Starting phenix.real_space_refine on Sat Jul 4 06:31:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kod_62473/07_2026/9kod_62473.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kod_62473/07_2026/9kod_62473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kod_62473/07_2026/9kod_62473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kod_62473/07_2026/9kod_62473.map" model { file = "/net/cci-nas-00/data/ceres_data/9kod_62473/07_2026/9kod_62473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kod_62473/07_2026/9kod_62473.cif" } resolution = 2.95 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= 0.113 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 128 5.16 5 C 12020 2.51 5 N 3256 2.21 5 O 3736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19148 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2984 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2984 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2984 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2984 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "H" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "J" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.68, per 1000 atoms: 0.19 Number of scatterers: 19148 At special positions: 0 Unit cell: (103.79, 127.07, 126.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 128 16.00 O 3736 8.00 N 3256 7.00 C 12020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.08 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.02 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.08 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.05 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.02 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.06 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.02 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.05 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.04 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.02 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.02 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.08 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.05 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 NAG-ASN " NAG A 501 " - " ASN A 146 " " NAG A 502 " - " ASN A 235 " " NAG B 501 " - " ASN B 146 " " NAG B 502 " - " ASN B 235 " " NAG C 501 " - " ASN C 146 " " NAG C 502 " - " ASN C 235 " " NAG D 501 " - " ASN D 146 " " NAG D 502 " - " ASN D 235 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 713.3 milliseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 52 sheets defined 4.4% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.528A pdb=" N ASN A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.531A pdb=" N ASN B 146 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.516A pdb=" N ASN C 146 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.520A pdb=" N ASN D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 80 through 84 removed outlier: 4.062A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.569A pdb=" N THR G 91 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 4.062A pdb=" N PHE H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.569A pdb=" N THR I 91 " --> pdb=" O VAL I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 removed outlier: 4.062A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.570A pdb=" N THR K 91 " --> pdb=" O VAL K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.682A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.489A pdb=" N SER A 444 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.953A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 157 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 6.224A pdb=" N TYR A 208 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 6.706A pdb=" N GLU A 259 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.431A pdb=" N GLU A 278 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A 293 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 353 removed outlier: 4.559A pdb=" N PHE A 349 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 360 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER A 369 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU A 395 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.489A pdb=" N SER B 444 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.954A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 157 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 185 removed outlier: 6.224A pdb=" N TYR B 208 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.707A pdb=" N GLU B 259 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 277 through 284 removed outlier: 5.431A pdb=" N GLU B 278 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG B 293 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 349 through 353 removed outlier: 4.559A pdb=" N PHE B 349 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 360 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER B 369 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU B 395 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.489A pdb=" N SER C 444 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.954A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 157 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 180 through 185 removed outlier: 6.225A pdb=" N TYR C 208 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AC1, first strand: chain 'C' and resid 224 through 225 removed outlier: 6.705A pdb=" N GLU C 259 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 277 through 284 removed outlier: 5.431A pdb=" N GLU C 278 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG C 293 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 349 through 353 removed outlier: 4.558A pdb=" N PHE C 349 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 360 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER C 369 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU C 395 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.489A pdb=" N SER D 444 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.954A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 180 through 185 removed outlier: 6.224A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AC8, first strand: chain 'D' and resid 224 through 225 removed outlier: 6.706A pdb=" N GLU D 259 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 277 through 284 removed outlier: 5.431A pdb=" N GLU D 278 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG D 293 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 349 through 353 removed outlier: 4.559A pdb=" N PHE D 349 " --> pdb=" O GLY D 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY D 360 " --> pdb=" O PHE D 349 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER D 369 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLU D 395 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 389 " --> pdb=" O TRP D 375 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.827A pdb=" N MET E 34 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N HIS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.581A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 54 through 55 removed outlier: 6.490A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.826A pdb=" N MET G 34 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AE2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.581A pdb=" N GLU H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 54 through 55 removed outlier: 6.490A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AE6, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.825A pdb=" N MET I 34 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AE8, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.581A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 54 through 55 removed outlier: 6.490A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU J 34 " --> pdb=" O ASP J 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.826A pdb=" N MET K 34 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N HIS K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.581A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.485A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU L 34 " --> pdb=" O ASP L 50 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3141 1.30 - 1.44: 5811 1.44 - 1.57: 10524 1.57 - 1.71: 0 1.71 - 1.84: 172 Bond restraints: 19648 Sorted by residual: bond pdb=" CA SER D 95 " pdb=" CB SER D 95 " ideal model delta sigma weight residual 1.533 1.429 0.104 1.60e-02 3.91e+03 4.20e+01 bond pdb=" CA SER D 336 " pdb=" CB SER D 336 " ideal model delta sigma weight residual 1.536 1.458 0.079 1.23e-02 6.61e+03 4.08e+01 bond pdb=" CA SER A 385 " pdb=" CB SER A 385 " ideal model delta sigma weight residual 1.538 1.457 0.081 1.35e-02 5.49e+03 3.61e+01 bond pdb=" C PRO D 93 " pdb=" O PRO D 93 " ideal model delta sigma weight residual 1.233 1.168 0.065 1.13e-02 7.83e+03 3.32e+01 bond pdb=" CA SER A 336 " pdb=" CB SER A 336 " ideal model delta sigma weight residual 1.538 1.466 0.072 1.29e-02 6.01e+03 3.11e+01 ... (remaining 19643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 25722 2.87 - 5.73: 868 5.73 - 8.60: 78 8.60 - 11.46: 15 11.46 - 14.33: 9 Bond angle restraints: 26692 Sorted by residual: angle pdb=" N ASN F 32 " pdb=" CA ASN F 32 " pdb=" C ASN F 32 " ideal model delta sigma weight residual 112.93 99.47 13.46 1.12e+00 7.97e-01 1.44e+02 angle pdb=" N ASN J 32 " pdb=" CA ASN J 32 " pdb=" C ASN J 32 " ideal model delta sigma weight residual 113.21 101.80 11.41 1.15e+00 7.56e-01 9.85e+01 angle pdb=" CA PRO B 431 " pdb=" N PRO B 431 " pdb=" CD PRO B 431 " ideal model delta sigma weight residual 111.50 98.19 13.31 1.40e+00 5.10e-01 9.04e+01 angle pdb=" N ASN L 32 " pdb=" CA ASN L 32 " pdb=" C ASN L 32 " ideal model delta sigma weight residual 112.92 101.35 11.57 1.23e+00 6.61e-01 8.85e+01 angle pdb=" CA PRO C 431 " pdb=" N PRO C 431 " pdb=" CD PRO C 431 " ideal model delta sigma weight residual 111.50 98.56 12.94 1.40e+00 5.10e-01 8.55e+01 ... (remaining 26687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 10570 17.22 - 34.44: 834 34.44 - 51.66: 158 51.66 - 68.88: 51 68.88 - 86.10: 7 Dihedral angle restraints: 11620 sinusoidal: 4640 harmonic: 6980 Sorted by residual: dihedral pdb=" CA ARG D 430 " pdb=" C ARG D 430 " pdb=" N PRO D 431 " pdb=" CA PRO D 431 " ideal model delta harmonic sigma weight residual 0.00 36.15 -36.15 0 5.00e+00 4.00e-02 5.23e+01 dihedral pdb=" CA ARG A 430 " pdb=" C ARG A 430 " pdb=" N PRO A 431 " pdb=" CA PRO A 431 " ideal model delta harmonic sigma weight residual 0.00 35.37 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" C CYS A 92 " pdb=" N CYS A 92 " pdb=" CA CYS A 92 " pdb=" CB CYS A 92 " ideal model delta harmonic sigma weight residual -122.60 -106.78 -15.82 0 2.50e+00 1.60e-01 4.01e+01 ... (remaining 11617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2461 0.098 - 0.196: 315 0.196 - 0.294: 51 0.294 - 0.392: 4 0.392 - 0.489: 5 Chirality restraints: 2836 Sorted by residual: chirality pdb=" CA THR F 54 " pdb=" N THR F 54 " pdb=" C THR F 54 " pdb=" CB THR F 54 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA GLU D 382 " pdb=" N GLU D 382 " pdb=" C GLU D 382 " pdb=" CB GLU D 382 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA GLU A 382 " pdb=" N GLU A 382 " pdb=" C GLU A 382 " pdb=" CB GLU A 382 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 2833 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 502 " 0.327 2.00e-02 2.50e+03 2.82e-01 9.94e+02 pdb=" C7 NAG D 502 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG D 502 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG D 502 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG D 502 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " 0.239 2.00e-02 2.50e+03 2.03e-01 5.16e+02 pdb=" C7 NAG C 502 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " -0.348 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 502 " -0.221 2.00e-02 2.50e+03 1.83e-01 4.17e+02 pdb=" C7 NAG A 502 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG A 502 " -0.154 2.00e-02 2.50e+03 pdb=" N2 NAG A 502 " 0.301 2.00e-02 2.50e+03 pdb=" O7 NAG A 502 " 0.019 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 50 2.30 - 2.95: 8999 2.95 - 3.60: 25353 3.60 - 4.25: 47645 4.25 - 4.90: 83636 Nonbonded interactions: 165683 Sorted by model distance: nonbonded pdb=" OD2 ASP A 384 " pdb="CA CA A 504 " model vdw 1.647 3.250 nonbonded pdb=" O TYR D 344 " pdb="CA CA D 503 " model vdw 1.688 3.250 nonbonded pdb=" O TYR A 344 " pdb="CA CA A 503 " model vdw 1.727 3.250 nonbonded pdb=" O TYR B 344 " pdb="CA CA B 503 " model vdw 1.858 3.250 nonbonded pdb=" O TYR C 344 " pdb="CA CA C 503 " model vdw 1.971 3.250 ... (remaining 165678 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 1.870 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.210 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.009 0.104 19696 Z= 0.509 Angle : 1.167 14.328 26796 Z= 0.745 Chirality : 0.070 0.489 2836 Planarity : 0.010 0.282 3448 Dihedral : 13.087 86.103 7084 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.17), residues: 2444 helix: -1.46 (1.03), residues: 24 sheet: -0.26 (0.17), residues: 948 loop : -0.91 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 103 TYR 0.032 0.003 TYR K 32 PHE 0.018 0.003 PHE A 406 TRP 0.021 0.002 TRP C 179 HIS 0.006 0.002 HIS F 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00879 / 0.51 (19648) covalent geometry : angle 1.13619 / 0.74 (26692) SS BOND : bond 0.01695 / 0.93 ( 40) SS BOND : angle 4.01367 / 2.58 ( 80) hydrogen bonds : bond 0.19816 / 13.50 ( 669) hydrogen bonds : angle 9.17285 / 6.63 ( 1737) link_NAG-ASN : bond 0.01384 / 0.80 ( 8) link_NAG-ASN : angle 5.65811 / 3.70 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8253 (mmt90) cc_final: 0.8034 (mmm-85) REVERT: A 269 MET cc_start: 0.8388 (mtp) cc_final: 0.8021 (mtp) REVERT: B 338 MET cc_start: 0.8360 (tpt) cc_final: 0.8099 (tpt) REVERT: B 382 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7102 (mm-30) REVERT: C 88 ASN cc_start: 0.7314 (t0) cc_final: 0.6844 (p0) REVERT: D 83 VAL cc_start: 0.4818 (OUTLIER) cc_final: 0.4523 (p) REVERT: D 248 ASN cc_start: 0.7846 (p0) cc_final: 0.7565 (m-40) REVERT: D 269 MET cc_start: 0.8440 (mtp) cc_final: 0.8211 (mtp) REVERT: D 398 ASP cc_start: 0.7781 (m-30) cc_final: 0.7526 (m-30) REVERT: F 73 THR cc_start: 0.8772 (m) cc_final: 0.8549 (p) outliers start: 2 outliers final: 0 residues processed: 340 average time/residue: 0.3962 time to fit residues: 157.8425 Evaluate side-chains 220 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN B 88 ASN B 171 ASN B 227 GLN C 341 ASN E 35 ASN E 39 GLN G 35 ASN H 91 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 HIS ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120663 restraints weight = 20212.819| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.67 r_work: 0.2961 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 19696 Z= 0.134 Angle : 0.648 12.779 26796 Z= 0.343 Chirality : 0.047 0.358 2836 Planarity : 0.004 0.051 3448 Dihedral : 5.526 38.583 2853 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.40 % Allowed : 8.93 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2444 helix: -0.32 (1.18), residues: 24 sheet: 0.00 (0.16), residues: 980 loop : -0.48 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 103 TYR 0.021 0.001 TYR A 402 PHE 0.019 0.002 PHE D 121 TRP 0.017 0.001 TRP B 179 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (19648) covalent geometry : angle 0.63089 / 0.34 (26692) SS BOND : bond 0.00476 / 0.26 ( 40) SS BOND : angle 2.10926 / 1.44 ( 80) hydrogen bonds : bond 0.04039 / 2.81 ( 669) hydrogen bonds : angle 6.80495 / 4.82 ( 1737) link_NAG-ASN : bond 0.00380 / 0.21 ( 8) link_NAG-ASN : angle 3.26106 / 2.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8371 (mmt90) cc_final: 0.7659 (mmm160) REVERT: A 247 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.8047 (m) REVERT: A 269 MET cc_start: 0.8589 (mtp) cc_final: 0.8229 (mtp) REVERT: B 235 ASN cc_start: 0.8612 (t0) cc_final: 0.8240 (t0) REVERT: B 382 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7514 (mm-30) REVERT: B 418 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7971 (mmt) REVERT: C 118 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8431 (ttp-170) REVERT: D 83 VAL cc_start: 0.4289 (OUTLIER) cc_final: 0.3929 (p) REVERT: D 118 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8492 (ttt-90) REVERT: D 248 ASN cc_start: 0.7901 (p0) cc_final: 0.7505 (m-40) REVERT: D 398 ASP cc_start: 0.8309 (m-30) cc_final: 0.7965 (m-30) REVERT: E 19 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7590 (ttp-170) REVERT: G 19 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8123 (ttm170) REVERT: G 25 SER cc_start: 0.8991 (t) cc_final: 0.8389 (m) REVERT: J 62 ARG cc_start: 0.7496 (ttp-110) cc_final: 0.7231 (ttp-110) REVERT: K 33 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: K 76 LYS cc_start: 0.7524 (ttmt) cc_final: 0.7066 (tttm) REVERT: L 75 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7502 (t) outliers start: 50 outliers final: 15 residues processed: 277 average time/residue: 0.4034 time to fit residues: 130.5943 Evaluate side-chains 232 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 119 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 210 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN B 88 ASN D 227 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN F 38 GLN G 35 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121527 restraints weight = 20377.087| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.57 r_work: 0.2952 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 19696 Z= 0.122 Angle : 0.598 14.914 26796 Z= 0.315 Chirality : 0.045 0.211 2836 Planarity : 0.004 0.042 3448 Dihedral : 5.324 39.141 2853 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.92 % Allowed : 11.28 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2444 helix: -0.39 (1.12), residues: 24 sheet: 0.20 (0.16), residues: 980 loop : -0.33 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 103 TYR 0.020 0.001 TYR A 402 PHE 0.016 0.001 PHE A 121 TRP 0.016 0.001 TRP B 179 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (19648) covalent geometry : angle 0.58706 / 0.31 (26692) SS BOND : bond 0.00526 / 0.30 ( 40) SS BOND : angle 1.57910 / 1.06 ( 80) hydrogen bonds : bond 0.03540 / 2.47 ( 669) hydrogen bonds : angle 6.31308 / 4.46 ( 1737) link_NAG-ASN : bond 0.00176 / 0.10 ( 8) link_NAG-ASN : angle 2.86296 / 1.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8354 (mmt90) cc_final: 0.7724 (mmm-85) REVERT: A 247 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8181 (m) REVERT: A 269 MET cc_start: 0.8686 (mtp) cc_final: 0.8306 (mtp) REVERT: A 309 ASN cc_start: 0.8848 (m-40) cc_final: 0.8503 (t0) REVERT: A 388 SER cc_start: 0.8945 (t) cc_final: 0.8707 (m) REVERT: B 235 ASN cc_start: 0.8495 (t0) cc_final: 0.8163 (t0) REVERT: B 382 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 418 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7687 (mmt) REVERT: C 284 ASP cc_start: 0.7581 (t0) cc_final: 0.6412 (p0) REVERT: C 392 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: D 83 VAL cc_start: 0.4066 (OUTLIER) cc_final: 0.3763 (p) REVERT: D 248 ASN cc_start: 0.7936 (p0) cc_final: 0.7607 (m-40) REVERT: D 398 ASP cc_start: 0.8306 (m-30) cc_final: 0.7973 (m-30) REVERT: E 19 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7820 (ttt-90) REVERT: E 110 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: G 19 ARG cc_start: 0.8634 (ttt180) cc_final: 0.8273 (ttm170) REVERT: G 25 SER cc_start: 0.8985 (t) cc_final: 0.8396 (m) REVERT: K 33 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7034 (mm-30) REVERT: K 76 LYS cc_start: 0.7537 (ttmt) cc_final: 0.7060 (tttt) REVERT: L 75 THR cc_start: 0.7440 (OUTLIER) cc_final: 0.7173 (t) outliers start: 40 outliers final: 16 residues processed: 253 average time/residue: 0.4183 time to fit residues: 123.8777 Evaluate side-chains 233 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 15 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 180 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 235 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN B 227 GLN C 341 ASN E 35 ASN F 38 GLN F 91 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121297 restraints weight = 19967.116| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.55 r_work: 0.2833 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 19696 Z= 0.182 Angle : 0.644 17.980 26796 Z= 0.338 Chirality : 0.047 0.300 2836 Planarity : 0.004 0.039 3448 Dihedral : 5.454 41.180 2853 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.50 % Allowed : 11.95 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2444 helix: -0.73 (1.04), residues: 24 sheet: 0.27 (0.17), residues: 936 loop : -0.33 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 46 TYR 0.021 0.002 TYR B 402 PHE 0.022 0.002 PHE D 121 TRP 0.018 0.002 TRP B 179 HIS 0.009 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (19648) covalent geometry : angle 0.63149 / 0.33 (26692) SS BOND : bond 0.00660 / 0.37 ( 40) SS BOND : angle 1.81211 / 1.23 ( 80) hydrogen bonds : bond 0.03862 / 2.69 ( 669) hydrogen bonds : angle 6.27368 / 4.44 ( 1737) link_NAG-ASN : bond 0.00259 / 0.16 ( 8) link_NAG-ASN : angle 2.94459 / 1.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8515 (mmt90) cc_final: 0.7747 (mmm-85) REVERT: A 247 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8190 (m) REVERT: A 269 MET cc_start: 0.8767 (mtp) cc_final: 0.8413 (mtp) REVERT: A 309 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8414 (t0) REVERT: B 235 ASN cc_start: 0.8629 (t0) cc_final: 0.8268 (t0) REVERT: B 311 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: B 382 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7532 (mm-30) REVERT: C 309 ASN cc_start: 0.8073 (t0) cc_final: 0.7384 (m110) REVERT: C 392 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: D 83 VAL cc_start: 0.4282 (OUTLIER) cc_final: 0.3989 (p) REVERT: D 398 ASP cc_start: 0.8388 (m-30) cc_final: 0.8039 (m-30) REVERT: E 19 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7792 (ttt-90) REVERT: E 110 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8081 (mtm) REVERT: G 25 SER cc_start: 0.8943 (t) cc_final: 0.8340 (m) REVERT: J 88 TYR cc_start: 0.8721 (m-80) cc_final: 0.8363 (m-80) REVERT: K 33 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: K 70 MET cc_start: 0.8586 (ttt) cc_final: 0.8184 (ttt) REVERT: K 76 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7112 (tttt) REVERT: L 75 THR cc_start: 0.7356 (OUTLIER) cc_final: 0.7118 (t) outliers start: 52 outliers final: 23 residues processed: 251 average time/residue: 0.4089 time to fit residues: 119.8435 Evaluate side-chains 236 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 174 optimal weight: 10.0000 chunk 229 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 239 optimal weight: 0.2980 chunk 194 optimal weight: 8.9990 chunk 197 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN B 409 HIS C 341 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 35 ASN ** 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 = 0.3795 r_free = 0.3795 target = 0.155145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122627 restraints weight = 19859.259| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.50 r_work: 0.2850 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 19696 Z= 0.156 Angle : 0.609 17.473 26796 Z= 0.319 Chirality : 0.046 0.267 2836 Planarity : 0.004 0.037 3448 Dihedral : 5.314 45.145 2853 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.21 % Allowed : 12.38 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2444 helix: -0.61 (1.04), residues: 24 sheet: 0.30 (0.17), residues: 932 loop : -0.29 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 293 TYR 0.015 0.002 TYR A 402 PHE 0.019 0.002 PHE A 121 TRP 0.019 0.001 TRP A 179 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (19648) covalent geometry : angle 0.59708 / 0.32 (26692) SS BOND : bond 0.00584 / 0.30 ( 40) SS BOND : angle 1.75038 / 1.15 ( 80) hydrogen bonds : bond 0.03550 / 2.47 ( 669) hydrogen bonds : angle 6.13191 / 4.33 ( 1737) link_NAG-ASN : bond 0.00229 / 0.15 ( 8) link_NAG-ASN : angle 2.76399 / 1.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8516 (mmt90) cc_final: 0.7727 (mmm160) REVERT: A 247 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8206 (m) REVERT: A 269 MET cc_start: 0.8751 (mtp) cc_final: 0.8404 (mtp) REVERT: A 295 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8701 (t0) REVERT: A 309 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8371 (t0) REVERT: A 388 SER cc_start: 0.8965 (t) cc_final: 0.8726 (m) REVERT: B 311 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: B 382 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 309 ASN cc_start: 0.8032 (t0) cc_final: 0.7309 (m110) REVERT: C 392 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: D 382 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: D 398 ASP cc_start: 0.8373 (m-30) cc_final: 0.8062 (m-30) REVERT: E 19 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7762 (ttt-90) REVERT: E 110 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8028 (mtm) REVERT: G 25 SER cc_start: 0.8945 (t) cc_final: 0.8356 (m) REVERT: G 67 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7492 (ttp80) REVERT: K 33 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7084 (mm-30) REVERT: K 76 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7088 (tttt) REVERT: L 75 THR cc_start: 0.7215 (OUTLIER) cc_final: 0.6988 (t) outliers start: 46 outliers final: 22 residues processed: 249 average time/residue: 0.4066 time to fit residues: 118.4666 Evaluate side-chains 227 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN C 227 GLN C 341 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 35 ASN ** 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 = 0.3824 r_free = 0.3824 target = 0.157622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125237 restraints weight = 19703.645| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.47 r_work: 0.2889 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 19696 Z= 0.112 Angle : 0.571 16.413 26796 Z= 0.300 Chirality : 0.045 0.246 2836 Planarity : 0.004 0.036 3448 Dihedral : 5.079 44.106 2852 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.06 % Allowed : 13.44 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2444 helix: -0.51 (1.02), residues: 24 sheet: 0.33 (0.17), residues: 932 loop : -0.18 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 103 TYR 0.011 0.001 TYR J 88 PHE 0.016 0.001 PHE A 121 TRP 0.016 0.001 TRP A 179 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (19648) covalent geometry : angle 0.55984 / 0.30 (26692) SS BOND : bond 0.00516 / 0.28 ( 40) SS BOND : angle 1.57897 / 1.03 ( 80) hydrogen bonds : bond 0.03214 / 2.24 ( 669) hydrogen bonds : angle 5.92715 / 4.17 ( 1737) link_NAG-ASN : bond 0.00158 / 0.10 ( 8) link_NAG-ASN : angle 2.56116 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8317 (pt0) cc_final: 0.7927 (pp20) REVERT: A 220 ARG cc_start: 0.8488 (mmt90) cc_final: 0.7954 (mmt90) REVERT: A 247 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.8072 (m) REVERT: A 269 MET cc_start: 0.8726 (mtp) cc_final: 0.8381 (mtp) REVERT: A 309 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8395 (t0) REVERT: A 318 CYS cc_start: 0.8410 (m) cc_final: 0.8103 (m) REVERT: B 235 ASN cc_start: 0.8610 (t0) cc_final: 0.8265 (t0) REVERT: B 311 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: B 382 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7580 (mm-30) REVERT: C 284 ASP cc_start: 0.7790 (t70) cc_final: 0.6532 (p0) REVERT: C 309 ASN cc_start: 0.8016 (t0) cc_final: 0.7274 (m110) REVERT: C 392 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: D 83 VAL cc_start: 0.4251 (OUTLIER) cc_final: 0.3986 (p) REVERT: D 398 ASP cc_start: 0.8318 (m-30) cc_final: 0.8008 (m-30) REVERT: E 19 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7899 (ttt-90) REVERT: E 110 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7749 (mtm) REVERT: G 25 SER cc_start: 0.8858 (t) cc_final: 0.8294 (m) REVERT: G 67 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7526 (ttp80) REVERT: I 104 ASP cc_start: 0.8652 (t0) cc_final: 0.8215 (t0) REVERT: K 32 TYR cc_start: 0.9073 (m-80) cc_final: 0.8755 (m-80) REVERT: K 33 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: K 76 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7130 (tttt) outliers start: 43 outliers final: 20 residues processed: 244 average time/residue: 0.4293 time to fit residues: 123.0763 Evaluate side-chains 233 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 76 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 230 optimal weight: 0.0980 chunk 236 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN C 297 HIS C 341 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 35 ASN ** 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 = 0.3781 r_free = 0.3781 target = 0.153824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121070 restraints weight = 19822.381| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.52 r_work: 0.3127 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 19696 Z= 0.206 Angle : 0.647 17.266 26796 Z= 0.338 Chirality : 0.048 0.284 2836 Planarity : 0.004 0.038 3448 Dihedral : 5.501 53.942 2852 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.21 % Allowed : 13.87 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2444 helix: -0.74 (1.01), residues: 24 sheet: 0.27 (0.17), residues: 940 loop : -0.29 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 103 TYR 0.015 0.002 TYR I 95 PHE 0.025 0.002 PHE D 121 TRP 0.019 0.002 TRP A 179 HIS 0.009 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (19648) covalent geometry : angle 0.63529 / 0.33 (26692) SS BOND : bond 0.00609 / 0.35 ( 40) SS BOND : angle 1.80003 / 1.21 ( 80) hydrogen bonds : bond 0.03851 / 2.68 ( 669) hydrogen bonds : angle 6.17284 / 4.36 ( 1737) link_NAG-ASN : bond 0.00316 / 0.20 ( 8) link_NAG-ASN : angle 2.87706 / 1.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8335 (pt0) cc_final: 0.7917 (pp20) REVERT: A 220 ARG cc_start: 0.8600 (mmt90) cc_final: 0.8113 (mmt90) REVERT: A 269 MET cc_start: 0.8739 (mtp) cc_final: 0.8395 (mtp) REVERT: A 309 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8389 (t0) REVERT: B 235 ASN cc_start: 0.8703 (t0) cc_final: 0.8349 (t0) REVERT: B 382 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7694 (mm-30) REVERT: C 220 ARG cc_start: 0.8256 (mmt90) cc_final: 0.7998 (mmt-90) REVERT: C 309 ASN cc_start: 0.8177 (t0) cc_final: 0.7465 (m110) REVERT: C 392 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: D 83 VAL cc_start: 0.4486 (OUTLIER) cc_final: 0.4116 (p) REVERT: D 398 ASP cc_start: 0.8341 (m-30) cc_final: 0.8077 (m-30) REVERT: E 110 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8019 (mtm) REVERT: E 115 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7891 (mm-40) REVERT: G 25 SER cc_start: 0.9024 (t) cc_final: 0.8491 (m) REVERT: G 67 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7984 (ttp80) REVERT: K 33 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: K 76 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7321 (tttt) outliers start: 46 outliers final: 24 residues processed: 234 average time/residue: 0.4103 time to fit residues: 113.0268 Evaluate side-chains 233 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 76 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN C 297 HIS C 341 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN I 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122310 restraints weight = 19767.210| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.47 r_work: 0.2835 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 19696 Z= 0.178 Angle : 0.623 17.126 26796 Z= 0.326 Chirality : 0.047 0.277 2836 Planarity : 0.004 0.039 3448 Dihedral : 5.488 60.808 2852 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.16 % Allowed : 14.25 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2444 helix: -0.66 (1.02), residues: 24 sheet: 0.27 (0.17), residues: 940 loop : -0.30 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.014 0.002 TYR I 95 PHE 0.023 0.002 PHE D 121 TRP 0.020 0.002 TRP A 179 HIS 0.007 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (19648) covalent geometry : angle 0.61130 / 0.32 (26692) SS BOND : bond 0.00566 / 0.32 ( 40) SS BOND : angle 1.67292 / 1.13 ( 80) hydrogen bonds : bond 0.03640 / 2.53 ( 669) hydrogen bonds : angle 6.11203 / 4.31 ( 1737) link_NAG-ASN : bond 0.00274 / 0.18 ( 8) link_NAG-ASN : angle 2.78079 / 1.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8281 (pt0) cc_final: 0.7842 (pp20) REVERT: A 220 ARG cc_start: 0.8490 (mmt90) cc_final: 0.7926 (mmt90) REVERT: A 269 MET cc_start: 0.8702 (mtp) cc_final: 0.8366 (mtp) REVERT: A 309 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8354 (t0) REVERT: B 235 ASN cc_start: 0.8697 (t0) cc_final: 0.8335 (t0) REVERT: B 311 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: B 382 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7557 (mm-30) REVERT: C 220 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7833 (mmt-90) REVERT: C 309 ASN cc_start: 0.8111 (t0) cc_final: 0.7349 (m110) REVERT: C 392 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: D 83 VAL cc_start: 0.4166 (OUTLIER) cc_final: 0.3796 (p) REVERT: D 398 ASP cc_start: 0.8361 (m-30) cc_final: 0.8077 (m-30) REVERT: E 110 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7971 (mtm) REVERT: E 115 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7926 (mm-40) REVERT: G 25 SER cc_start: 0.8923 (t) cc_final: 0.8361 (m) REVERT: G 67 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7854 (ttp80) REVERT: H 11 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6179 (tt) REVERT: I 104 ASP cc_start: 0.8546 (t0) cc_final: 0.8303 (t0) REVERT: J 49 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8153 (mt) REVERT: K 33 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: K 76 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7095 (tttt) outliers start: 45 outliers final: 27 residues processed: 233 average time/residue: 0.3927 time to fit residues: 107.5948 Evaluate side-chains 239 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 76 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN C 297 HIS C 341 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120259 restraints weight = 19900.496| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.60 r_work: 0.2823 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 19696 Z= 0.187 Angle : 0.632 17.179 26796 Z= 0.331 Chirality : 0.047 0.279 2836 Planarity : 0.004 0.039 3448 Dihedral : 5.661 67.799 2852 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.21 % Allowed : 14.30 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2444 helix: -0.71 (1.02), residues: 24 sheet: 0.26 (0.17), residues: 940 loop : -0.32 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.014 0.002 TYR D 344 PHE 0.024 0.002 PHE D 121 TRP 0.020 0.002 TRP B 179 HIS 0.008 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (19648) covalent geometry : angle 0.62088 / 0.33 (26692) SS BOND : bond 0.00586 / 0.33 ( 40) SS BOND : angle 1.71499 / 1.16 ( 80) hydrogen bonds : bond 0.03710 / 2.58 ( 669) hydrogen bonds : angle 6.13727 / 4.33 ( 1737) link_NAG-ASN : bond 0.00296 / 0.20 ( 8) link_NAG-ASN : angle 2.82830 / 1.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8295 (pt0) cc_final: 0.8072 (pt0) REVERT: A 220 ARG cc_start: 0.8508 (mmt90) cc_final: 0.7927 (mmt90) REVERT: A 269 MET cc_start: 0.8697 (mtp) cc_final: 0.8357 (mtp) REVERT: A 309 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8354 (t0) REVERT: B 235 ASN cc_start: 0.8707 (t0) cc_final: 0.8352 (t0) REVERT: B 311 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: B 382 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7573 (mm-30) REVERT: C 309 ASN cc_start: 0.8101 (t0) cc_final: 0.7340 (m110) REVERT: C 392 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: D 83 VAL cc_start: 0.4303 (OUTLIER) cc_final: 0.3907 (p) REVERT: D 103 ASP cc_start: 0.8319 (p0) cc_final: 0.8109 (p0) REVERT: D 118 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7228 (ttt-90) REVERT: D 398 ASP cc_start: 0.8347 (m-30) cc_final: 0.8067 (m-30) REVERT: E 110 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7990 (mtm) REVERT: E 115 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7922 (mm-40) REVERT: G 25 SER cc_start: 0.8857 (t) cc_final: 0.8304 (m) REVERT: G 67 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7861 (ttp80) REVERT: H 11 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6161 (tt) REVERT: I 104 ASP cc_start: 0.8543 (t0) cc_final: 0.8295 (t0) REVERT: J 49 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8149 (mt) REVERT: K 33 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: K 76 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7149 (tttt) REVERT: L 75 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.7114 (t) outliers start: 46 outliers final: 28 residues processed: 234 average time/residue: 0.3921 time to fit residues: 108.0366 Evaluate side-chains 240 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 76 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 3 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 163 optimal weight: 0.0570 chunk 102 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 88 ASN C 297 HIS C 341 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122675 restraints weight = 19860.966| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.54 r_work: 0.2869 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 19696 Z= 0.127 Angle : 0.581 16.292 26796 Z= 0.305 Chirality : 0.045 0.252 2836 Planarity : 0.004 0.037 3448 Dihedral : 5.410 66.884 2852 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.11 % Allowed : 14.73 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2444 helix: -0.55 (1.01), residues: 24 sheet: 0.31 (0.17), residues: 940 loop : -0.24 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 103 TYR 0.013 0.001 TYR J 92 PHE 0.018 0.002 PHE D 121 TRP 0.018 0.001 TRP A 179 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (19648) covalent geometry : angle 0.57072 / 0.30 (26692) SS BOND : bond 0.00490 / 0.27 ( 40) SS BOND : angle 1.52125 / 1.01 ( 80) hydrogen bonds : bond 0.03305 / 2.30 ( 669) hydrogen bonds : angle 5.94099 / 4.18 ( 1737) link_NAG-ASN : bond 0.00208 / 0.14 ( 8) link_NAG-ASN : angle 2.55285 / 1.61 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8714 (p) cc_final: 0.8507 (m) REVERT: A 128 GLU cc_start: 0.8276 (pt0) cc_final: 0.7872 (pp20) REVERT: A 220 ARG cc_start: 0.8442 (mmt90) cc_final: 0.7879 (mmt90) REVERT: A 269 MET cc_start: 0.8682 (mtp) cc_final: 0.8330 (mtp) REVERT: A 309 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8361 (t0) REVERT: B 235 ASN cc_start: 0.8636 (t0) cc_final: 0.8279 (t0) REVERT: B 311 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: B 382 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7582 (mm-30) REVERT: C 309 ASN cc_start: 0.8096 (t0) cc_final: 0.7330 (m110) REVERT: C 392 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: D 83 VAL cc_start: 0.4482 (OUTLIER) cc_final: 0.4083 (p) REVERT: D 118 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7114 (ttt-90) REVERT: D 398 ASP cc_start: 0.8334 (m-30) cc_final: 0.8075 (m-30) REVERT: E 110 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7713 (mtm) REVERT: E 115 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7911 (mm-40) REVERT: G 25 SER cc_start: 0.8831 (t) cc_final: 0.8295 (m) REVERT: G 67 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7585 (ttp80) REVERT: H 11 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6086 (tt) REVERT: I 104 ASP cc_start: 0.8519 (t0) cc_final: 0.8281 (t0) REVERT: J 49 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7967 (mt) REVERT: K 32 TYR cc_start: 0.9066 (m-80) cc_final: 0.8834 (m-80) REVERT: K 33 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: L 75 THR cc_start: 0.7244 (OUTLIER) cc_final: 0.7038 (t) outliers start: 44 outliers final: 23 residues processed: 235 average time/residue: 0.3889 time to fit residues: 107.8046 Evaluate side-chains 234 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 76 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 227 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 229 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 0.0770 chunk 194 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN C 297 HIS C 341 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120940 restraints weight = 20109.898| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.61 r_work: 0.2848 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 19696 Z= 0.174 Angle : 0.631 16.923 26796 Z= 0.331 Chirality : 0.046 0.270 2836 Planarity : 0.004 0.039 3448 Dihedral : 5.590 69.420 2852 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.82 % Allowed : 15.07 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2444 helix: -0.63 (1.01), residues: 24 sheet: 0.29 (0.17), residues: 940 loop : -0.29 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.017 0.002 TYR J 33 PHE 0.022 0.002 PHE D 121 TRP 0.020 0.002 TRP A 179 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (19648) covalent geometry : angle 0.61809 / 0.33 (26692) SS BOND : bond 0.00561 / 0.32 ( 40) SS BOND : angle 1.97859 / 1.33 ( 80) hydrogen bonds : bond 0.03584 / 2.49 ( 669) hydrogen bonds : angle 6.03601 / 4.26 ( 1737) link_NAG-ASN : bond 0.00274 / 0.18 ( 8) link_NAG-ASN : angle 2.67833 / 1.69 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4859.87 seconds wall clock time: 83 minutes 56.44 seconds (5036.44 seconds total)