Starting phenix.real_space_refine on Sat Sep 12 01:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hjn_0234/09_2026/6hjn_0234.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjn_0234/09_2026/6hjn_0234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2026/6hjn_0234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2026/6hjn_0234.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2026/6hjn_0234.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2026/6hjn_0234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2026/6hjn_0234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2026/6hjn_0234.map" } resolution = 3.3 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= 0.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7701 2.51 5 N 2031 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12309 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "B" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1395 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "D" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1395 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "F" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1395 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "E" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.17, per 1000 atoms: 0.26 Number of scatterers: 12309 At special positions: 0 Unit cell: (92.708, 91.63, 150.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2526 8.00 N 2031 7.00 C 7701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS C 8 " distance=2.05 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS E 8 " distance=2.05 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.02 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 3 " " NAG S 1 " - " FUC S 3 " NAG-ASN " NAG G 1 " - " ASN A 15 " " NAG H 1 " - " ASN A 27 " " NAG I 1 " - " ASN A 91 " " NAG J 1 " - " ASN A 290 " " NAG K 1 " - " ASN B 154 " " NAG L 1 " - " ASN D 154 " " NAG M 1 " - " ASN F 154 " " NAG N 1 " - " ASN C 15 " " NAG O 1 " - " ASN C 27 " " NAG P 1 " - " ASN C 91 " " NAG Q 1 " - " ASN C 290 " " NAG R 1 " - " ASN E 15 " " NAG S 1 " - " ASN E 27 " " NAG T 1 " - " ASN E 91 " " NAG U 1 " - " ASN E 290 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 613.0 milliseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2742 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 33 sheets defined 25.8% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 101 through 110 removed outlier: 3.582A pdb=" N LEU A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 39 through 59 removed outlier: 4.015A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.671A pdb=" N GLN B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.597A pdb=" N MET B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.632A pdb=" N SER B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 59 removed outlier: 4.015A pdb=" N ASN D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 126 removed outlier: 3.669A pdb=" N GLN D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.597A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.632A pdb=" N SER D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 59 removed outlier: 4.015A pdb=" N ASN F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.671A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.597A pdb=" N MET F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 Processing helix chain 'F' and resid 162 through 173 removed outlier: 3.631A pdb=" N SER F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 101 through 110 removed outlier: 3.582A pdb=" N LEU C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 101 through 110 removed outlier: 3.582A pdb=" N LEU E 105 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11 removed outlier: 3.516A pdb=" N GLY A 10 " --> pdb=" O GLY B 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.763A pdb=" N LEU A 46 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 280 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 7.004A pdb=" N LEU A 54 " --> pdb=" O ILE A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 99 removed outlier: 7.127A pdb=" N GLU A 98 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N TRP A 234 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 118 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 261 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER A 114 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AB2, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB3, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.519A pdb=" N GLY C 10 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB6, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB8, first strand: chain 'C' and resid 46 through 49 removed outlier: 5.763A pdb=" N LEU C 46 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 280 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 54 through 55 removed outlier: 7.003A pdb=" N LEU C 54 " --> pdb=" O ILE C 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 97 through 99 removed outlier: 7.127A pdb=" N GLU C 98 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N TRP C 234 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 258 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 118 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 261 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER C 114 " --> pdb=" O ASN C 261 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 168 Processing sheet with id=AC5, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AC6, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC7, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AC8, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AC9, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.763A pdb=" N LEU E 46 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N CYS E 278 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 280 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 54 through 55 removed outlier: 7.004A pdb=" N LEU E 54 " --> pdb=" O ILE E 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 97 through 99 removed outlier: 7.127A pdb=" N GLU E 98 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N TRP E 234 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE E 118 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN E 261 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER E 114 " --> pdb=" O ASN E 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 168 Processing sheet with id=AD6, first strand: chain 'E' and resid 282 through 283 403 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3736 1.33 - 1.45: 2147 1.45 - 1.57: 6627 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 12576 Sorted by residual: bond pdb=" N ASN A 290 " pdb=" CA ASN A 290 " ideal model delta sigma weight residual 1.460 1.405 0.055 1.17e-02 7.31e+03 2.20e+01 bond pdb=" N ASN E 290 " pdb=" CA ASN E 290 " ideal model delta sigma weight residual 1.460 1.406 0.054 1.17e-02 7.31e+03 2.16e+01 bond pdb=" N ASN C 290 " pdb=" CA ASN C 290 " ideal model delta sigma weight residual 1.460 1.406 0.054 1.17e-02 7.31e+03 2.15e+01 bond pdb=" N LYS F 131 " pdb=" CA LYS F 131 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.47e+00 bond pdb=" N LYS B 131 " pdb=" CA LYS B 131 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.43e+00 ... (remaining 12571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 16066 2.33 - 4.66: 856 4.66 - 6.98: 96 6.98 - 9.31: 25 9.31 - 11.64: 6 Bond angle restraints: 17049 Sorted by residual: angle pdb=" CA ASP F 158 " pdb=" CB ASP F 158 " pdb=" CG ASP F 158 " ideal model delta sigma weight residual 112.60 118.11 -5.51 1.00e+00 1.00e+00 3.03e+01 angle pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " pdb=" CG ASP B 158 " ideal model delta sigma weight residual 112.60 117.77 -5.17 1.00e+00 1.00e+00 2.67e+01 angle pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " pdb=" CG ASP D 158 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" C ASP F 158 " pdb=" N TYR F 159 " pdb=" CA TYR F 159 " ideal model delta sigma weight residual 120.58 126.39 -5.81 1.32e+00 5.74e-01 1.94e+01 angle pdb=" C ASP B 158 " pdb=" N TYR B 159 " pdb=" CA TYR B 159 " ideal model delta sigma weight residual 120.58 126.36 -5.78 1.32e+00 5.74e-01 1.92e+01 ... (remaining 17044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 6492 15.32 - 30.64: 498 30.64 - 45.96: 132 45.96 - 61.27: 15 61.27 - 76.59: 6 Dihedral angle restraints: 7143 sinusoidal: 2847 harmonic: 4296 Sorted by residual: dihedral pdb=" C ASP D 158 " pdb=" N ASP D 158 " pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " ideal model delta harmonic sigma weight residual -122.60 -136.75 14.15 0 2.50e+00 1.60e-01 3.20e+01 dihedral pdb=" C ASP B 158 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " ideal model delta harmonic sigma weight residual -122.60 -136.61 14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA ASN B 129 " pdb=" C ASN B 129 " pdb=" N ALA B 130 " pdb=" CA ALA B 130 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 7140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 1953 0.287 - 0.574: 9 0.574 - 0.860: 3 0.860 - 1.147: 3 1.147 - 1.434: 3 Chirality restraints: 1971 Sorted by residual: chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.90e+03 chirality pdb=" C1 MAN I 4 " pdb=" O3 BMA I 3 " pdb=" C2 MAN I 4 " pdb=" O5 MAN I 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.89e+03 chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.89e+03 ... (remaining 1968 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG G 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.513 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG N 2 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.086 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG R 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.512 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.165 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 18 2.37 - 3.00: 6072 3.00 - 3.63: 17379 3.63 - 4.27: 25745 4.27 - 4.90: 43195 Nonbonded interactions: 92409 Sorted by model distance: nonbonded pdb=" CE2 TYR C 161 " pdb=" O THR C 248 " model vdw 1.734 3.340 nonbonded pdb=" CE2 TYR E 161 " pdb=" O THR E 248 " model vdw 1.735 3.340 nonbonded pdb=" CE2 TYR A 161 " pdb=" O THR A 248 " model vdw 1.735 3.340 nonbonded pdb=" OD1 ASN D 128 " pdb=" NH1 ARG D 170 " model vdw 2.051 3.120 nonbonded pdb=" OD1 ASN F 128 " pdb=" NH1 ARG F 170 " model vdw 2.051 3.120 ... (remaining 92404 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'T' } 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: 13.060 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.850 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 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 : 0.008 0.057 12639 Z= 0.526 Angle : 1.346 22.399 17220 Z= 0.719 Chirality : 0.111 1.434 1971 Planarity : 0.022 0.287 2148 Dihedral : 12.086 76.592 4347 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.80 % Allowed : 4.44 % Favored : 92.76 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -3.22 (0.17), residues: 1476 helix: -0.02 (0.24), residues: 351 sheet: -2.26 (0.28), residues: 258 loop : -3.19 (0.15), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 170 TYR 0.016 0.003 TYR D 157 PHE 0.013 0.003 PHE B 140 TRP 0.024 0.004 TRP C 153 HIS 0.004 0.002 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.53 (12576) covalent geometry : angle 1.23077 / 0.70 (17049) SS BOND : bond 0.00877 / 0.59 ( 18) SS BOND : angle 1.62224 / 0.97 ( 36) hydrogen bonds : bond 0.17725 / 11.80 ( 403) hydrogen bonds : angle 6.17035 / 4.11 ( 1101) link_ALPHA1-3 : bond 0.03367 / 1.69 ( 3) link_ALPHA1-3 : angle 8.09519 / 4.46 ( 9) link_ALPHA1-6 : bond 0.01391 / 0.70 ( 3) link_ALPHA1-6 : angle 3.40510 / 1.68 ( 9) link_BETA1-4 : bond 0.00519 / 0.33 ( 21) link_BETA1-4 : angle 3.61952 / 2.37 ( 63) link_BETA1-6 : bond 0.00125 / 0.06 ( 3) link_BETA1-6 : angle 1.74271 / 0.92 ( 9) link_NAG-ASN : bond 0.01015 / 0.60 ( 15) link_NAG-ASN : angle 9.12498 / 5.85 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8801 (tm-30) REVERT: B 59 MET cc_start: 0.8838 (mmm) cc_final: 0.8537 (mmm) REVERT: B 149 MET cc_start: 0.9351 (mmt) cc_final: 0.9131 (mmp) REVERT: D 59 MET cc_start: 0.8923 (mmm) cc_final: 0.8621 (mmm) REVERT: D 149 MET cc_start: 0.9385 (mmt) cc_final: 0.9147 (mmp) REVERT: F 59 MET cc_start: 0.8823 (mmm) cc_final: 0.8554 (mmm) REVERT: F 149 MET cc_start: 0.9361 (mmt) cc_final: 0.9147 (mmp) REVERT: C 192 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8800 (tm-30) outliers start: 36 outliers final: 6 residues processed: 147 average time/residue: 0.1462 time to fit residues: 29.0572 Evaluate side-chains 64 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS A 192 GLN A 286 HIS A 299 HIS B 169 ASN D 169 ASN F 169 ASN C 184 HIS C 192 GLN C 286 HIS C 299 HIS E 184 HIS E 286 HIS E 299 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.044516 restraints weight = 35205.110| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 3.88 r_work: 0.2409 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12639 Z= 0.156 Angle : 0.806 15.189 17220 Z= 0.361 Chirality : 0.051 0.433 1971 Planarity : 0.004 0.034 2148 Dihedral : 6.269 59.891 1641 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.49 % Allowed : 7.55 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.00 (0.20), residues: 1476 helix: 2.01 (0.28), residues: 351 sheet: -1.40 (0.31), residues: 219 loop : -2.89 (0.16), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 116 TYR 0.015 0.001 TYR C 161 PHE 0.009 0.001 PHE B 140 TRP 0.015 0.001 TRP C 255 HIS 0.003 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12576) covalent geometry : angle 0.75003 / 0.35 (17049) SS BOND : bond 0.00574 / 0.32 ( 18) SS BOND : angle 0.86289 / 0.55 ( 36) hydrogen bonds : bond 0.07295 / 5.03 ( 403) hydrogen bonds : angle 4.48897 / 3.00 ( 1101) link_ALPHA1-3 : bond 0.02826 / 1.42 ( 3) link_ALPHA1-3 : angle 4.10393 / 2.15 ( 9) link_ALPHA1-6 : bond 0.00608 / 0.31 ( 3) link_ALPHA1-6 : angle 1.38761 / 0.87 ( 9) link_BETA1-4 : bond 0.00912 / 0.56 ( 21) link_BETA1-4 : angle 2.02153 / 1.34 ( 63) link_BETA1-6 : bond 0.00617 / 0.31 ( 3) link_BETA1-6 : angle 1.17993 / 0.77 ( 9) link_NAG-ASN : bond 0.00323 / 0.20 ( 15) link_NAG-ASN : angle 4.98171 / 3.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.9052 (tt0) cc_final: 0.8672 (pt0) REVERT: B 59 MET cc_start: 0.8770 (mmm) cc_final: 0.8521 (mmm) REVERT: D 59 MET cc_start: 0.8897 (mmm) cc_final: 0.8653 (mmm) REVERT: D 149 MET cc_start: 0.9212 (mmt) cc_final: 0.8982 (mmp) REVERT: F 59 MET cc_start: 0.8794 (mmm) cc_final: 0.8541 (mmm) REVERT: F 149 MET cc_start: 0.9238 (mmt) cc_final: 0.9004 (mmp) REVERT: C 115 PHE cc_start: 0.8423 (m-10) cc_final: 0.8099 (m-10) outliers start: 32 outliers final: 12 residues processed: 93 average time/residue: 0.1496 time to fit residues: 19.0117 Evaluate side-chains 71 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 0.0370 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS A 184 HIS F 25 HIS C 184 HIS E 130 HIS E 184 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.044265 restraints weight = 35287.849| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 3.82 r_work: 0.2396 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12639 Z= 0.154 Angle : 0.696 10.990 17220 Z= 0.325 Chirality : 0.045 0.270 1971 Planarity : 0.004 0.030 2148 Dihedral : 5.521 59.407 1633 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.57 % Allowed : 7.63 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.42 (0.20), residues: 1476 helix: 2.73 (0.27), residues: 351 sheet: -0.88 (0.33), residues: 219 loop : -2.68 (0.16), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 116 TYR 0.013 0.001 TYR C 195 PHE 0.011 0.001 PHE D 9 TRP 0.011 0.001 TRP F 92 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (12576) covalent geometry : angle 0.65746 / 0.32 (17049) SS BOND : bond 0.00419 / 0.25 ( 18) SS BOND : angle 1.04564 / 0.62 ( 36) hydrogen bonds : bond 0.06793 / 4.70 ( 403) hydrogen bonds : angle 4.06304 / 2.74 ( 1101) link_ALPHA1-3 : bond 0.01922 / 0.96 ( 3) link_ALPHA1-3 : angle 3.28851 / 2.02 ( 9) link_ALPHA1-6 : bond 0.00493 / 0.25 ( 3) link_ALPHA1-6 : angle 1.37545 / 0.89 ( 9) link_BETA1-4 : bond 0.00747 / 0.46 ( 21) link_BETA1-4 : angle 1.63582 / 1.06 ( 63) link_BETA1-6 : bond 0.00479 / 0.24 ( 3) link_BETA1-6 : angle 1.22188 / 0.80 ( 9) link_NAG-ASN : bond 0.00332 / 0.21 ( 15) link_NAG-ASN : angle 3.78667 / 2.44 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8877 (mp) cc_final: 0.8504 (tp) REVERT: A 305 GLU cc_start: 0.9067 (tt0) cc_final: 0.8588 (pt0) REVERT: B 149 MET cc_start: 0.9209 (mmp) cc_final: 0.8967 (mmp) REVERT: C 7 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8603 (tp) REVERT: C 115 PHE cc_start: 0.8332 (m-10) cc_final: 0.8044 (m-10) REVERT: C 296 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8898 (tm-30) REVERT: E 7 ILE cc_start: 0.8816 (mp) cc_final: 0.8508 (tp) REVERT: E 115 PHE cc_start: 0.8399 (m-10) cc_final: 0.8102 (m-10) outliers start: 33 outliers final: 14 residues processed: 90 average time/residue: 0.1061 time to fit residues: 14.2517 Evaluate side-chains 77 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 296 GLN Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN C 231 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.042771 restraints weight = 35470.481| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 3.87 r_work: 0.2361 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12639 Z= 0.188 Angle : 0.684 9.609 17220 Z= 0.324 Chirality : 0.045 0.280 1971 Planarity : 0.003 0.029 2148 Dihedral : 5.420 55.818 1633 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.26 % Allowed : 9.27 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.05 (0.21), residues: 1476 helix: 3.00 (0.27), residues: 351 sheet: -0.50 (0.34), residues: 216 loop : -2.46 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 211 TYR 0.013 0.001 TYR C 195 PHE 0.013 0.001 PHE D 9 TRP 0.010 0.001 TRP F 92 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (12576) covalent geometry : angle 0.65469 / 0.32 (17049) SS BOND : bond 0.00464 / 0.29 ( 18) SS BOND : angle 1.26877 / 0.75 ( 36) hydrogen bonds : bond 0.06873 / 4.77 ( 403) hydrogen bonds : angle 4.02617 / 2.73 ( 1101) link_ALPHA1-3 : bond 0.00831 / 0.42 ( 3) link_ALPHA1-3 : angle 2.50848 / 1.66 ( 9) link_ALPHA1-6 : bond 0.00421 / 0.21 ( 3) link_ALPHA1-6 : angle 1.41649 / 0.92 ( 9) link_BETA1-4 : bond 0.00594 / 0.36 ( 21) link_BETA1-4 : angle 1.48774 / 0.97 ( 63) link_BETA1-6 : bond 0.00479 / 0.24 ( 3) link_BETA1-6 : angle 1.21268 / 0.80 ( 9) link_NAG-ASN : bond 0.00218 / 0.14 ( 15) link_NAG-ASN : angle 3.18860 / 2.07 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8882 (mp) cc_final: 0.8625 (tp) REVERT: A 184 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.7744 (p90) REVERT: B 27 GLN cc_start: 0.9359 (tp-100) cc_final: 0.9091 (tp-100) REVERT: F 2 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8701 (tm) REVERT: C 115 PHE cc_start: 0.8438 (m-10) cc_final: 0.8106 (m-10) REVERT: E 7 ILE cc_start: 0.8802 (mp) cc_final: 0.8576 (tp) REVERT: E 296 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.9051 (tm-30) outliers start: 29 outliers final: 14 residues processed: 86 average time/residue: 0.1132 time to fit residues: 14.5909 Evaluate side-chains 71 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 146 optimal weight: 0.0170 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 0.0670 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.9158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN C 130 HIS ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS E 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.043098 restraints weight = 35542.690| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 3.91 r_work: 0.2364 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12639 Z= 0.158 Angle : 0.659 9.543 17220 Z= 0.314 Chirality : 0.045 0.276 1971 Planarity : 0.003 0.027 2148 Dihedral : 5.206 52.368 1631 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.41 % Allowed : 8.80 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.79 (0.21), residues: 1476 helix: 3.26 (0.27), residues: 351 sheet: -0.32 (0.35), residues: 216 loop : -2.32 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 211 TYR 0.010 0.001 TYR E 102 PHE 0.012 0.001 PHE D 9 TRP 0.008 0.001 TRP F 92 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (12576) covalent geometry : angle 0.63288 / 0.31 (17049) SS BOND : bond 0.00549 / 0.30 ( 18) SS BOND : angle 1.65343 / 1.01 ( 36) hydrogen bonds : bond 0.06664 / 4.63 ( 403) hydrogen bonds : angle 3.98299 / 2.71 ( 1101) link_ALPHA1-3 : bond 0.00653 / 0.33 ( 3) link_ALPHA1-3 : angle 1.73094 / 1.14 ( 9) link_ALPHA1-6 : bond 0.00398 / 0.20 ( 3) link_ALPHA1-6 : angle 1.40651 / 0.90 ( 9) link_BETA1-4 : bond 0.00541 / 0.33 ( 21) link_BETA1-4 : angle 1.36473 / 0.88 ( 63) link_BETA1-6 : bond 0.00477 / 0.24 ( 3) link_BETA1-6 : angle 1.20542 / 0.79 ( 9) link_NAG-ASN : bond 0.00190 / 0.12 ( 15) link_NAG-ASN : angle 2.91572 / 1.89 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.7639 (p90) REVERT: A 196 GLN cc_start: 0.8351 (tt0) cc_final: 0.7796 (mp10) REVERT: B 27 GLN cc_start: 0.9315 (tp-100) cc_final: 0.9090 (tp-100) REVERT: F 2 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8626 (tm) REVERT: E 7 ILE cc_start: 0.8784 (mp) cc_final: 0.8570 (tp) REVERT: E 184 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.6400 (p90) REVERT: E 296 GLN cc_start: 0.9489 (OUTLIER) cc_final: 0.9148 (pp30) outliers start: 31 outliers final: 16 residues processed: 91 average time/residue: 0.1219 time to fit residues: 16.5169 Evaluate side-chains 75 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.058367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.043955 restraints weight = 35529.309| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 3.88 r_work: 0.2378 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12639 Z= 0.147 Angle : 0.654 9.555 17220 Z= 0.311 Chirality : 0.045 0.270 1971 Planarity : 0.003 0.026 2148 Dihedral : 5.066 48.680 1631 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.26 % Allowed : 8.96 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.59 (0.21), residues: 1476 helix: 3.46 (0.27), residues: 351 sheet: -0.19 (0.35), residues: 216 loop : -2.21 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 127 TYR 0.009 0.001 TYR C 102 PHE 0.011 0.001 PHE D 9 TRP 0.008 0.001 TRP D 92 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12576) covalent geometry : angle 0.62670 / 0.30 (17049) SS BOND : bond 0.00369 / 0.23 ( 18) SS BOND : angle 2.24842 / 1.42 ( 36) hydrogen bonds : bond 0.06505 / 4.52 ( 403) hydrogen bonds : angle 3.97294 / 2.70 ( 1101) link_ALPHA1-3 : bond 0.00689 / 0.35 ( 3) link_ALPHA1-3 : angle 1.36173 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00410 / 0.21 ( 3) link_ALPHA1-6 : angle 1.40959 / 0.89 ( 9) link_BETA1-4 : bond 0.00515 / 0.32 ( 21) link_BETA1-4 : angle 1.30763 / 0.84 ( 63) link_BETA1-6 : bond 0.00480 / 0.24 ( 3) link_BETA1-6 : angle 1.19186 / 0.78 ( 9) link_NAG-ASN : bond 0.00184 / 0.11 ( 15) link_NAG-ASN : angle 2.69370 / 1.74 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.7656 (p90) REVERT: B 27 GLN cc_start: 0.9300 (tp-100) cc_final: 0.9084 (tp-100) REVERT: F 2 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8598 (tm) REVERT: C 7 ILE cc_start: 0.8797 (mp) cc_final: 0.8533 (tp) REVERT: C 239 GLN cc_start: 0.9019 (mp10) cc_final: 0.8708 (mp10) REVERT: E 7 ILE cc_start: 0.8772 (mp) cc_final: 0.8551 (tp) REVERT: E 184 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.6446 (p90) REVERT: E 296 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.9061 (pp30) outliers start: 29 outliers final: 16 residues processed: 88 average time/residue: 0.1079 time to fit residues: 14.5332 Evaluate side-chains 76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.044133 restraints weight = 35214.489| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 3.90 r_work: 0.2405 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12639 Z= 0.124 Angle : 0.653 9.561 17220 Z= 0.311 Chirality : 0.045 0.273 1971 Planarity : 0.003 0.024 2148 Dihedral : 5.051 44.369 1631 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.87 % Allowed : 9.97 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1476 helix: 3.64 (0.26), residues: 351 sheet: -0.08 (0.35), residues: 216 loop : -2.09 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 127 TYR 0.010 0.001 TYR E 195 PHE 0.010 0.001 PHE B 9 TRP 0.007 0.001 TRP D 92 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (12576) covalent geometry : angle 0.62556 / 0.30 (17049) SS BOND : bond 0.00247 / 0.16 ( 18) SS BOND : angle 2.56664 / 1.66 ( 36) hydrogen bonds : bond 0.06203 / 4.32 ( 403) hydrogen bonds : angle 3.96962 / 2.71 ( 1101) link_ALPHA1-3 : bond 0.00697 / 0.35 ( 3) link_ALPHA1-3 : angle 1.25385 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00417 / 0.21 ( 3) link_ALPHA1-6 : angle 1.42206 / 0.89 ( 9) link_BETA1-4 : bond 0.00513 / 0.32 ( 21) link_BETA1-4 : angle 1.27052 / 0.81 ( 63) link_BETA1-6 : bond 0.00494 / 0.25 ( 3) link_BETA1-6 : angle 1.16312 / 0.75 ( 9) link_NAG-ASN : bond 0.00163 / 0.10 ( 15) link_NAG-ASN : angle 2.48437 / 1.60 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 CYS cc_start: 0.5830 (OUTLIER) cc_final: 0.5617 (p) REVERT: B 27 GLN cc_start: 0.9276 (tp-100) cc_final: 0.9066 (tp-100) REVERT: F 2 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8576 (tm) REVERT: C 239 GLN cc_start: 0.9038 (mp10) cc_final: 0.8720 (mp10) REVERT: E 47 CYS cc_start: 0.5686 (OUTLIER) cc_final: 0.5355 (p) REVERT: E 184 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.6464 (p90) REVERT: E 196 GLN cc_start: 0.8230 (tt0) cc_final: 0.8012 (mt0) REVERT: E 239 GLN cc_start: 0.9192 (mp10) cc_final: 0.8828 (mp10) REVERT: E 296 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.8980 (pp30) outliers start: 24 outliers final: 13 residues processed: 89 average time/residue: 0.1015 time to fit residues: 13.9718 Evaluate side-chains 74 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 0.5980 chunk 88 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 140 optimal weight: 0.4980 chunk 142 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.044408 restraints weight = 35300.762| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 3.90 r_work: 0.2412 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12639 Z= 0.124 Angle : 0.639 9.562 17220 Z= 0.305 Chirality : 0.045 0.264 1971 Planarity : 0.003 0.024 2148 Dihedral : 4.900 38.850 1631 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.79 % Allowed : 10.67 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1476 helix: 3.74 (0.26), residues: 351 sheet: 0.06 (0.36), residues: 216 loop : -2.02 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 127 TYR 0.008 0.001 TYR E 195 PHE 0.020 0.001 PHE D 140 TRP 0.007 0.001 TRP D 92 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12576) covalent geometry : angle 0.61481 / 0.30 (17049) SS BOND : bond 0.00281 / 0.18 ( 18) SS BOND : angle 2.37439 / 1.52 ( 36) hydrogen bonds : bond 0.06035 / 4.20 ( 403) hydrogen bonds : angle 3.89611 / 2.66 ( 1101) link_ALPHA1-3 : bond 0.00764 / 0.38 ( 3) link_ALPHA1-3 : angle 1.26705 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00412 / 0.21 ( 3) link_ALPHA1-6 : angle 1.41571 / 0.89 ( 9) link_BETA1-4 : bond 0.00504 / 0.31 ( 21) link_BETA1-4 : angle 1.23578 / 0.79 ( 63) link_BETA1-6 : bond 0.00487 / 0.24 ( 3) link_BETA1-6 : angle 1.15758 / 0.75 ( 9) link_NAG-ASN : bond 0.00156 / 0.10 ( 15) link_NAG-ASN : angle 2.35745 / 1.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.7601 (p90) REVERT: B 27 GLN cc_start: 0.9297 (tp-100) cc_final: 0.9036 (tp-100) REVERT: F 2 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8536 (tm) REVERT: C 239 GLN cc_start: 0.9017 (mp10) cc_final: 0.8704 (mp10) REVERT: E 184 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.6357 (p90) REVERT: E 196 GLN cc_start: 0.8207 (tt0) cc_final: 0.8002 (mt0) REVERT: E 239 GLN cc_start: 0.9196 (mp10) cc_final: 0.8833 (mp10) REVERT: E 296 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8924 (pp30) outliers start: 23 outliers final: 13 residues processed: 82 average time/residue: 0.1113 time to fit residues: 13.7732 Evaluate side-chains 73 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 1 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.0570 chunk 65 optimal weight: 0.0060 chunk 120 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.044827 restraints weight = 34942.102| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 3.87 r_work: 0.2425 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12639 Z= 0.122 Angle : 0.648 10.794 17220 Z= 0.308 Chirality : 0.044 0.262 1971 Planarity : 0.003 0.024 2148 Dihedral : 4.851 38.102 1631 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.56 % Allowed : 10.90 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.22), residues: 1476 helix: 3.77 (0.26), residues: 351 sheet: -0.06 (0.35), residues: 225 loop : -1.95 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 127 TYR 0.009 0.001 TYR E 195 PHE 0.019 0.001 PHE D 140 TRP 0.006 0.001 TRP D 92 HIS 0.004 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (12576) covalent geometry : angle 0.62047 / 0.30 (17049) SS BOND : bond 0.00352 / 0.18 ( 18) SS BOND : angle 2.88655 / 1.85 ( 36) hydrogen bonds : bond 0.05901 / 4.12 ( 403) hydrogen bonds : angle 3.96158 / 2.71 ( 1101) link_ALPHA1-3 : bond 0.00769 / 0.39 ( 3) link_ALPHA1-3 : angle 1.26693 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00418 / 0.21 ( 3) link_ALPHA1-6 : angle 1.42115 / 0.89 ( 9) link_BETA1-4 : bond 0.00496 / 0.31 ( 21) link_BETA1-4 : angle 1.21038 / 0.77 ( 63) link_BETA1-6 : bond 0.00485 / 0.24 ( 3) link_BETA1-6 : angle 1.15203 / 0.74 ( 9) link_NAG-ASN : bond 0.00151 / 0.09 ( 15) link_NAG-ASN : angle 2.24895 / 1.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.7593 (p90) REVERT: B 27 GLN cc_start: 0.9299 (tp-100) cc_final: 0.9053 (tp-100) REVERT: F 2 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8523 (tm) REVERT: C 239 GLN cc_start: 0.9003 (mp10) cc_final: 0.8697 (mp10) REVERT: E 184 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.6344 (p90) REVERT: E 196 GLN cc_start: 0.8164 (tt0) cc_final: 0.7955 (mt0) REVERT: E 296 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8929 (pp30) outliers start: 20 outliers final: 10 residues processed: 80 average time/residue: 0.1070 time to fit residues: 13.1546 Evaluate side-chains 70 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 32 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.043348 restraints weight = 35528.765| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 3.90 r_work: 0.2384 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12639 Z= 0.187 Angle : 0.677 13.122 17220 Z= 0.323 Chirality : 0.045 0.254 1971 Planarity : 0.003 0.024 2148 Dihedral : 4.894 37.498 1631 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.40 % Allowed : 11.21 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1476 helix: 3.72 (0.26), residues: 351 sheet: 0.16 (0.36), residues: 216 loop : -1.96 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 127 TYR 0.010 0.001 TYR A 102 PHE 0.020 0.002 PHE D 140 TRP 0.008 0.001 TRP F 92 HIS 0.004 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (12576) covalent geometry : angle 0.65292 / 0.32 (17049) SS BOND : bond 0.00361 / 0.24 ( 18) SS BOND : angle 2.57171 / 1.65 ( 36) hydrogen bonds : bond 0.06329 / 4.41 ( 403) hydrogen bonds : angle 3.98447 / 2.72 ( 1101) link_ALPHA1-3 : bond 0.00740 / 0.37 ( 3) link_ALPHA1-3 : angle 1.33650 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00453 / 0.23 ( 3) link_ALPHA1-6 : angle 1.42213 / 0.89 ( 9) link_BETA1-4 : bond 0.00461 / 0.28 ( 21) link_BETA1-4 : angle 1.21459 / 0.78 ( 63) link_BETA1-6 : bond 0.00442 / 0.22 ( 3) link_BETA1-6 : angle 1.21436 / 0.79 ( 9) link_NAG-ASN : bond 0.00219 / 0.14 ( 15) link_NAG-ASN : angle 2.32776 / 1.51 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7568 (p90) REVERT: B 27 GLN cc_start: 0.9308 (tp-100) cc_final: 0.9053 (tp-100) REVERT: F 2 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8497 (tm) REVERT: E 184 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.6379 (p90) REVERT: E 296 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.8917 (pp30) outliers start: 18 outliers final: 11 residues processed: 72 average time/residue: 0.1140 time to fit residues: 12.4458 Evaluate side-chains 68 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.043159 restraints weight = 35325.943| |-----------------------------------------------------------------------------| r_work (start): 0.2531 rms_B_bonded: 3.89 r_work: 0.2377 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12639 Z= 0.174 Angle : 0.678 13.837 17220 Z= 0.324 Chirality : 0.046 0.254 1971 Planarity : 0.003 0.025 2148 Dihedral : 4.888 36.860 1631 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.40 % Allowed : 11.21 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1476 helix: 3.70 (0.26), residues: 351 sheet: -0.03 (0.35), residues: 225 loop : -1.94 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 127 TYR 0.010 0.001 TYR C 102 PHE 0.017 0.001 PHE D 140 TRP 0.008 0.001 TRP F 92 HIS 0.004 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (12576) covalent geometry : angle 0.65319 / 0.32 (17049) SS BOND : bond 0.00331 / 0.23 ( 18) SS BOND : angle 2.70723 / 1.69 ( 36) hydrogen bonds : bond 0.06443 / 4.49 ( 403) hydrogen bonds : angle 4.02840 / 2.76 ( 1101) link_ALPHA1-3 : bond 0.00734 / 0.37 ( 3) link_ALPHA1-3 : angle 1.30592 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00442 / 0.22 ( 3) link_ALPHA1-6 : angle 1.40486 / 0.87 ( 9) link_BETA1-4 : bond 0.00466 / 0.29 ( 21) link_BETA1-4 : angle 1.19795 / 0.76 ( 63) link_BETA1-6 : bond 0.00449 / 0.23 ( 3) link_BETA1-6 : angle 1.21311 / 0.79 ( 9) link_NAG-ASN : bond 0.00195 / 0.12 ( 15) link_NAG-ASN : angle 2.29680 / 1.49 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.45 seconds wall clock time: 40 minutes 35.22 seconds (2435.22 seconds total)