Starting phenix.real_space_refine on Wed Sep 17 16:14:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9do2_47071/09_2025/9do2_47071.cif Found real_map, /net/cci-nas-00/data/ceres_data/9do2_47071/09_2025/9do2_47071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9do2_47071/09_2025/9do2_47071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9do2_47071/09_2025/9do2_47071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9do2_47071/09_2025/9do2_47071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9do2_47071/09_2025/9do2_47071.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 39 5.16 5 C 5829 2.51 5 N 1536 2.21 5 O 1923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9327 Number of models: 1 Model: "" Number of chains: 23 Chain: "H" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 963 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 797 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2408 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 285} Chain breaks: 1 Chain: "B" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2408 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 285} Chain breaks: 1 Chain: "C" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2142 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 255} Chain breaks: 4 Chain: "D" 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: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" 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: "K" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "P" 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: "Q" 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: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 Time building chain proxies: 2.24, per 1000 atoms: 0.24 Number of scatterers: 9327 At special positions: 0 Unit cell: (93.102, 94.154, 127.818, 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 39 16.00 O 1923 8.00 N 1536 7.00 C 5829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " 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 ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA R 3 " - " MAN R 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " 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 P 1 " - " NAG P 2 " " 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 T 1 " - " NAG T 2 " NAG-ASN " NAG A 601 " - " ASN A 126 " " NAG A 602 " - " ASN A 122 " " NAG A 603 " - " ASN A 158 " " NAG B 601 " - " ASN B 126 " " NAG B 602 " - " ASN B 122 " " NAG B 603 " - " ASN B 158 " " NAG C 601 " - " ASN C 126 " " NAG C 602 " - " ASN C 122 " " NAG D 1 " - " ASN A 133 " " NAG E 1 " - " ASN A 63 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 246 " " NAG I 1 " - " ASN A 285 " " NAG J 1 " - " ASN B 133 " " NAG K 1 " - " ASN B 63 " " NAG M 1 " - " ASN B 165 " " NAG N 1 " - " ASN B 246 " " NAG O 1 " - " ASN B 285 " " NAG P 1 " - " ASN C 133 " " NAG Q 1 " - " ASN C 63 " " NAG R 1 " - " ASN C 165 " " NAG S 1 " - " ASN C 246 " " NAG T 1 " - " ASN C 285 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 265.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 30 sheets defined 16.8% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.721A pdb=" N THR H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 112C through 113 removed outlier: 3.557A pdb=" N PHE H 113 " --> pdb=" O TYR H 112B" (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.763A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.736A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.930A pdb=" N LEU A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 removed outlier: 3.984A pdb=" N GLU A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.741A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY B 78 " --> pdb=" O GLN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 222 through 226 removed outlier: 4.269A pdb=" N ASP B 225 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 424 removed outlier: 4.049A pdb=" N GLU B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.578A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 404 through 425 removed outlier: 3.761A pdb=" N GLU C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.556A pdb=" N LYS H 24 " --> pdb=" O MET H 5 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL H 19 " --> pdb=" O MET H 91 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 77 " --> pdb=" O GLU H 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.939A pdb=" N ARG H 13 " --> pdb=" O SER H 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 51 through 57 removed outlier: 5.468A pdb=" N TRP H 52 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR H 102 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR H 122 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 105 through 107 removed outlier: 6.822A pdb=" N SER H 106 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.059A pdb=" N GLN L 43 " --> pdb=" O TYR L 52 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.625A pdb=" N VAL L 19 " --> pdb=" O ILE L 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.352A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.400A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AB1, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB2, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.139A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB4, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.634A pdb=" N LEU A 243 " --> pdb=" O MET A 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 176 through 184 Processing sheet with id=AB6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB7, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.428A pdb=" N ILE B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 61 removed outlier: 5.916A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.102A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 3.711A pdb=" N SER B 146 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA B 138 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N SER B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 153 Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AC6, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.733A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 58 through 61 removed outlier: 5.755A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.931A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AD1, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.446A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'C' and resid 294 through 295 259 hydrogen bonds defined for protein. 678 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: 1.41 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2882 1.34 - 1.46: 2410 1.46 - 1.58: 4187 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 9529 Sorted by residual: bond pdb=" CA ASP C 53 " pdb=" CB ASP C 53 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.21e-02 6.83e+03 9.05e-01 bond pdb=" CA CYS C 305 " pdb=" C CYS C 305 " ideal model delta sigma weight residual 1.518 1.526 -0.008 9.60e-03 1.09e+04 7.20e-01 bond pdb=" C LEU A 164 " pdb=" N ASN A 165 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.58e-02 4.01e+03 6.75e-01 bond pdb=" CB CYS C 281 " pdb=" SG CYS C 281 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.60e-01 bond pdb=" CB CYS A 281 " pdb=" SG CYS A 281 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.45e-01 ... (remaining 9524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 12433 1.34 - 2.68: 400 2.68 - 4.02: 67 4.02 - 5.36: 19 5.36 - 6.69: 4 Bond angle restraints: 12923 Sorted by residual: angle pdb=" C GLY A 404 " pdb=" N ARG A 405 " pdb=" CA ARG A 405 " ideal model delta sigma weight residual 120.38 124.79 -4.41 1.37e+00 5.33e-01 1.04e+01 angle pdb=" C LEU L 53 " pdb=" N MET L 54 " pdb=" CA MET L 54 " ideal model delta sigma weight residual 121.62 116.77 4.85 1.83e+00 2.99e-01 7.02e+00 angle pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " pdb=" SG CYS C 97 " ideal model delta sigma weight residual 114.40 120.41 -6.01 2.30e+00 1.89e-01 6.83e+00 angle pdb=" C CYS C 97 " pdb=" N TYR C 98 " pdb=" CA TYR C 98 " ideal model delta sigma weight residual 121.80 127.79 -5.99 2.44e+00 1.68e-01 6.03e+00 angle pdb=" N CYS C 305 " pdb=" CA CYS C 305 " pdb=" C CYS C 305 " ideal model delta sigma weight residual 108.14 110.80 -2.66 1.15e+00 7.56e-01 5.37e+00 ... (remaining 12918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5779 17.64 - 35.27: 365 35.27 - 52.91: 96 52.91 - 70.55: 29 70.55 - 88.18: 10 Dihedral angle restraints: 6279 sinusoidal: 3076 harmonic: 3203 Sorted by residual: dihedral pdb=" CA CYS B 305 " pdb=" C CYS B 305 " pdb=" N PRO B 306 " pdb=" CA PRO B 306 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA CYS B 97 " pdb=" CB CYS B 97 " pdb=" SG CYS B 97 " pdb=" SG CYS B 139 " ideal model delta sinusoidal sigma weight residual 79.00 17.54 61.46 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" CA CYS A 97 " pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 139 " ideal model delta sinusoidal sigma weight residual 79.00 18.96 60.04 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 6276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1089 0.041 - 0.082: 297 0.082 - 0.123: 125 0.123 - 0.163: 15 0.163 - 0.204: 7 Chirality restraints: 1533 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.63e+00 chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 1.59e+00 chirality pdb=" C1 MAN R 5 " pdb=" O2 MAN R 4 " pdb=" C2 MAN R 5 " pdb=" O5 MAN R 5 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.55e+00 ... (remaining 1530 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 214 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ILE A 214 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 214 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 215 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 220 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 221 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 214 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO A 215 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.023 5.00e-02 4.00e+02 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 4712 2.97 - 3.45: 8718 3.45 - 3.94: 15123 3.94 - 4.42: 16605 4.42 - 4.90: 28208 Nonbonded interactions: 73366 Sorted by model distance: nonbonded pdb=" O4 NAG F 2 " pdb=" O2 BMA F 3 " model vdw 2.491 2.432 nonbonded pdb=" O4 NAG M 2 " pdb=" O2 BMA M 3 " model vdw 2.513 2.432 nonbonded pdb=" O5 MAN R 5 " pdb=" O6 MAN R 5 " model vdw 2.521 2.432 nonbonded pdb=" C THR C 167 " pdb=" OG1 THR C 167 " model vdw 2.564 2.616 nonbonded pdb=" CB ARG C 224 " pdb=" NE ARG C 224 " model vdw 2.573 2.816 ... (remaining 73361 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 154 or resid 163 through 184 or resid 202 throu \ gh 215 or resid 224 through 602)) selection = (chain 'B' and (resid 44 through 154 or resid 163 through 184 or resid 202 throu \ gh 215 or resid 224 through 602)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'F' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 42.710 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: 0.340 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.350 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9588 Z= 0.119 Angle : 0.615 6.695 13086 Z= 0.302 Chirality : 0.046 0.204 1533 Planarity : 0.004 0.042 1605 Dihedral : 12.846 88.185 4185 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.05 % Allowed : 7.49 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.24), residues: 1087 helix: 1.01 (0.46), residues: 142 sheet: -0.53 (0.32), residues: 227 loop : -0.75 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 150 TYR 0.009 0.001 TYR C 178 PHE 0.010 0.001 PHE C 120 TRP 0.007 0.001 TRP L 107 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9529) covalent geometry : angle 0.58876 (12923) SS BOND : bond 0.00422 ( 14) SS BOND : angle 1.11022 ( 28) hydrogen bonds : bond 0.16045 ( 259) hydrogen bonds : angle 8.84789 ( 678) link_ALPHA1-2 : bond 0.00497 ( 2) link_ALPHA1-2 : angle 2.02731 ( 6) link_ALPHA1-3 : bond 0.00824 ( 1) link_ALPHA1-3 : angle 1.98561 ( 3) link_ALPHA1-6 : bond 0.00380 ( 1) link_ALPHA1-6 : angle 1.82966 ( 3) link_BETA1-4 : bond 0.00490 ( 18) link_BETA1-4 : angle 2.13176 ( 54) link_NAG-ASN : bond 0.00461 ( 23) link_NAG-ASN : angle 1.44510 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7960 (mtt-85) REVERT: A 418 ILE cc_start: 0.7886 (mp) cc_final: 0.7471 (mp) REVERT: B 419 ASP cc_start: 0.7996 (m-30) cc_final: 0.7544 (m-30) REVERT: C 119 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 173 GLN cc_start: 0.8500 (mm-40) cc_final: 0.7676 (tm-30) REVERT: C 229 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7444 (mtp85) REVERT: C 282 ILE cc_start: 0.7763 (tp) cc_final: 0.7520 (mt) REVERT: C 396 GLU cc_start: 0.7878 (tt0) cc_final: 0.7594 (tt0) outliers start: 20 outliers final: 7 residues processed: 131 average time/residue: 0.0915 time to fit residues: 16.6622 Evaluate side-chains 104 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 229 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112AASN L 55 GLN A 394 GLN A 407 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.171475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149133 restraints weight = 14161.290| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.79 r_work: 0.3782 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 9588 Z= 0.279 Angle : 0.746 9.261 13086 Z= 0.373 Chirality : 0.050 0.268 1533 Planarity : 0.005 0.049 1605 Dihedral : 8.374 74.074 2157 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.80 % Allowed : 11.29 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.24), residues: 1087 helix: 0.81 (0.44), residues: 142 sheet: -0.57 (0.32), residues: 234 loop : -0.95 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 224 TYR 0.017 0.002 TYR L 52 PHE 0.016 0.002 PHE A 120 TRP 0.013 0.002 TRP A 180 HIS 0.009 0.002 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00657 ( 9529) covalent geometry : angle 0.71944 (12923) SS BOND : bond 0.00656 ( 14) SS BOND : angle 1.68884 ( 28) hydrogen bonds : bond 0.04528 ( 259) hydrogen bonds : angle 7.41016 ( 678) link_ALPHA1-2 : bond 0.00379 ( 2) link_ALPHA1-2 : angle 1.85247 ( 6) link_ALPHA1-3 : bond 0.01084 ( 1) link_ALPHA1-3 : angle 0.99785 ( 3) link_ALPHA1-6 : bond 0.00471 ( 1) link_ALPHA1-6 : angle 1.69046 ( 3) link_BETA1-4 : bond 0.00374 ( 18) link_BETA1-4 : angle 2.16181 ( 54) link_NAG-ASN : bond 0.00451 ( 23) link_NAG-ASN : angle 1.81013 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8287 (mp) cc_final: 0.7785 (mp) REVERT: B 193 PHE cc_start: 0.7302 (t80) cc_final: 0.7026 (t80) REVERT: C 119 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: C 173 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7757 (tm-30) outliers start: 37 outliers final: 24 residues processed: 134 average time/residue: 0.1086 time to fit residues: 19.7040 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 422 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.173678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151521 restraints weight = 13915.259| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.77 r_work: 0.3812 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9588 Z= 0.141 Angle : 0.620 8.924 13086 Z= 0.307 Chirality : 0.046 0.211 1533 Planarity : 0.005 0.051 1605 Dihedral : 7.316 64.272 2153 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.77 % Allowed : 13.45 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.25), residues: 1087 helix: 1.16 (0.46), residues: 142 sheet: -0.63 (0.32), residues: 235 loop : -0.86 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 75 TYR 0.019 0.001 TYR L 52 PHE 0.013 0.001 PHE C 87 TRP 0.011 0.001 TRP B 421 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9529) covalent geometry : angle 0.59403 (12923) SS BOND : bond 0.00567 ( 14) SS BOND : angle 2.01439 ( 28) hydrogen bonds : bond 0.03433 ( 259) hydrogen bonds : angle 6.71325 ( 678) link_ALPHA1-2 : bond 0.00470 ( 2) link_ALPHA1-2 : angle 1.73982 ( 6) link_ALPHA1-3 : bond 0.01218 ( 1) link_ALPHA1-3 : angle 1.48268 ( 3) link_ALPHA1-6 : bond 0.00772 ( 1) link_ALPHA1-6 : angle 1.80079 ( 3) link_BETA1-4 : bond 0.00397 ( 18) link_BETA1-4 : angle 1.75385 ( 54) link_NAG-ASN : bond 0.00253 ( 23) link_NAG-ASN : angle 1.52119 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8268 (mp) cc_final: 0.7750 (mp) REVERT: B 193 PHE cc_start: 0.7242 (t80) cc_final: 0.7023 (t80) REVERT: B 204 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8314 (p) REVERT: B 419 ASP cc_start: 0.7902 (m-30) cc_final: 0.7606 (m-30) REVERT: C 85 ASP cc_start: 0.7354 (t0) cc_final: 0.7135 (t0) REVERT: C 173 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7759 (tm-30) REVERT: C 414 GLU cc_start: 0.7189 (tp30) cc_final: 0.6920 (mm-30) outliers start: 27 outliers final: 19 residues processed: 125 average time/residue: 0.1056 time to fit residues: 17.9801 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 260 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.0670 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111BASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152560 restraints weight = 14318.232| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.93 r_work: 0.3823 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9588 Z= 0.124 Angle : 0.586 7.285 13086 Z= 0.289 Chirality : 0.045 0.208 1533 Planarity : 0.004 0.048 1605 Dihedral : 6.839 60.019 2150 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.39 % Allowed : 14.17 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.25), residues: 1087 helix: 1.38 (0.46), residues: 142 sheet: -0.58 (0.33), residues: 235 loop : -0.83 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 224 TYR 0.017 0.001 TYR L 52 PHE 0.012 0.001 PHE C 87 TRP 0.010 0.001 TRP B 421 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9529) covalent geometry : angle 0.56185 (12923) SS BOND : bond 0.00402 ( 14) SS BOND : angle 1.66985 ( 28) hydrogen bonds : bond 0.03087 ( 259) hydrogen bonds : angle 6.27212 ( 678) link_ALPHA1-2 : bond 0.00457 ( 2) link_ALPHA1-2 : angle 1.73180 ( 6) link_ALPHA1-3 : bond 0.01193 ( 1) link_ALPHA1-3 : angle 1.81849 ( 3) link_ALPHA1-6 : bond 0.00851 ( 1) link_ALPHA1-6 : angle 1.83089 ( 3) link_BETA1-4 : bond 0.00376 ( 18) link_BETA1-4 : angle 1.63949 ( 54) link_NAG-ASN : bond 0.00252 ( 23) link_NAG-ASN : angle 1.49330 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: A 176 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7665 (ptmt) REVERT: A 418 ILE cc_start: 0.8261 (mp) cc_final: 0.7746 (mp) REVERT: B 193 PHE cc_start: 0.7232 (t80) cc_final: 0.7001 (t80) REVERT: B 419 ASP cc_start: 0.7920 (m-30) cc_final: 0.7629 (m-30) REVERT: C 85 ASP cc_start: 0.7467 (t0) cc_final: 0.7140 (t0) REVERT: C 173 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7715 (tm-30) REVERT: C 208 ARG cc_start: 0.8092 (mpt180) cc_final: 0.7796 (mpt180) REVERT: C 241 ASP cc_start: 0.7389 (t0) cc_final: 0.7099 (t0) REVERT: C 282 ILE cc_start: 0.7949 (tp) cc_final: 0.7636 (mt) REVERT: C 410 GLU cc_start: 0.8116 (pt0) cc_final: 0.7804 (mt-10) REVERT: C 414 GLU cc_start: 0.7193 (tp30) cc_final: 0.6934 (mm-30) outliers start: 33 outliers final: 21 residues processed: 133 average time/residue: 0.1148 time to fit residues: 20.3416 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 422 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.171846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.148731 restraints weight = 14117.370| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.88 r_work: 0.3815 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9588 Z= 0.200 Angle : 0.655 9.113 13086 Z= 0.324 Chirality : 0.047 0.238 1533 Planarity : 0.005 0.048 1605 Dihedral : 6.930 60.361 2146 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.00 % Allowed : 15.09 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.25), residues: 1087 helix: 1.29 (0.45), residues: 142 sheet: -0.65 (0.33), residues: 235 loop : -0.95 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 110 TYR 0.017 0.002 TYR L 52 PHE 0.013 0.001 PHE A 120 TRP 0.015 0.002 TRP B 421 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9529) covalent geometry : angle 0.63006 (12923) SS BOND : bond 0.00748 ( 14) SS BOND : angle 2.02920 ( 28) hydrogen bonds : bond 0.03534 ( 259) hydrogen bonds : angle 6.42891 ( 678) link_ALPHA1-2 : bond 0.00332 ( 2) link_ALPHA1-2 : angle 1.71950 ( 6) link_ALPHA1-3 : bond 0.01294 ( 1) link_ALPHA1-3 : angle 1.47554 ( 3) link_ALPHA1-6 : bond 0.00797 ( 1) link_ALPHA1-6 : angle 1.92427 ( 3) link_BETA1-4 : bond 0.00358 ( 18) link_BETA1-4 : angle 1.70378 ( 54) link_NAG-ASN : bond 0.00292 ( 23) link_NAG-ASN : angle 1.58382 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: A 176 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7714 (ptmt) REVERT: A 201 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7205 (ptt90) REVERT: A 418 ILE cc_start: 0.8293 (mp) cc_final: 0.7774 (mp) REVERT: B 193 PHE cc_start: 0.7266 (t80) cc_final: 0.7054 (t80) REVERT: B 419 ASP cc_start: 0.7918 (m-30) cc_final: 0.7639 (m-30) REVERT: C 85 ASP cc_start: 0.7528 (t0) cc_final: 0.7165 (t0) REVERT: C 173 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7702 (tm-30) REVERT: C 208 ARG cc_start: 0.8103 (mpt180) cc_final: 0.7848 (mpt180) REVERT: C 241 ASP cc_start: 0.7481 (t0) cc_final: 0.7254 (t0) REVERT: C 414 GLU cc_start: 0.7294 (tp30) cc_final: 0.7000 (mm-30) outliers start: 39 outliers final: 26 residues processed: 131 average time/residue: 0.1074 time to fit residues: 19.3488 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 422 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 104 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.173238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.150399 restraints weight = 14149.853| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.87 r_work: 0.3806 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9588 Z= 0.146 Angle : 0.622 9.144 13086 Z= 0.305 Chirality : 0.046 0.213 1533 Planarity : 0.004 0.047 1605 Dihedral : 6.733 59.034 2146 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.70 % Allowed : 16.22 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.25), residues: 1087 helix: 1.41 (0.46), residues: 142 sheet: -0.64 (0.33), residues: 235 loop : -0.95 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 110 TYR 0.017 0.001 TYR L 52 PHE 0.011 0.001 PHE C 87 TRP 0.016 0.001 TRP B 421 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9529) covalent geometry : angle 0.59802 (12923) SS BOND : bond 0.00534 ( 14) SS BOND : angle 2.06632 ( 28) hydrogen bonds : bond 0.03138 ( 259) hydrogen bonds : angle 6.22121 ( 678) link_ALPHA1-2 : bond 0.00387 ( 2) link_ALPHA1-2 : angle 1.75489 ( 6) link_ALPHA1-3 : bond 0.01203 ( 1) link_ALPHA1-3 : angle 1.60676 ( 3) link_ALPHA1-6 : bond 0.00901 ( 1) link_ALPHA1-6 : angle 1.88518 ( 3) link_BETA1-4 : bond 0.00383 ( 18) link_BETA1-4 : angle 1.59586 ( 54) link_NAG-ASN : bond 0.00232 ( 23) link_NAG-ASN : angle 1.48146 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: A 176 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7687 (ptmt) REVERT: A 418 ILE cc_start: 0.8279 (mp) cc_final: 0.7759 (mp) REVERT: B 193 PHE cc_start: 0.7230 (t80) cc_final: 0.7024 (t80) REVERT: B 204 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8300 (p) REVERT: B 419 ASP cc_start: 0.7929 (m-30) cc_final: 0.7653 (m-30) REVERT: C 85 ASP cc_start: 0.7520 (t0) cc_final: 0.7142 (t0) REVERT: C 173 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7654 (tm-30) REVERT: C 414 GLU cc_start: 0.7263 (tp30) cc_final: 0.6983 (mm-30) outliers start: 36 outliers final: 27 residues processed: 133 average time/residue: 0.1082 time to fit residues: 19.6035 Evaluate side-chains 129 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 422 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.172421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.149938 restraints weight = 14079.780| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.83 r_work: 0.3795 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9588 Z= 0.177 Angle : 0.643 8.661 13086 Z= 0.316 Chirality : 0.046 0.231 1533 Planarity : 0.005 0.048 1605 Dihedral : 6.773 56.245 2146 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.70 % Allowed : 16.32 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1087 helix: 1.33 (0.46), residues: 142 sheet: -0.69 (0.33), residues: 235 loop : -1.02 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 110 TYR 0.016 0.002 TYR L 52 PHE 0.012 0.001 PHE A 120 TRP 0.017 0.001 TRP B 421 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9529) covalent geometry : angle 0.61985 (12923) SS BOND : bond 0.00630 ( 14) SS BOND : angle 1.98559 ( 28) hydrogen bonds : bond 0.03267 ( 259) hydrogen bonds : angle 6.26099 ( 678) link_ALPHA1-2 : bond 0.00313 ( 2) link_ALPHA1-2 : angle 1.73977 ( 6) link_ALPHA1-3 : bond 0.01260 ( 1) link_ALPHA1-3 : angle 1.51201 ( 3) link_ALPHA1-6 : bond 0.00891 ( 1) link_ALPHA1-6 : angle 1.89758 ( 3) link_BETA1-4 : bond 0.00364 ( 18) link_BETA1-4 : angle 1.63147 ( 54) link_NAG-ASN : bond 0.00273 ( 23) link_NAG-ASN : angle 1.51640 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: H 53 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7346 (ptm) REVERT: A 123 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: A 176 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7662 (ptmt) REVERT: A 201 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7185 (ptt90) REVERT: A 418 ILE cc_start: 0.8286 (mp) cc_final: 0.7763 (mp) REVERT: B 193 PHE cc_start: 0.7276 (t80) cc_final: 0.7075 (t80) REVERT: B 204 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8298 (p) REVERT: B 295 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6153 (pt0) REVERT: B 419 ASP cc_start: 0.7955 (m-30) cc_final: 0.7689 (m-30) REVERT: C 85 ASP cc_start: 0.7551 (t0) cc_final: 0.7130 (t0) REVERT: C 173 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7621 (tm-30) REVERT: C 208 ARG cc_start: 0.8107 (mpt180) cc_final: 0.7759 (mpt180) REVERT: C 241 ASP cc_start: 0.7492 (t0) cc_final: 0.7182 (t0) REVERT: C 414 GLU cc_start: 0.7329 (tp30) cc_final: 0.7028 (mm-30) outliers start: 36 outliers final: 25 residues processed: 130 average time/residue: 0.1078 time to fit residues: 19.0960 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 422 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.175220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.152252 restraints weight = 14038.293| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.90 r_work: 0.3829 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9588 Z= 0.120 Angle : 0.621 8.567 13086 Z= 0.305 Chirality : 0.046 0.227 1533 Planarity : 0.004 0.047 1605 Dihedral : 6.451 52.385 2146 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.29 % Allowed : 17.25 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.25), residues: 1087 helix: 1.62 (0.46), residues: 142 sheet: -0.63 (0.33), residues: 235 loop : -0.97 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 110 TYR 0.018 0.001 TYR L 52 PHE 0.010 0.001 PHE C 120 TRP 0.018 0.001 TRP B 421 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9529) covalent geometry : angle 0.59558 (12923) SS BOND : bond 0.00575 ( 14) SS BOND : angle 2.42651 ( 28) hydrogen bonds : bond 0.02828 ( 259) hydrogen bonds : angle 5.96645 ( 678) link_ALPHA1-2 : bond 0.00417 ( 2) link_ALPHA1-2 : angle 1.83356 ( 6) link_ALPHA1-3 : bond 0.01182 ( 1) link_ALPHA1-3 : angle 1.75589 ( 3) link_ALPHA1-6 : bond 0.01034 ( 1) link_ALPHA1-6 : angle 1.80163 ( 3) link_BETA1-4 : bond 0.00401 ( 18) link_BETA1-4 : angle 1.51693 ( 54) link_NAG-ASN : bond 0.00222 ( 23) link_NAG-ASN : angle 1.40335 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: H 53 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7232 (ptm) REVERT: H 72 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7210 (tm-30) REVERT: A 123 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: A 176 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7653 (ptmt) REVERT: A 418 ILE cc_start: 0.8263 (mp) cc_final: 0.7728 (mp) REVERT: B 204 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8291 (p) REVERT: B 419 ASP cc_start: 0.7925 (m-30) cc_final: 0.7616 (m-30) REVERT: C 85 ASP cc_start: 0.7525 (t0) cc_final: 0.7098 (t0) REVERT: C 173 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7612 (tm-30) REVERT: C 414 GLU cc_start: 0.7319 (tp30) cc_final: 0.7043 (mm-30) outliers start: 32 outliers final: 22 residues processed: 127 average time/residue: 0.1106 time to fit residues: 19.1715 Evaluate side-chains 124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 260 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 0.0040 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.175265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151806 restraints weight = 14102.534| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.96 r_work: 0.3825 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9588 Z= 0.133 Angle : 0.625 8.380 13086 Z= 0.307 Chirality : 0.046 0.227 1533 Planarity : 0.005 0.047 1605 Dihedral : 6.283 51.006 2143 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.29 % Allowed : 17.15 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.25), residues: 1087 helix: 1.61 (0.46), residues: 142 sheet: -0.60 (0.33), residues: 235 loop : -1.00 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 110 TYR 0.017 0.001 TYR L 52 PHE 0.011 0.001 PHE A 120 TRP 0.020 0.001 TRP B 421 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9529) covalent geometry : angle 0.60083 (12923) SS BOND : bond 0.00578 ( 14) SS BOND : angle 2.27918 ( 28) hydrogen bonds : bond 0.02872 ( 259) hydrogen bonds : angle 5.90381 ( 678) link_ALPHA1-2 : bond 0.00249 ( 2) link_ALPHA1-2 : angle 1.91814 ( 6) link_ALPHA1-3 : bond 0.01162 ( 1) link_ALPHA1-3 : angle 1.75226 ( 3) link_ALPHA1-6 : bond 0.01005 ( 1) link_ALPHA1-6 : angle 1.83281 ( 3) link_BETA1-4 : bond 0.00375 ( 18) link_BETA1-4 : angle 1.52637 ( 54) link_NAG-ASN : bond 0.00217 ( 23) link_NAG-ASN : angle 1.39911 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: H 53 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7230 (ptm) REVERT: H 72 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7245 (tm-30) REVERT: A 123 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: A 176 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7978 (ptmt) REVERT: A 201 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7102 (ptt90) REVERT: A 418 ILE cc_start: 0.8270 (mp) cc_final: 0.7745 (mp) REVERT: B 204 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8303 (p) REVERT: B 419 ASP cc_start: 0.7887 (m-30) cc_final: 0.7615 (m-30) REVERT: C 85 ASP cc_start: 0.7516 (t0) cc_final: 0.7072 (t0) REVERT: C 173 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7580 (tm-30) REVERT: C 208 ARG cc_start: 0.8109 (mpt180) cc_final: 0.7813 (mpt180) REVERT: C 241 ASP cc_start: 0.7457 (t0) cc_final: 0.7248 (t0) REVERT: C 414 GLU cc_start: 0.7318 (tp30) cc_final: 0.7033 (mm-30) outliers start: 32 outliers final: 23 residues processed: 123 average time/residue: 0.1085 time to fit residues: 18.0630 Evaluate side-chains 124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 260 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.175511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.152216 restraints weight = 14129.870| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.96 r_work: 0.3829 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9588 Z= 0.131 Angle : 0.614 8.584 13086 Z= 0.301 Chirality : 0.046 0.232 1533 Planarity : 0.005 0.047 1605 Dihedral : 6.108 48.082 2143 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.18 % Allowed : 17.45 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.25), residues: 1087 helix: 1.70 (0.46), residues: 142 sheet: -0.58 (0.33), residues: 235 loop : -0.99 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 261 TYR 0.018 0.001 TYR C 308 PHE 0.011 0.001 PHE A 120 TRP 0.021 0.001 TRP B 421 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9529) covalent geometry : angle 0.59137 (12923) SS BOND : bond 0.00527 ( 14) SS BOND : angle 2.00239 ( 28) hydrogen bonds : bond 0.02823 ( 259) hydrogen bonds : angle 5.80836 ( 678) link_ALPHA1-2 : bond 0.00303 ( 2) link_ALPHA1-2 : angle 1.86393 ( 6) link_ALPHA1-3 : bond 0.01251 ( 1) link_ALPHA1-3 : angle 1.65858 ( 3) link_ALPHA1-6 : bond 0.01029 ( 1) link_ALPHA1-6 : angle 1.81468 ( 3) link_BETA1-4 : bond 0.00383 ( 18) link_BETA1-4 : angle 1.50666 ( 54) link_NAG-ASN : bond 0.00220 ( 23) link_NAG-ASN : angle 1.40511 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: H 53 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7228 (ptm) REVERT: H 72 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7224 (tm-30) REVERT: A 123 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: A 176 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7611 (ptmt) REVERT: A 201 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7091 (ptt90) REVERT: A 418 ILE cc_start: 0.8280 (mp) cc_final: 0.7768 (mp) REVERT: B 204 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 276 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7766 (mmtm) REVERT: B 419 ASP cc_start: 0.7900 (m-30) cc_final: 0.7631 (m-30) REVERT: C 85 ASP cc_start: 0.7529 (t0) cc_final: 0.7087 (t0) REVERT: C 173 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7558 (tm-30) REVERT: C 208 ARG cc_start: 0.8111 (mpt180) cc_final: 0.7904 (mpt180) REVERT: C 414 GLU cc_start: 0.7335 (tp30) cc_final: 0.7039 (mm-30) outliers start: 31 outliers final: 25 residues processed: 124 average time/residue: 0.1090 time to fit residues: 18.4197 Evaluate side-chains 127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 97 CYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 422 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 69 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.175527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.152961 restraints weight = 14009.674| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.87 r_work: 0.3834 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9588 Z= 0.126 Angle : 0.613 8.929 13086 Z= 0.301 Chirality : 0.045 0.233 1533 Planarity : 0.005 0.047 1605 Dihedral : 6.009 46.637 2143 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.29 % Allowed : 17.56 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.25), residues: 1087 helix: 1.74 (0.45), residues: 142 sheet: -0.58 (0.33), residues: 235 loop : -0.97 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 110 TYR 0.016 0.001 TYR L 52 PHE 0.011 0.001 PHE A 120 TRP 0.019 0.001 TRP B 421 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9529) covalent geometry : angle 0.59309 (12923) SS BOND : bond 0.00499 ( 14) SS BOND : angle 1.68759 ( 28) hydrogen bonds : bond 0.02784 ( 259) hydrogen bonds : angle 5.75045 ( 678) link_ALPHA1-2 : bond 0.00346 ( 2) link_ALPHA1-2 : angle 1.84324 ( 6) link_ALPHA1-3 : bond 0.01113 ( 1) link_ALPHA1-3 : angle 1.63194 ( 3) link_ALPHA1-6 : bond 0.01053 ( 1) link_ALPHA1-6 : angle 1.78804 ( 3) link_BETA1-4 : bond 0.00388 ( 18) link_BETA1-4 : angle 1.48665 ( 54) link_NAG-ASN : bond 0.00226 ( 23) link_NAG-ASN : angle 1.40120 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.23 seconds wall clock time: 48 minutes 52.20 seconds (2932.20 seconds total)