Starting phenix.real_space_refine on Thu Sep 18 18:06:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kod_62473/09_2025/9kod_62473.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kod_62473/09_2025/9kod_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kod_62473/09_2025/9kod_62473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kod_62473/09_2025/9kod_62473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kod_62473/09_2025/9kod_62473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kod_62473/09_2025/9kod_62473.map" } 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-2.0-5805/lib/python3.9/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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.09, per 1000 atoms: 0.21 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: 1.28 Conformation dependent library (CDL) restraints added in 818.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.73 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: 3.92 Time building geometry restraints manager: 1.81 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 2.510 nonbonded pdb=" O TYR D 344 " pdb="CA CA D 503 " model vdw 1.688 2.510 nonbonded pdb=" O TYR A 344 " pdb="CA CA A 503 " model vdw 1.727 2.510 nonbonded pdb=" O TYR B 344 " pdb="CA CA B 503 " model vdw 1.858 2.510 nonbonded pdb=" O TYR C 344 " pdb="CA CA C 503 " model vdw 1.971 2.510 ... (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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.350 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:9.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 aren 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 covalent geometry : bond 0.00879 (19648) covalent geometry : angle 1.13619 (26692) SS BOND : bond 0.01695 ( 40) SS BOND : angle 4.01367 ( 80) hydrogen bonds : bond 0.19816 ( 669) hydrogen bonds : angle 9.17285 ( 1737) link_NAG-ASN : bond 0.01384 ( 8) link_NAG-ASN : angle 5.65811 ( 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 : 0.661 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: 0.7564 (m-40) REVERT: D 269 MET cc_start: 0.8440 (mtp) cc_final: 0.8211 (mtp) REVERT: D 398 ASP cc_start: 0.7782 (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: 0.4231 time to fit residues: 168.1148 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 : 0.618 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3765 r_free = 0.3765 target = 0.152531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120045 restraints weight = 20239.661| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.53 r_work: 0.2941 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 19696 Z= 0.138 Angle : 0.649 11.106 26796 Z= 0.344 Chirality : 0.047 0.356 2836 Planarity : 0.005 0.049 3448 Dihedral : 5.527 39.908 2853 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.30 % Allowed : 9.12 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.17), residues: 2444 helix: -0.30 (1.19), 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 K 103 TYR 0.020 0.001 TYR A 402 PHE 0.019 0.002 PHE D 121 TRP 0.017 0.001 TRP B 179 HIS 0.007 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00323 (19648) covalent geometry : angle 0.63351 (26692) SS BOND : bond 0.00461 ( 40) SS BOND : angle 1.97681 ( 80) hydrogen bonds : bond 0.04144 ( 669) hydrogen bonds : angle 6.79816 ( 1737) link_NAG-ASN : bond 0.00302 ( 8) link_NAG-ASN : angle 3.33288 ( 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 295 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8358 (mmt90) cc_final: 0.7683 (mmm160) REVERT: A 247 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8088 (m) REVERT: A 269 MET cc_start: 0.8597 (mtp) cc_final: 0.8219 (mtp) REVERT: B 235 ASN cc_start: 0.8598 (t0) cc_final: 0.8228 (t0) REVERT: B 338 MET cc_start: 0.8211 (tpt) cc_final: 0.8009 (tpt) REVERT: B 382 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7502 (mm-30) REVERT: B 418 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8001 (mmt) REVERT: C 118 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8448 (ttp-170) REVERT: D 83 VAL cc_start: 0.4252 (OUTLIER) cc_final: 0.3905 (p) REVERT: D 103 ASP cc_start: 0.7902 (p0) cc_final: 0.7685 (p0) REVERT: D 118 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8482 (ttt-90) REVERT: D 248 ASN cc_start: 0.7919 (p0) cc_final: 0.7522 (m-40) REVERT: D 392 ASP cc_start: 0.7828 (m-30) cc_final: 0.7628 (m-30) REVERT: D 398 ASP cc_start: 0.8296 (m-30) cc_final: 0.7958 (m-30) REVERT: E 19 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7625 (ttp-170) REVERT: F 83 ASP cc_start: 0.7926 (m-30) cc_final: 0.7723 (m-30) REVERT: G 19 ARG cc_start: 0.8523 (ttt180) cc_final: 0.8122 (ttm170) REVERT: G 25 SER cc_start: 0.9015 (t) cc_final: 0.8419 (m) REVERT: J 62 ARG cc_start: 0.7537 (ttp-110) cc_final: 0.7274 (ttp-110) REVERT: K 33 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: K 76 LYS cc_start: 0.7567 (ttmt) cc_final: 0.7111 (tttm) REVERT: L 75 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7536 (t) outliers start: 48 outliers final: 13 residues processed: 277 average time/residue: 0.4340 time to fit residues: 140.1795 Evaluate side-chains 232 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 210 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 215 optimal weight: 3.9990 chunk 123 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN C 88 ASN D 227 GLN E 35 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119094 restraints weight = 20408.210| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.53 r_work: 0.2922 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 19696 Z= 0.133 Angle : 0.611 15.611 26796 Z= 0.322 Chirality : 0.045 0.207 2836 Planarity : 0.004 0.041 3448 Dihedral : 5.361 39.538 2853 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.92 % Allowed : 11.37 % Favored : 86.71 % 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 aren not related in a simple way. whole: -0.25 (0.17), residues: 2444 helix: -0.45 (1.12), residues: 24 sheet: 0.19 (0.16), residues: 980 loop : -0.35 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.022 0.001 TYR A 402 PHE 0.018 0.002 PHE D 121 TRP 0.017 0.001 TRP B 179 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00315 (19648) covalent geometry : angle 0.59762 (26692) SS BOND : bond 0.00725 ( 40) SS BOND : angle 1.78791 ( 80) hydrogen bonds : bond 0.03632 ( 669) hydrogen bonds : angle 6.34772 ( 1737) link_NAG-ASN : bond 0.00208 ( 8) link_NAG-ASN : angle 2.92612 ( 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 265 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8356 (mmt90) cc_final: 0.7766 (mmm-85) REVERT: A 247 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8181 (m) REVERT: A 269 MET cc_start: 0.8697 (mtp) cc_final: 0.8332 (mtp) REVERT: A 309 ASN cc_start: 0.8840 (m-40) cc_final: 0.8498 (t0) REVERT: A 388 SER cc_start: 0.8964 (t) cc_final: 0.8723 (m) REVERT: B 235 ASN cc_start: 0.8513 (t0) cc_final: 0.8178 (t0) REVERT: B 382 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 418 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7711 (mmt) REVERT: C 284 ASP cc_start: 0.7576 (t0) cc_final: 0.6497 (p0) REVERT: C 334 SER cc_start: 0.7363 (t) cc_final: 0.7161 (p) REVERT: C 392 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: D 83 VAL cc_start: 0.4142 (OUTLIER) cc_final: 0.3842 (p) REVERT: D 118 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8517 (ttt-90) REVERT: D 248 ASN cc_start: 0.7956 (p0) cc_final: 0.7644 (m-40) REVERT: D 398 ASP cc_start: 0.8265 (m-30) cc_final: 0.7933 (m-30) REVERT: E 19 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7771 (ttt-90) REVERT: E 110 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7952 (mtm) REVERT: G 19 ARG cc_start: 0.8641 (ttt180) cc_final: 0.8278 (ttm170) REVERT: G 25 SER cc_start: 0.9003 (t) cc_final: 0.8420 (m) REVERT: I 104 ASP cc_start: 0.8418 (t0) cc_final: 0.8210 (t0) REVERT: K 33 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: K 76 LYS cc_start: 0.7590 (ttmt) cc_final: 0.7112 (tttt) REVERT: L 75 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7252 (t) outliers start: 40 outliers final: 16 residues processed: 249 average time/residue: 0.4403 time to fit residues: 126.6376 Evaluate side-chains 234 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 118 ARG Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 267 VAL 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 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: 0.7980 chunk 106 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 235 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 227 GLN F 38 GLN ** 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 = 0.3745 r_free = 0.3745 target = 0.150915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118566 restraints weight = 20165.921| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.56 r_work: 0.2794 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 19696 Z= 0.266 Angle : 0.714 19.201 26796 Z= 0.374 Chirality : 0.050 0.320 2836 Planarity : 0.005 0.039 3448 Dihedral : 5.804 48.736 2853 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.69 % Allowed : 12.14 % Favored : 85.17 % 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 aren not related in a simple way. whole: -0.37 (0.17), residues: 2444 helix: -0.83 (1.05), residues: 24 sheet: 0.13 (0.17), residues: 940 loop : -0.44 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 46 TYR 0.023 0.002 TYR B 402 PHE 0.026 0.002 PHE D 121 TRP 0.022 0.002 TRP A 179 HIS 0.013 0.002 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00651 (19648) covalent geometry : angle 0.69924 (26692) SS BOND : bond 0.00767 ( 40) SS BOND : angle 2.13215 ( 80) hydrogen bonds : bond 0.04320 ( 669) hydrogen bonds : angle 6.51473 ( 1737) link_NAG-ASN : bond 0.00377 ( 8) link_NAG-ASN : angle 3.23177 ( 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 274 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: A 220 ARG cc_start: 0.8534 (mmt90) cc_final: 0.7747 (mmm-85) REVERT: A 247 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8292 (m) REVERT: A 309 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8457 (t0) REVERT: B 235 ASN cc_start: 0.8624 (t0) cc_final: 0.8274 (t0) REVERT: B 311 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: B 382 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7523 (mm-30) REVERT: C 309 ASN cc_start: 0.8098 (t0) cc_final: 0.7414 (m110) REVERT: C 392 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: D 83 VAL cc_start: 0.4228 (OUTLIER) cc_final: 0.3936 (p) REVERT: D 262 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8129 (mmtm) REVERT: D 398 ASP cc_start: 0.8362 (m-30) cc_final: 0.8023 (m-30) REVERT: E 19 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7826 (ttt-90) REVERT: E 110 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: G 25 SER cc_start: 0.8966 (t) cc_final: 0.8356 (m) REVERT: I 104 ASP cc_start: 0.8546 (t0) cc_final: 0.8323 (t0) REVERT: K 33 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7184 (mm-30) REVERT: K 76 LYS cc_start: 0.7670 (ttmt) cc_final: 0.7175 (tttm) REVERT: L 75 THR cc_start: 0.7547 (OUTLIER) cc_final: 0.7314 (t) outliers start: 56 outliers final: 28 residues processed: 252 average time/residue: 0.4064 time to fit residues: 119.8691 Evaluate side-chains 237 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 128 GLU 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 D residue 384 ASP Chi-restraints excluded: chain D residue 392 ASP 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 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 34 LEU 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: 7.9990 chunk 229 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 197 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 88 ASN B 409 HIS C 227 GLN C 341 ASN F 91 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122403 restraints weight = 19971.644| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.59 r_work: 0.2830 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19696 Z= 0.153 Angle : 0.617 17.579 26796 Z= 0.324 Chirality : 0.046 0.275 2836 Planarity : 0.004 0.038 3448 Dihedral : 5.466 51.565 2853 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.30 % Allowed : 13.00 % Favored : 84.69 % 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 aren not related in a simple way. whole: -0.22 (0.17), residues: 2444 helix: -0.63 (1.05), residues: 24 sheet: 0.28 (0.17), residues: 924 loop : -0.37 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.014 0.002 TYR A 402 PHE 0.020 0.002 PHE A 121 TRP 0.021 0.001 TRP A 179 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00370 (19648) covalent geometry : angle 0.60452 (26692) SS BOND : bond 0.00584 ( 40) SS BOND : angle 1.77599 ( 80) hydrogen bonds : bond 0.03571 ( 669) hydrogen bonds : angle 6.20720 ( 1737) link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 2.85253 ( 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 260 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.8009 (pt0) REVERT: A 220 ARG cc_start: 0.8504 (mmt90) cc_final: 0.7725 (mmm160) REVERT: A 309 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8385 (t0) REVERT: A 388 SER cc_start: 0.8954 (t) cc_final: 0.8713 (m) REVERT: B 311 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: B 382 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7549 (mm-30) REVERT: C 309 ASN cc_start: 0.8025 (t0) cc_final: 0.7296 (m110) REVERT: C 392 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: D 83 VAL cc_start: 0.4071 (OUTLIER) cc_final: 0.3844 (p) REVERT: D 262 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8136 (mmtm) REVERT: D 268 GLU cc_start: 0.8273 (tt0) cc_final: 0.8025 (tp30) REVERT: D 382 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: D 398 ASP cc_start: 0.8379 (m-30) cc_final: 0.8059 (m-30) REVERT: E 19 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7790 (ttt-90) REVERT: E 110 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7983 (mtm) REVERT: G 25 SER cc_start: 0.8963 (t) cc_final: 0.8377 (m) REVERT: G 67 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7440 (ttp80) REVERT: K 32 TYR cc_start: 0.9080 (m-80) cc_final: 0.8850 (m-80) REVERT: K 76 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7043 (tttt) REVERT: L 75 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7210 (t) outliers start: 48 outliers final: 25 residues processed: 243 average time/residue: 0.4333 time to fit residues: 122.2439 Evaluate side-chains 231 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 128 GLU 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 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 83 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 392 ASP 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 G residue 67 ARG Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 22 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 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: 1.9990 chunk 76 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 88 ASN C 341 ASN E 115 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122845 restraints weight = 19754.035| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.45 r_work: 0.2853 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 19696 Z= 0.138 Angle : 0.594 16.837 26796 Z= 0.312 Chirality : 0.046 0.263 2836 Planarity : 0.004 0.037 3448 Dihedral : 5.305 53.733 2853 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.69 % Allowed : 13.39 % Favored : 83.93 % 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 aren not related in a simple way. whole: -0.15 (0.17), residues: 2444 helix: -0.57 (1.04), residues: 24 sheet: 0.31 (0.17), residues: 932 loop : -0.30 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.018 0.001 TYR D 344 PHE 0.018 0.002 PHE A 121 TRP 0.019 0.001 TRP A 179 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00330 (19648) covalent geometry : angle 0.58355 (26692) SS BOND : bond 0.00522 ( 40) SS BOND : angle 1.59554 ( 80) hydrogen bonds : bond 0.03434 ( 669) hydrogen bonds : angle 6.06730 ( 1737) link_NAG-ASN : bond 0.00202 ( 8) link_NAG-ASN : angle 2.70843 ( 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 268 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.716 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: 0.8434 (mmt90) cc_final: 0.7922 (mmt90) REVERT: A 309 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8409 (t0) REVERT: A 318 CYS cc_start: 0.8388 (m) cc_final: 0.8077 (m) REVERT: A 388 SER cc_start: 0.8959 (t) cc_final: 0.8746 (m) REVERT: B 235 ASN cc_start: 0.8592 (t0) cc_final: 0.8254 (t0) REVERT: B 311 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: B 382 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7573 (mm-30) REVERT: C 284 ASP cc_start: 0.7820 (t70) cc_final: 0.6611 (p0) REVERT: C 309 ASN cc_start: 0.8042 (t0) cc_final: 0.7280 (m110) REVERT: C 392 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: D 262 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8104 (mmtm) REVERT: D 398 ASP cc_start: 0.8354 (m-30) cc_final: 0.8047 (m-30) REVERT: E 19 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7786 (ttt-90) REVERT: E 110 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7794 (mtm) REVERT: G 25 SER cc_start: 0.8948 (t) cc_final: 0.8374 (m) REVERT: G 67 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7826 (ttp80) REVERT: K 76 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7109 (tttt) REVERT: L 75 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.7073 (t) outliers start: 56 outliers final: 27 residues processed: 248 average time/residue: 0.4225 time to fit residues: 122.0677 Evaluate side-chains 236 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 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 231 CYS Chi-restraints excluded: chain D residue 392 ASP 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 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 22 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 35 ASN Chi-restraints excluded: chain L residue 75 THR 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: 9.9990 chunk 149 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 234 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN C 341 ASN E 115 GLN ** 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 = 0.3802 r_free = 0.3802 target = 0.155865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123781 restraints weight = 19920.799| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.44 r_work: 0.2866 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2586 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= 0.124 Angle : 0.577 16.427 26796 Z= 0.302 Chirality : 0.045 0.254 2836 Planarity : 0.004 0.037 3448 Dihedral : 5.157 54.821 2852 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.26 % Allowed : 13.92 % Favored : 83.83 % 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 aren not related in a simple way. whole: -0.09 (0.17), residues: 2444 helix: -0.59 (1.02), residues: 24 sheet: 0.29 (0.17), residues: 940 loop : -0.22 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 103 TYR 0.019 0.001 TYR D 344 PHE 0.017 0.002 PHE A 121 TRP 0.018 0.001 TRP A 179 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00296 (19648) covalent geometry : angle 0.56734 (26692) SS BOND : bond 0.00481 ( 40) SS BOND : angle 1.44824 ( 80) hydrogen bonds : bond 0.03300 ( 669) hydrogen bonds : angle 5.94641 ( 1737) link_NAG-ASN : bond 0.00196 ( 8) link_NAG-ASN : angle 2.55111 ( 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 258 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.682 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: 0.8412 (mmt90) cc_final: 0.7902 (mmt90) REVERT: A 237 SER cc_start: 0.8263 (m) cc_final: 0.8058 (t) REVERT: A 309 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8380 (t0) REVERT: B 235 ASN cc_start: 0.8585 (t0) cc_final: 0.8255 (t0) REVERT: B 311 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: B 382 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7598 (mm-30) REVERT: C 284 ASP cc_start: 0.7827 (t70) cc_final: 0.6642 (p0) REVERT: C 309 ASN cc_start: 0.8046 (t0) cc_final: 0.7276 (m110) REVERT: C 392 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: D 398 ASP cc_start: 0.8337 (m-30) cc_final: 0.8043 (m-30) REVERT: E 110 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7779 (mtm) REVERT: G 25 SER cc_start: 0.8872 (t) cc_final: 0.8320 (m) REVERT: G 67 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7875 (ttp80) REVERT: K 76 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7118 (tttt) outliers start: 47 outliers final: 29 residues processed: 240 average time/residue: 0.3887 time to fit residues: 110.2533 Evaluate side-chains 235 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 231 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 452 THR 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 14 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 22 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 35 ASN 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: 0.8980 chunk 182 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 213 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 88 ASN C 341 ASN E 115 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121663 restraints weight = 20028.486| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.58 r_work: 0.2820 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 19696 Z= 0.149 Angle : 0.596 16.719 26796 Z= 0.312 Chirality : 0.046 0.267 2836 Planarity : 0.004 0.037 3448 Dihedral : 5.308 58.358 2852 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.06 % Allowed : 14.78 % 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 aren not related in a simple way. whole: -0.11 (0.17), residues: 2444 helix: -0.56 (1.02), residues: 24 sheet: 0.29 (0.17), residues: 940 loop : -0.24 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.025 0.001 TYR D 344 PHE 0.020 0.002 PHE D 121 TRP 0.018 0.001 TRP A 179 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00360 (19648) covalent geometry : angle 0.58572 (26692) SS BOND : bond 0.00524 ( 40) SS BOND : angle 1.52269 ( 80) hydrogen bonds : bond 0.03471 ( 669) hydrogen bonds : angle 5.99053 ( 1737) link_NAG-ASN : bond 0.00235 ( 8) link_NAG-ASN : angle 2.62332 ( 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 243 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.624 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: 0.8406 (pt0) cc_final: 0.7974 (pp20) REVERT: A 220 ARG cc_start: 0.8473 (mmt90) cc_final: 0.7923 (mmt90) REVERT: A 309 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8383 (t0) REVERT: B 235 ASN cc_start: 0.8636 (t0) cc_final: 0.8311 (t0) REVERT: B 311 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: B 382 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 309 ASN cc_start: 0.8082 (t0) cc_final: 0.7309 (m110) REVERT: C 392 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: D 83 VAL cc_start: 0.4139 (OUTLIER) cc_final: 0.3785 (p) REVERT: D 398 ASP cc_start: 0.8379 (m-30) cc_final: 0.8114 (m-30) REVERT: E 110 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7911 (mtm) REVERT: G 25 SER cc_start: 0.8878 (t) cc_final: 0.8328 (m) REVERT: G 67 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (ttp80) REVERT: H 11 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6180 (tt) REVERT: K 33 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: K 76 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7100 (tttt) outliers start: 43 outliers final: 26 residues processed: 230 average time/residue: 0.4079 time to fit residues: 110.2344 Evaluate side-chains 234 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 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 392 ASP Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 110 MET 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 22 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 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: 3.9990 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 234 optimal weight: 0.5980 chunk 192 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 295 ASN B 88 ASN 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 = 0.3766 r_free = 0.3766 target = 0.152948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121106 restraints weight = 20064.308| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.54 r_work: 0.2791 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2653 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= 0.184 Angle : 0.640 17.114 26796 Z= 0.334 Chirality : 0.047 0.280 2836 Planarity : 0.004 0.039 3448 Dihedral : 5.574 64.834 2852 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.30 % Allowed : 14.59 % Favored : 83.11 % 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 aren not related in a simple way. whole: -0.13 (0.17), residues: 2444 helix: -0.64 (1.02), residues: 24 sheet: 0.33 (0.17), residues: 932 loop : -0.29 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.029 0.002 TYR D 344 PHE 0.023 0.002 PHE D 121 TRP 0.019 0.002 TRP A 179 HIS 0.008 0.002 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00449 (19648) covalent geometry : angle 0.62645 (26692) SS BOND : bond 0.00548 ( 40) SS BOND : angle 1.97482 ( 80) hydrogen bonds : bond 0.03670 ( 669) hydrogen bonds : angle 6.08004 ( 1737) link_NAG-ASN : bond 0.00288 ( 8) link_NAG-ASN : angle 2.74903 ( 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 246 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.685 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: 0.8398 (pt0) cc_final: 0.7942 (pp20) REVERT: A 220 ARG cc_start: 0.8503 (mmt90) cc_final: 0.7909 (mmt90) REVERT: A 309 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8409 (t0) REVERT: B 235 ASN cc_start: 0.8712 (t0) cc_final: 0.8360 (t0) REVERT: B 311 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: B 382 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7623 (mm-30) REVERT: C 309 ASN cc_start: 0.8138 (t0) cc_final: 0.7372 (m110) REVERT: C 344 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6713 (t80) REVERT: C 392 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: D 83 VAL cc_start: 0.4281 (OUTLIER) cc_final: 0.3895 (p) REVERT: D 398 ASP cc_start: 0.8411 (m-30) cc_final: 0.8136 (m-30) REVERT: E 110 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8072 (mtm) REVERT: E 115 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8068 (mm-40) REVERT: G 25 SER cc_start: 0.8938 (t) cc_final: 0.8376 (m) REVERT: G 67 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7839 (ttp80) REVERT: H 11 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6145 (tt) REVERT: K 33 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: K 76 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7108 (tttt) outliers start: 48 outliers final: 26 residues processed: 229 average time/residue: 0.4075 time to fit residues: 109.3513 Evaluate side-chains 230 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 392 ASP Chi-restraints excluded: chain D residue 418 MET 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 22 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 L residue 34 LEU 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: 0.8980 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 0.0070 chunk 111 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 88 ASN 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 = 0.3808 r_free = 0.3808 target = 0.156467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124097 restraints weight = 19959.553| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.58 r_work: 0.2870 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19696 Z= 0.108 Angle : 0.569 15.956 26796 Z= 0.299 Chirality : 0.044 0.247 2836 Planarity : 0.004 0.038 3448 Dihedral : 5.245 62.766 2852 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.68 % Allowed : 15.55 % Favored : 82.77 % 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 aren not related in a simple way. whole: 0.01 (0.17), residues: 2444 helix: -0.40 (1.02), residues: 24 sheet: 0.39 (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 0.018 0.001 TYR D 344 PHE 0.017 0.001 PHE A 121 TRP 0.016 0.001 TRP B 179 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00255 (19648) covalent geometry : angle 0.55873 (26692) SS BOND : bond 0.00455 ( 40) SS BOND : angle 1.56734 ( 80) hydrogen bonds : bond 0.03134 ( 669) hydrogen bonds : angle 5.83253 ( 1737) link_NAG-ASN : bond 0.00176 ( 8) link_NAG-ASN : angle 2.40897 ( 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 243 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.672 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: 0.8315 (pt0) cc_final: 0.7908 (pp20) REVERT: A 220 ARG cc_start: 0.8455 (mmt90) cc_final: 0.7892 (mmt90) REVERT: A 309 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8374 (t0) REVERT: B 235 ASN cc_start: 0.8627 (t0) cc_final: 0.8299 (t0) REVERT: B 311 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: B 382 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7620 (mm-30) REVERT: C 309 ASN cc_start: 0.8095 (t0) cc_final: 0.7298 (m110) REVERT: C 392 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: D 83 VAL cc_start: 0.4516 (OUTLIER) cc_final: 0.4112 (p) REVERT: D 398 ASP cc_start: 0.8361 (m-30) cc_final: 0.8102 (m-30) REVERT: E 110 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7755 (mtm) REVERT: E 115 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8053 (mm-40) REVERT: G 25 SER cc_start: 0.8851 (t) cc_final: 0.8311 (m) REVERT: G 67 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7622 (ttp80) REVERT: H 11 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6131 (tt) REVERT: H 22 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8145 (t) REVERT: I 104 ASP cc_start: 0.8564 (t0) cc_final: 0.8314 (t0) REVERT: K 33 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.6839 (mm-30) outliers start: 35 outliers final: 21 residues processed: 233 average time/residue: 0.4198 time to fit residues: 115.0036 Evaluate side-chains 226 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 392 ASP Chi-restraints excluded: chain D residue 418 MET 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 H residue 11 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 22 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 J residue 64 SER Chi-restraints excluded: chain K residue 33 GLU 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: 3.9990 chunk 28 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 220 optimal weight: 0.0770 chunk 229 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 295 ASN B 88 ASN C 341 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122388 restraints weight = 20176.550| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.57 r_work: 0.2819 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 19696 Z= 0.147 Angle : 0.594 16.377 26796 Z= 0.312 Chirality : 0.046 0.259 2836 Planarity : 0.004 0.037 3448 Dihedral : 5.358 65.288 2852 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.58 % Allowed : 15.64 % Favored : 82.77 % 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 aren not related in a simple way. whole: -0.00 (0.17), residues: 2444 helix: -0.47 (1.02), residues: 24 sheet: 0.40 (0.17), residues: 932 loop : -0.19 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 103 TYR 0.025 0.001 TYR D 344 PHE 0.020 0.002 PHE D 121 TRP 0.019 0.001 TRP A 179 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00356 (19648) covalent geometry : angle 0.58295 (26692) SS BOND : bond 0.00508 ( 40) SS BOND : angle 1.69820 ( 80) hydrogen bonds : bond 0.03429 ( 669) hydrogen bonds : angle 5.91300 ( 1737) link_NAG-ASN : bond 0.00236 ( 8) link_NAG-ASN : angle 2.52306 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5256.73 seconds wall clock time: 90 minutes 34.05 seconds (5434.05 seconds total)