ARG cc_start: 0.3205 (mtt180) cc_final: 0.1042 (ptt90) REVERT: C 56 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7277 (mptt) REVERT: C 117 ASP cc_start: 0.8344 (p0) cc_final: 0.8080 (p0) REVERT: C 229 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: C 235 GLU cc_start: 0.8127 (tt0) cc_final: 0.7598 (tm-30) REVERT: C 291 TRP cc_start: 0.5976 (p90) cc_final: 0.5261 (p90) REVERT: F 545 GLU cc_start: 0.8021 (mp0) cc_final: 0.7761 (mp0) REVERT: F 587 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8004 (ttm-80) REVERT: I 34 MET cc_start: 0.8312 (mmm) cc_final: 0.8035 (mmm) REVERT: I 48 MET cc_start: 0.6901 (mmm) cc_final: 0.6605 (tpp) REVERT: I 54 ASP cc_start: 0.8143 (p0) cc_final: 0.7718 (p0) REVERT: I 104 TYR cc_start: 0.8381 (m-10) cc_final: 0.8049 (m-10) REVERT: L 67 SER cc_start: 0.7938 (t) cc_final: 0.7671 (p) REVERT: L 104 LEU cc_start: 0.8658 (tp) cc_final: 0.7890 (tt) REVERT: L 108 ARG cc_start: 0.3154 (mtt180) cc_final: 0.1015 (ptt90) outliers start: 36 outliers final: 23 residues processed: 343 average time/residue: 0.5049 time to fit residues: 245.8268 Evaluate side-chains 320 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 2 VAL 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 22 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.118572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091015 restraints weight = 27991.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.093969 restraints weight = 16739.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096021 restraints weight = 11905.312| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14044 Z= 0.158 Angle : 0.702 8.469 19130 Z= 0.340 Chirality : 0.046 0.200 2205 Planarity : 0.004 0.051 2370 Dihedral : 7.755 58.339 2622 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.54 % Allowed : 17.09 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.21), residues: 1644 helix: 1.15 (0.39), residues: 183 sheet: -1.02 (0.20), residues: 645 loop : -1.06 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 597 HIS 0.003 0.001 HIS G 35 PHE 0.027 0.002 PHE D 592 TYR 0.017 0.001 TYR J 96 ARG 0.005 0.001 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 15) link_NAG-ASN : angle 2.57810 ( 45) link_ALPHA1-6 : bond 0.01102 ( 3) link_ALPHA1-6 : angle 1.20586 ( 9) link_BETA1-4 : bond 0.00335 ( 15) link_BETA1-4 : angle 1.67953 ( 45) link_ALPHA1-3 : bond 0.01043 ( 6) link_ALPHA1-3 : angle 1.79594 ( 18) hydrogen bonds : bond 0.03168 ( 429) hydrogen bonds : angle 5.97488 ( 1143) SS BOND : bond 0.00258 ( 7) SS BOND : angle 1.32190 ( 14) covalent geometry : bond 0.00363 (13998) covalent geometry : angle 0.68486 (18999) *********************** 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 336 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 300 time to evaluate : 1.524 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: 0.7527 (mmmt) cc_final: 0.7292 (mptt) REVERT: A 117 ASP cc_start: 0.8440 (p0) cc_final: 0.8136 (p0) REVERT: A 229 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7465 (pp20) REVERT: A 235 GLU cc_start: 0.8034 (tt0) cc_final: 0.7559 (tm-30) REVERT: D 587 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8138 (ttm-80) REVERT: G 43 LYS cc_start: 0.7761 (mmmm) cc_final: 0.7554 (mmmt) REVERT: G 54 ASP cc_start: 0.8242 (p0) cc_final: 0.7847 (p0) REVERT: J 37 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: J 67 SER cc_start: 0.8163 (t) cc_final: 0.7789 (p) REVERT: J 70 ASP cc_start: 0.8598 (t70) cc_final: 0.8254 (t70) REVERT: J 90 GLN cc_start: 0.8834 (pp30) cc_final: 0.8395 (pp30) REVERT: J 92 LYS cc_start: 0.8884 (tttm) cc_final: 0.8612 (tttp) REVERT: J 108 ARG cc_start: 0.3528 (mtt180) cc_final: 0.1495 (ptt90) REVERT: B 56 LYS cc_start: 0.7214 (mptt) cc_final: 0.6975 (mptt) REVERT: B 117 ASP cc_start: 0.8244 (p0) cc_final: 0.7893 (p0) REVERT: B 235 GLU cc_start: 0.8181 (tt0) cc_final: 0.7712 (tm-30) REVERT: E 587 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7786 (ttm-80) REVERT: H 6 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5627 (mt-10) REVERT: H 43 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7477 (mmmt) REVERT: H 54 ASP cc_start: 0.8173 (p0) cc_final: 0.7742 (p0) REVERT: H 57 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8312 (mmtp) REVERT: K 37 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: K 67 SER cc_start: 0.8048 (t) cc_final: 0.7765 (p) REVERT: K 90 GLN cc_start: 0.8770 (pp30) cc_final: 0.8300 (pp30) REVERT: K 94 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7648 (t80) REVERT: K 108 ARG cc_start: 0.3194 (mtt180) cc_final: 0.1025 (ptt90) REVERT: C 56 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7300 (mptt) REVERT: C 117 ASP cc_start: 0.8367 (p0) cc_final: 0.8091 (p0) REVERT: C 229 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7489 (pp20) REVERT: C 235 GLU cc_start: 0.8144 (tt0) cc_final: 0.7613 (tm-30) REVERT: F 545 GLU cc_start: 0.8072 (mp0) cc_final: 0.7828 (mp0) REVERT: F 587 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7951 (ttm-80) REVERT: I 34 MET cc_start: 0.8223 (mmm) cc_final: 0.7964 (mmm) REVERT: I 43 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7804 (mmmt) REVERT: I 46 GLU cc_start: 0.7320 (pt0) cc_final: 0.7082 (pt0) REVERT: I 54 ASP cc_start: 0.8162 (p0) cc_final: 0.7757 (p0) REVERT: I 104 TYR cc_start: 0.8415 (m-10) cc_final: 0.8080 (m-10) REVERT: L 67 SER cc_start: 0.7949 (t) cc_final: 0.7633 (p) REVERT: L 90 GLN cc_start: 0.8862 (pp30) cc_final: 0.8309 (pp30) REVERT: L 94 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7611 (t80) REVERT: L 104 LEU cc_start: 0.8587 (tp) cc_final: 0.7793 (tt) REVERT: L 108 ARG cc_start: 0.3095 (mtt180) cc_final: 0.1027 (ptt90) outliers start: 36 outliers final: 22 residues processed: 320 average time/residue: 0.2944 time to fit residues: 131.1723 Evaluate side-chains 316 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 J residue 28 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 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 2 VAL Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 114 optimal weight: 0.0980 chunk 100 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN C 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089847 restraints weight = 27958.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.092713 restraints weight = 16998.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.094725 restraints weight = 12296.240| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.004 0.033 14044 Z= 0.180 Angle : 0.723 11.430 19130 Z= 0.349 Chirality : 0.047 0.195 2205 Planarity : 0.004 0.054 2370 Dihedral : 7.433 57.768 2622 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.97 % Allowed : 16.95 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1644 helix: 1.34 (0.39), residues: 183 sheet: -0.96 (0.20), residues: 645 loop : -1.04 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 597 HIS 0.003 0.001 HIS G 35 PHE 0.016 0.002 PHE L 94 TYR 0.018 0.001 TYR G 115 ARG 0.004 0.000 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 15) link_NAG-ASN : angle 2.59260 ( 45) link_ALPHA1-6 : bond 0.01044 ( 3) link_ALPHA1-6 : angle 1.16931 ( 9) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 1.64538 ( 45) link_ALPHA1-3 : bond 0.00974 ( 6) link_ALPHA1-3 : angle 1.71637 ( 18) hydrogen bonds : bond 0.03187 ( 429) hydrogen bonds : angle 5.90726 ( 1143) SS BOND : bond 0.00185 ( 7) SS BOND : angle 1.39035 ( 14) covalent geometry : bond 0.00416 (13998) covalent geometry : angle 0.70627 (18999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7335 (mptt) REVERT: A 117 ASP cc_start: 0.8469 (p0) cc_final: 0.8189 (p0) REVERT: A 229 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: A 235 GLU cc_start: 0.8034 (tt0) cc_final: 0.7570 (tm-30) REVERT: D 587 ARG cc_start: 0.8418 (mtp85) cc_final: 0.8151 (ttm-80) REVERT: D 588 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7826 (mmmt) REVERT: G 43 LYS cc_start: 0.7906 (mmmm) cc_final: 0.7688 (mmmt) REVERT: G 54 ASP cc_start: 0.8219 (p0) cc_final: 0.7811 (p0) REVERT: J 37 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: J 67 SER cc_start: 0.8144 (t) cc_final: 0.7812 (p) REVERT: J 70 ASP cc_start: 0.8612 (t70) cc_final: 0.8238 (t70) REVERT: J 90 GLN cc_start: 0.8868 (pp30) cc_final: 0.8398 (pp30) REVERT: J 92 LYS cc_start: 0.8938 (tttm) cc_final: 0.8651 (tttm) REVERT: J 108 ARG cc_start: 0.3524 (mtt180) cc_final: 0.1538 (ptt90) REVERT: B 69 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7716 (t0) REVERT: B 117 ASP cc_start: 0.8287 (p0) cc_final: 0.7928 (p0) REVERT: B 235 GLU cc_start: 0.8122 (tt0) cc_final: 0.7682 (tm-30) REVERT: E 587 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7748 (ttm-80) REVERT: H 43 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7460 (mmmt) REVERT: H 54 ASP cc_start: 0.8196 (p0) cc_final: 0.7765 (p0) REVERT: K 67 SER cc_start: 0.8190 (t) cc_final: 0.7911 (p) REVERT: K 90 GLN cc_start: 0.8801 (pp30) cc_final: 0.8339 (pp30) REVERT: K 92 LYS cc_start: 0.8699 (tttm) cc_final: 0.8229 (ttmt) REVERT: K 94 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7598 (t80) REVERT: K 108 ARG cc_start: 0.3065 (mtt180) cc_final: 0.0940 (ptt90) REVERT: C 56 LYS cc_start: 0.7736 (mmmt) cc_final: 0.7349 (mptt) REVERT: C 117 ASP cc_start: 0.8404 (p0) cc_final: 0.8126 (p0) REVERT: C 130 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8384 (mmm160) REVERT: C 229 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7376 (pp20) REVERT: C 235 GLU cc_start: 0.8181 (tt0) cc_final: 0.7623 (tm-30) REVERT: F 587 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7969 (ttm-80) REVERT: I 34 MET cc_start: 0.8258 (mmm) cc_final: 0.7965 (mmm) REVERT: I 43 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7879 (mmmt) REVERT: I 54 ASP cc_start: 0.8159 (p0) cc_final: 0.7792 (p0) REVERT: I 104 TYR cc_start: 0.8438 (m-10) cc_final: 0.8010 (m-10) REVERT: L 67 SER cc_start: 0.7999 (t) cc_final: 0.7605 (p) REVERT: L 94 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7660 (t80) REVERT: L 104 LEU cc_start: 0.8668 (tp) cc_final: 0.7851 (tt) REVERT: L 108 ARG cc_start: 0.3048 (mtt180) cc_final: 0.1042 (ptt90) outliers start: 42 outliers final: 29 residues processed: 310 average time/residue: 0.3692 time to fit residues: 159.8640 Evaluate side-chains 311 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 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 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 244 LEU 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 69 THR 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 K residue 94 PHE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 104 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 F residue 548 MET Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 57 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN ** 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** K 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.115619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.087615 restraints weight = 28228.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090552 restraints weight = 16800.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092539 restraints weight = 11987.450| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14044 Z= 0.231 Angle : 0.777 9.984 19130 Z= 0.374 Chirality : 0.048 0.193 2205 Planarity : 0.005 0.053 2370 Dihedral : 7.361 57.227 2622 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.61 % Allowed : 17.51 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.21), residues: 1644 helix: 1.31 (0.38), residues: 183 sheet: -1.08 (0.20), residues: 648 loop : -1.15 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 597 HIS 0.004 0.001 HIS C 154 PHE 0.028 0.002 PHE D 592 TYR 0.020 0.002 TYR I 115 ARG 0.005 0.001 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 15) link_NAG-ASN : angle 2.68288 ( 45) link_ALPHA1-6 : bond 0.01012 ( 3) link_ALPHA1-6 : angle 1.19327 ( 9) link_BETA1-4 : bond 0.00336 ( 15) link_BETA1-4 : angle 1.65635 ( 45) link_ALPHA1-3 : bond 0.00910 ( 6) link_ALPHA1-3 : angle 1.63268 ( 18) hydrogen bonds : bond 0.03430 ( 429) hydrogen bonds : angle 6.01696 ( 1143) SS BOND : bond 0.00342 ( 7) SS BOND : angle 1.55990 ( 14) covalent geometry : bond 0.00535 (13998) covalent geometry : angle 0.76160 (18999) *********************** 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 315 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 1.818 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 56 LYS cc_start: 0.7559 (mmmt) cc_final: 0.7357 (mptt) REVERT: A 117 ASP cc_start: 0.8346 (p0) cc_final: 0.8146 (p0) REVERT: A 229 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: A 235 GLU cc_start: 0.8037 (tt0) cc_final: 0.7550 (tm-30) REVERT: D 552 ASP cc_start: 0.7493 (t0) cc_final: 0.7227 (t0) REVERT: D 587 ARG cc_start: 0.8361 (mtp85) cc_final: 0.8075 (ttm-80) REVERT: G 43 LYS cc_start: 0.7987 (mmmm) cc_final: 0.7749 (mmmt) REVERT: G 54 ASP cc_start: 0.8208 (p0) cc_final: 0.7812 (p0) REVERT: G 57 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8582 (mmtp) REVERT: J 18 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8363 (ttp80) REVERT: J 37 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: J 67 SER cc_start: 0.8183 (t) cc_final: 0.7784 (p) REVERT: J 70 ASP cc_start: 0.8570 (t70) cc_final: 0.8117 (t70) REVERT: J 90 GLN cc_start: 0.8873 (pp30) cc_final: 0.8446 (pp30) REVERT: J 92 LYS cc_start: 0.8934 (tttm) cc_final: 0.8663 (tttm) REVERT: J 108 ARG cc_start: 0.3536 (mtt180) cc_final: 0.1493 (ptt90) REVERT: B 56 LYS cc_start: 0.7320 (mptt) cc_final: 0.6966 (mmtt) REVERT: B 69 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7787 (t0) REVERT: B 117 ASP cc_start: 0.8287 (p0) cc_final: 0.7936 (p0) REVERT: B 235 GLU cc_start: 0.8135 (tt0) cc_final: 0.7697 (tm-30) REVERT: E 552 ASP cc_start: 0.7217 (t0) cc_final: 0.7003 (t0) REVERT: E 587 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7698 (ttm-80) REVERT: E 591 ASP cc_start: 0.8173 (t0) cc_final: 0.7906 (t0) REVERT: H 43 LYS cc_start: 0.7878 (mtpp) cc_final: 0.7567 (mmmt) REVERT: H 54 ASP cc_start: 0.8133 (p0) cc_final: 0.7708 (p0) REVERT: H 57 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8416 (mmtp) REVERT: K 67 SER cc_start: 0.8067 (t) cc_final: 0.7670 (p) REVERT: K 70 ASP cc_start: 0.8889 (t0) cc_final: 0.8314 (t0) REVERT: K 94 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7622 (t80) REVERT: K 108 ARG cc_start: 0.2965 (mtt180) cc_final: 0.0916 (ptt90) REVERT: C 56 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7414 (mptt) REVERT: C 117 ASP cc_start: 0.8384 (p0) cc_final: 0.8140 (p0) REVERT: C 229 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: C 235 GLU cc_start: 0.8184 (tt0) cc_final: 0.7637 (tm-30) REVERT: F 587 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7962 (ttm-80) REVERT: I 43 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7936 (mmmt) REVERT: I 54 ASP cc_start: 0.8191 (p0) cc_final: 0.7845 (p0) REVERT: I 104 TYR cc_start: 0.8459 (m-10) cc_final: 0.8005 (m-10) REVERT: L 67 SER cc_start: 0.8084 (t) cc_final: 0.7746 (p) REVERT: L 94 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7775 (t80) REVERT: L 104 LEU cc_start: 0.8701 (tp) cc_final: 0.7896 (tt) REVERT: L 108 ARG cc_start: 0.3053 (mtt180) cc_final: 0.1063 (ptt90) outliers start: 37 outliers final: 26 residues processed: 301 average time/residue: 0.3501 time to fit residues: 145.1680 Evaluate side-chains 301 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 118 LEU 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 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 156 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.090691 restraints weight = 27884.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.093657 restraints weight = 16930.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.095673 restraints weight = 12168.721| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14044 Z= 0.133 Angle : 0.718 9.447 19130 Z= 0.345 Chirality : 0.046 0.174 2205 Planarity : 0.004 0.056 2370 Dihedral : 7.086 56.282 2622 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.26 % Allowed : 18.15 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1644 helix: 1.55 (0.39), residues: 183 sheet: -0.96 (0.20), residues: 651 loop : -0.93 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 597 HIS 0.003 0.001 HIS I 35 PHE 0.016 0.002 PHE I 68 TYR 0.017 0.001 TYR G 115 ARG 0.005 0.000 ARG I 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 15) link_NAG-ASN : angle 2.54342 ( 45) link_ALPHA1-6 : bond 0.00968 ( 3) link_ALPHA1-6 : angle 1.12377 ( 9) link_BETA1-4 : bond 0.00374 ( 15) link_BETA1-4 : angle 1.53444 ( 45) link_ALPHA1-3 : bond 0.00882 ( 6) link_ALPHA1-3 : angle 1.55501 ( 18) hydrogen bonds : bond 0.03020 ( 429) hydrogen bonds : angle 5.86450 ( 1143) SS BOND : bond 0.00311 ( 7) SS BOND : angle 1.23962 ( 14) covalent geometry : bond 0.00298 (13998) covalent geometry : angle 0.70334 (18999) *********************** 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 327 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 1.498 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 229 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: A 235 GLU cc_start: 0.7963 (tt0) cc_final: 0.7508 (tm-30) REVERT: D 552 ASP cc_start: 0.7591 (t0) cc_final: 0.7371 (t0) REVERT: D 587 ARG cc_start: 0.8312 (mtp85) cc_final: 0.8070 (ttm-80) REVERT: D 588 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7841 (mmmt) REVERT: G 43 LYS cc_start: 0.7956 (mmmm) cc_final: 0.7709 (mmmt) REVERT: G 54 ASP cc_start: 0.8184 (p0) cc_final: 0.7761 (p0) REVERT: J 18 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8361 (ttp80) REVERT: J 37 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: J 67 SER cc_start: 0.8137 (t) cc_final: 0.7750 (p) REVERT: J 70 ASP cc_start: 0.8647 (t70) cc_final: 0.8184 (t70) REVERT: J 90 GLN cc_start: 0.8749 (pp30) cc_final: 0.8452 (pp30) REVERT: J 92 LYS cc_start: 0.8934 (tttm) cc_final: 0.8707 (tttm) REVERT: J 108 ARG cc_start: 0.3424 (mtt180) cc_final: 0.1472 (ptt90) REVERT: B 56 LYS cc_start: 0.7303 (mptt) cc_final: 0.7094 (mptt) REVERT: B 117 ASP cc_start: 0.8313 (p0) cc_final: 0.7949 (p0) REVERT: B 235 GLU cc_start: 0.8068 (tt0) cc_final: 0.7613 (tm-30) REVERT: E 587 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7710 (ttm-80) REVERT: H 43 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7535 (mmmt) REVERT: H 54 ASP cc_start: 0.8117 (p0) cc_final: 0.7748 (p0) REVERT: H 57 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8296 (mmmm) REVERT: K 24 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7648 (mmm160) REVERT: K 67 SER cc_start: 0.8113 (t) cc_final: 0.7693 (p) REVERT: K 90 GLN cc_start: 0.8745 (pp30) cc_final: 0.8222 (pp30) REVERT: K 94 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7648 (t80) REVERT: K 108 ARG cc_start: 0.2920 (mtt180) cc_final: 0.0892 (ptt90) REVERT: C 56 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7421 (mptt) REVERT: C 117 ASP cc_start: 0.8357 (p0) cc_final: 0.8111 (p0) REVERT: C 130 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8465 (mmm160) REVERT: C 229 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7385 (pp20) REVERT: C 235 GLU cc_start: 0.8148 (tt0) cc_final: 0.7606 (tm-30) REVERT: F 587 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7931 (ttm-80) REVERT: I 43 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7951 (mmmt) REVERT: I 54 ASP cc_start: 0.8210 (p0) cc_final: 0.7836 (p0) REVERT: I 104 TYR cc_start: 0.8423 (m-10) cc_final: 0.7982 (m-10) REVERT: L 67 SER cc_start: 0.7987 (t) cc_final: 0.7583 (p) REVERT: L 90 GLN cc_start: 0.8754 (pp30) cc_final: 0.8186 (pp30) REVERT: L 94 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7564 (t80) REVERT: L 104 LEU cc_start: 0.8645 (tp) cc_final: 0.7824 (tt) REVERT: L 108 ARG cc_start: 0.2992 (mtt180) cc_final: 0.1007 (ptt90) outliers start: 32 outliers final: 22 residues processed: 315 average time/residue: 0.4437 time to fit residues: 197.7311 Evaluate side-chains 312 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 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 23 CYS 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 27 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 2 optimal weight: 0.0270 chunk 156 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 129 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 109 optimal weight: 0.0670 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.120440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092484 restraints weight = 27732.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.095501 restraints weight = 16722.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097545 restraints weight = 11969.243| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14044 Z= 0.121 Angle : 0.715 10.727 19130 Z= 0.342 Chirality : 0.045 0.168 2205 Planarity : 0.004 0.057 2370 Dihedral : 6.831 55.380 2622 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.84 % Allowed : 18.86 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1644 helix: 1.66 (0.40), residues: 183 sheet: -0.86 (0.20), residues: 651 loop : -0.85 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 597 HIS 0.003 0.001 HIS H 35 PHE 0.027 0.002 PHE D 592 TYR 0.015 0.001 TYR J 96 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 15) link_NAG-ASN : angle 2.48764 ( 45) link_ALPHA1-6 : bond 0.00769 ( 3) link_ALPHA1-6 : angle 1.06464 ( 9) link_BETA1-4 : bond 0.00435 ( 15) link_BETA1-4 : angle 1.49984 ( 45) link_ALPHA1-3 : bond 0.00818 ( 6) link_ALPHA1-3 : angle 1.48216 ( 18) hydrogen bonds : bond 0.02935 ( 429) hydrogen bonds : angle 5.68410 ( 1143) SS BOND : bond 0.00348 ( 7) SS BOND : angle 1.21039 ( 14) covalent geometry : bond 0.00270 (13998) covalent geometry : angle 0.70126 (18999) ********************** 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 : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7221 (mptt) cc_final: 0.6996 (mmtt) REVERT: A 229 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: A 235 GLU cc_start: 0.7951 (tt0) cc_final: 0.7513 (tm-30) REVERT: D 552 ASP cc_start: 0.7591 (t0) cc_final: 0.7368 (t0) REVERT: D 587 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7964 (ttm-80) REVERT: D 588 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7812 (mmmt) REVERT: G 43 LYS cc_start: 0.7922 (mmmm) cc_final: 0.7685 (mmmt) REVERT: G 54 ASP cc_start: 0.8171 (p0) cc_final: 0.7740 (p0) REVERT: G 57 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8349 (mmmm) REVERT: J 5 THR cc_start: 0.9016 (p) cc_final: 0.8775 (t) REVERT: J 18 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8493 (ttp80) REVERT: J 37 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: J 67 SER cc_start: 0.8106 (t) cc_final: 0.7692 (p) REVERT: J 70 ASP cc_start: 0.8601 (t70) cc_final: 0.8187 (t70) REVERT: J 90 GLN cc_start: 0.8759 (pp30) cc_final: 0.8487 (pp30) REVERT: J 108 ARG cc_start: 0.3475 (mtt180) cc_final: 0.1679 (ptt90) REVERT: B 56 LYS cc_start: 0.7269 (mptt) cc_final: 0.6903 (mmtt) REVERT: B 117 ASP cc_start: 0.8284 (p0) cc_final: 0.7921 (p0) REVERT: B 235 GLU cc_start: 0.8051 (tt0) cc_final: 0.7667 (tm-30) REVERT: E 587 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7762 (ttm-80) REVERT: H 34 MET cc_start: 0.8453 (mmm) cc_final: 0.7478 (mmm) REVERT: H 43 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7537 (mmmt) REVERT: H 54 ASP cc_start: 0.8164 (p0) cc_final: 0.7814 (p0) REVERT: H 57 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8310 (mmmm) REVERT: H 83 MET cc_start: 0.7126 (mmm) cc_final: 0.6581 (mmm) REVERT: K 24 ARG cc_start: 0.7861 (mmm160) cc_final: 0.7509 (mmm160) REVERT: K 67 SER cc_start: 0.8108 (t) cc_final: 0.7657 (p) REVERT: K 90 GLN cc_start: 0.8666 (pp30) cc_final: 0.8312 (pp30) REVERT: K 108 ARG cc_start: 0.2931 (mtt180) cc_final: 0.0923 (ptt90) REVERT: C 56 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7375 (mptt) REVERT: C 117 ASP cc_start: 0.8285 (p0) cc_final: 0.8039 (p0) REVERT: C 130 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8437 (mmm160) REVERT: C 229 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: C 235 GLU cc_start: 0.8134 (tt0) cc_final: 0.7677 (tm-30) REVERT: F 587 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7944 (ttm110) REVERT: I 43 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7988 (mmmt) REVERT: I 54 ASP cc_start: 0.8208 (p0) cc_final: 0.7799 (p0) REVERT: I 104 TYR cc_start: 0.8381 (m-10) cc_final: 0.7949 (m-10) REVERT: L 67 SER cc_start: 0.8008 (t) cc_final: 0.7585 (p) REVERT: L 90 GLN cc_start: 0.8689 (pp30) cc_final: 0.8225 (pp30) REVERT: L 104 LEU cc_start: 0.8524 (tp) cc_final: 0.7764 (tt) REVERT: L 108 ARG cc_start: 0.2981 (mtt180) cc_final: 0.1028 (ptt90) outliers start: 26 outliers final: 16 residues processed: 311 average time/residue: 0.4391 time to fit residues: 189.9639 Evaluate side-chains 301 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 282 time to evaluate : 3.101 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 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 I residue 68 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 0.0470 chunk 3 optimal weight: 0.0980 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 chunk 113 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093930 restraints weight = 27805.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096984 restraints weight = 16543.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099086 restraints weight = 11731.030| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14044 Z= 0.120 Angle : 0.733 12.802 19130 Z= 0.351 Chirality : 0.045 0.174 2205 Planarity : 0.004 0.059 2370 Dihedral : 6.619 54.583 2622 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.41 % Allowed : 19.49 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1644 helix: 1.71 (0.39), residues: 183 sheet: -0.56 (0.21), residues: 627 loop : -0.88 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 597 HIS 0.004 0.001 HIS I 35 PHE 0.030 0.002 PHE E 592 TYR 0.021 0.001 TYR J 96 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 15) link_NAG-ASN : angle 2.52729 ( 45) link_ALPHA1-6 : bond 0.00893 ( 3) link_ALPHA1-6 : angle 1.10710 ( 9) link_BETA1-4 : bond 0.00431 ( 15) link_BETA1-4 : angle 1.49219 ( 45) link_ALPHA1-3 : bond 0.00770 ( 6) link_ALPHA1-3 : angle 1.45466 ( 18) hydrogen bonds : bond 0.02902 ( 429) hydrogen bonds : angle 5.56649 ( 1143) SS BOND : bond 0.00325 ( 7) SS BOND : angle 1.07691 ( 14) covalent geometry : bond 0.00262 (13998) covalent geometry : angle 0.71942 (18999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5241.29 seconds wall clock time: 97 minutes 47.97 seconds (5867.97 seconds total)