Starting phenix.real_space_refine on Thu Sep 18 00:54:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hjn_0234/09_2025/6hjn_0234.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjn_0234/09_2025/6hjn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2025/6hjn_0234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2025/6hjn_0234.map" model { file = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2025/6hjn_0234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjn_0234/09_2025/6hjn_0234.cif" } 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-2.0-5805/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 6 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: 24 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: 24 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: 24 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.59, per 1000 atoms: 0.29 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: 1.42 Conformation dependent library (CDL) restraints added in 597.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.45 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: 2.64 Time building geometry restraints manager: 1.80 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 - 20.72: 7529 20.72 - 41.44: 385 41.44 - 62.16: 72 62.16 - 82.88: 42 82.88 - 103.60: 24 Dihedral angle restraints: 8052 sinusoidal: 3756 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 8049 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: 0.03 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: 12.790 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.620 Find NCS groups from input model: 0.320 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:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 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 : 15.251 103.604 5256 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 aren 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 covalent geometry : bond 0.00814 (12576) covalent geometry : angle 1.23077 (17049) SS BOND : bond 0.00877 ( 18) SS BOND : angle 1.62224 ( 36) hydrogen bonds : bond 0.17725 ( 403) hydrogen bonds : angle 6.17035 ( 1101) link_ALPHA1-3 : bond 0.03367 ( 3) link_ALPHA1-3 : angle 8.09519 ( 9) link_ALPHA1-6 : bond 0.01391 ( 3) link_ALPHA1-6 : angle 3.40510 ( 9) link_BETA1-4 : bond 0.00519 ( 21) link_BETA1-4 : angle 3.61952 ( 63) link_BETA1-6 : bond 0.00125 ( 3) link_BETA1-6 : angle 1.74271 ( 9) link_NAG-ASN : bond 0.01015 ( 15) link_NAG-ASN : angle 9.12498 ( 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 : 0.508 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: 0.1708 time to fit residues: 33.2401 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 : 0.581 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 130 HIS 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 130 HIS E 184 HIS E 286 HIS E 299 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.044514 restraints weight = 35204.267| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 3.88 r_work: 0.2408 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12639 Z= 0.162 Angle : 0.817 15.498 17220 Z= 0.365 Chirality : 0.050 0.412 1971 Planarity : 0.004 0.033 2148 Dihedral : 13.034 78.982 2550 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.57 % Allowed : 7.48 % 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 aren not related in a simple way. whole: -2.00 (0.20), residues: 1476 helix: 2.01 (0.28), residues: 351 sheet: -1.41 (0.31), residues: 219 loop : -2.90 (0.16), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 116 TYR 0.016 0.001 TYR C 161 PHE 0.013 0.001 PHE B 140 TRP 0.015 0.001 TRP A 255 HIS 0.003 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00331 (12576) covalent geometry : angle 0.75658 (17049) SS BOND : bond 0.00512 ( 18) SS BOND : angle 0.88540 ( 36) hydrogen bonds : bond 0.07256 ( 403) hydrogen bonds : angle 4.50231 ( 1101) link_ALPHA1-3 : bond 0.03946 ( 3) link_ALPHA1-3 : angle 4.71697 ( 9) link_ALPHA1-6 : bond 0.00282 ( 3) link_ALPHA1-6 : angle 1.62748 ( 9) link_BETA1-4 : bond 0.00901 ( 21) link_BETA1-4 : angle 2.34842 ( 63) link_BETA1-6 : bond 0.00691 ( 3) link_BETA1-6 : angle 1.08492 ( 9) link_NAG-ASN : bond 0.00371 ( 15) link_NAG-ASN : angle 5.00442 ( 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 102 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.515 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: 0.9045 (tt0) cc_final: 0.8670 (pt0) REVERT: B 59 MET cc_start: 0.8784 (mmm) cc_final: 0.8527 (mmm) REVERT: D 59 MET cc_start: 0.8895 (mmm) cc_final: 0.8648 (mmm) REVERT: D 149 MET cc_start: 0.9195 (mmt) cc_final: 0.8960 (mmp) REVERT: F 59 MET cc_start: 0.8791 (mmm) cc_final: 0.8537 (mmm) REVERT: F 149 MET cc_start: 0.9226 (mmt) cc_final: 0.8988 (mmp) REVERT: C 115 PHE cc_start: 0.8438 (m-10) cc_final: 0.8117 (m-10) outliers start: 33 outliers final: 12 residues processed: 94 average time/residue: 0.1684 time to fit residues: 21.3258 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 : 0.491 ------------------------------------------------------------------------------- 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: 2.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 231 ASN ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS C 184 HIS C 231 ASN E 184 HIS E 231 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.041038 restraints weight = 35993.182| |-----------------------------------------------------------------------------| r_work (start): 0.2468 rms_B_bonded: 3.90 r_work: 0.2308 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 12639 Z= 0.296 Angle : 0.793 11.469 17220 Z= 0.378 Chirality : 0.049 0.274 1971 Planarity : 0.004 0.034 2148 Dihedral : 11.254 67.352 2542 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.80 % Allowed : 7.94 % Favored : 89.25 % 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 aren not related in a simple way. whole: -1.49 (0.20), residues: 1476 helix: 2.54 (0.27), residues: 351 sheet: -0.96 (0.32), residues: 231 loop : -2.67 (0.16), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 116 TYR 0.015 0.002 TYR E 102 PHE 0.017 0.002 PHE D 110 TRP 0.014 0.002 TRP A 255 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00693 (12576) covalent geometry : angle 0.74923 (17049) SS BOND : bond 0.00620 ( 18) SS BOND : angle 1.17795 ( 36) hydrogen bonds : bond 0.07764 ( 403) hydrogen bonds : angle 4.33463 ( 1101) link_ALPHA1-3 : bond 0.03697 ( 3) link_ALPHA1-3 : angle 4.08790 ( 9) link_ALPHA1-6 : bond 0.00363 ( 3) link_ALPHA1-6 : angle 1.63743 ( 9) link_BETA1-4 : bond 0.00679 ( 21) link_BETA1-4 : angle 2.02237 ( 63) link_BETA1-6 : bond 0.00558 ( 3) link_BETA1-6 : angle 1.18542 ( 9) link_NAG-ASN : bond 0.00511 ( 15) link_NAG-ASN : angle 4.12924 ( 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 95 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8832 (tm) REVERT: B 59 MET cc_start: 0.8753 (mmm) cc_final: 0.8505 (mmm) REVERT: B 98 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8998 (tm) REVERT: F 2 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8778 (tm) REVERT: F 59 MET cc_start: 0.8725 (mmm) cc_final: 0.8507 (mmm) REVERT: C 7 ILE cc_start: 0.8988 (mp) cc_final: 0.8638 (tp) REVERT: C 296 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8885 (tm-30) outliers start: 36 outliers final: 15 residues processed: 88 average time/residue: 0.1249 time to fit residues: 16.1845 Evaluate side-chains 72 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 98 LEU 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 2 LEU 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 Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS 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: 1.9990 chunk 40 optimal weight: 0.5980 chunk 89 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 296 GLN C 184 HIS ** C 250 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.043111 restraints weight = 35196.068| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 3.86 r_work: 0.2364 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12639 Z= 0.141 Angle : 0.690 9.802 17220 Z= 0.322 Chirality : 0.046 0.273 1971 Planarity : 0.003 0.037 2148 Dihedral : 10.258 58.707 2542 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.95 % Allowed : 9.42 % Favored : 88.63 % 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 aren not related in a simple way. whole: -1.08 (0.21), residues: 1476 helix: 3.01 (0.27), residues: 351 sheet: -0.52 (0.34), residues: 216 loop : -2.49 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 281 TYR 0.012 0.001 TYR E 195 PHE 0.011 0.001 PHE D 9 TRP 0.009 0.001 TRP B 92 HIS 0.014 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00285 (12576) covalent geometry : angle 0.65393 (17049) SS BOND : bond 0.00375 ( 18) SS BOND : angle 1.29139 ( 36) hydrogen bonds : bond 0.06874 ( 403) hydrogen bonds : angle 4.01659 ( 1101) link_ALPHA1-3 : bond 0.03541 ( 3) link_ALPHA1-3 : angle 3.68282 ( 9) link_ALPHA1-6 : bond 0.00445 ( 3) link_ALPHA1-6 : angle 1.87151 ( 9) link_BETA1-4 : bond 0.00656 ( 21) link_BETA1-4 : angle 1.72664 ( 63) link_BETA1-6 : bond 0.00592 ( 3) link_BETA1-6 : angle 1.11447 ( 9) link_NAG-ASN : bond 0.00192 ( 15) link_NAG-ASN : angle 3.29420 ( 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 85 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.530 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: 0.8353 (OUTLIER) cc_final: 0.7564 (p90) REVERT: B 2 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8817 (tm) REVERT: B 27 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9082 (tp-100) REVERT: B 59 MET cc_start: 0.8762 (mmm) cc_final: 0.8529 (mmm) REVERT: B 98 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8893 (tm) REVERT: F 2 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8656 (tm) REVERT: F 59 MET cc_start: 0.8719 (mmm) cc_final: 0.8516 (mmm) REVERT: C 196 GLN cc_start: 0.8432 (tt0) cc_final: 0.7803 (mp10) REVERT: C 317 MET cc_start: 0.9331 (ttt) cc_final: 0.9126 (ttt) REVERT: E 7 ILE cc_start: 0.8795 (mp) cc_final: 0.8437 (tp) REVERT: E 296 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8832 (tm-30) outliers start: 25 outliers final: 11 residues processed: 82 average time/residue: 0.1321 time to fit residues: 15.6995 Evaluate side-chains 68 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 45 ILE Chi-restraints excluded: chain B residue 98 LEU 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 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 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: 0.6980 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** 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 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.043288 restraints weight = 35341.687| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 3.89 r_work: 0.2371 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12639 Z= 0.143 Angle : 0.673 9.576 17220 Z= 0.314 Chirality : 0.045 0.259 1971 Planarity : 0.003 0.026 2148 Dihedral : 9.435 57.152 2542 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.49 % Allowed : 8.64 % Favored : 88.86 % 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 aren not related in a simple way. whole: -0.82 (0.21), residues: 1476 helix: 3.24 (0.27), residues: 351 sheet: -0.36 (0.35), residues: 216 loop : -2.34 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 211 TYR 0.010 0.001 TYR E 195 PHE 0.011 0.001 PHE D 9 TRP 0.007 0.001 TRP D 92 HIS 0.005 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00302 (12576) covalent geometry : angle 0.63916 (17049) SS BOND : bond 0.00272 ( 18) SS BOND : angle 1.71434 ( 36) hydrogen bonds : bond 0.06584 ( 403) hydrogen bonds : angle 3.95185 ( 1101) link_ALPHA1-3 : bond 0.03405 ( 3) link_ALPHA1-3 : angle 3.45568 ( 9) link_ALPHA1-6 : bond 0.00582 ( 3) link_ALPHA1-6 : angle 1.81072 ( 9) link_BETA1-4 : bond 0.00586 ( 21) link_BETA1-4 : angle 1.62531 ( 63) link_BETA1-6 : bond 0.00584 ( 3) link_BETA1-6 : angle 1.10480 ( 9) link_NAG-ASN : bond 0.00207 ( 15) link_NAG-ASN : angle 3.04976 ( 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: 32 poor density : 63 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7617 (p90) REVERT: A 305 GLU cc_start: 0.9105 (tt0) cc_final: 0.8619 (pt0) REVERT: B 2 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8824 (tm) REVERT: B 27 GLN cc_start: 0.9316 (tp-100) cc_final: 0.9085 (tp-100) REVERT: B 59 MET cc_start: 0.8786 (mmm) cc_final: 0.8561 (mmm) REVERT: B 98 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8889 (tm) REVERT: F 2 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8606 (tm) REVERT: F 59 MET cc_start: 0.8697 (mmm) cc_final: 0.8488 (mmm) REVERT: C 317 MET cc_start: 0.9351 (ttt) cc_final: 0.9142 (ttt) REVERT: E 7 ILE cc_start: 0.8802 (mp) cc_final: 0.8496 (tp) REVERT: E 184 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.6605 (p90) outliers start: 32 outliers final: 13 residues processed: 89 average time/residue: 0.1220 time to fit residues: 15.9862 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 : 0.494 ------------------------------------------------------------------------------- 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 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 140 PHE 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 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 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 105 optimal weight: 0.0170 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 196 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.043858 restraints weight = 35225.802| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 3.88 r_work: 0.2394 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12639 Z= 0.137 Angle : 0.667 9.579 17220 Z= 0.311 Chirality : 0.045 0.253 1971 Planarity : 0.003 0.030 2148 Dihedral : 8.564 57.173 2542 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.41 % Allowed : 9.11 % 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 aren not related in a simple way. whole: -0.59 (0.21), residues: 1476 helix: 3.44 (0.27), residues: 351 sheet: -0.19 (0.35), residues: 216 loop : -2.20 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 127 TYR 0.011 0.001 TYR A 195 PHE 0.011 0.001 PHE D 9 TRP 0.007 0.001 TRP D 92 HIS 0.005 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00286 (12576) covalent geometry : angle 0.63452 (17049) SS BOND : bond 0.00296 ( 18) SS BOND : angle 2.24676 ( 36) hydrogen bonds : bond 0.06280 ( 403) hydrogen bonds : angle 3.89702 ( 1101) link_ALPHA1-3 : bond 0.03394 ( 3) link_ALPHA1-3 : angle 3.39269 ( 9) link_ALPHA1-6 : bond 0.00879 ( 3) link_ALPHA1-6 : angle 1.40622 ( 9) link_BETA1-4 : bond 0.00551 ( 21) link_BETA1-4 : angle 1.51084 ( 63) link_BETA1-6 : bond 0.00576 ( 3) link_BETA1-6 : angle 1.09438 ( 9) link_NAG-ASN : bond 0.00185 ( 15) link_NAG-ASN : angle 2.76346 ( 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 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.7641 (p90) REVERT: A 239 GLN cc_start: 0.9258 (mp10) cc_final: 0.8984 (mp10) REVERT: B 2 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8779 (tm) REVERT: B 27 GLN cc_start: 0.9311 (tp-100) cc_final: 0.9099 (tp-100) REVERT: B 59 MET cc_start: 0.8773 (mmm) cc_final: 0.8538 (mmm) REVERT: B 98 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8875 (tm) REVERT: F 2 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8585 (tm) REVERT: F 59 MET cc_start: 0.8731 (mmm) cc_final: 0.8505 (mmm) REVERT: C 196 GLN cc_start: 0.8320 (tt0) cc_final: 0.7703 (mp10) REVERT: C 317 MET cc_start: 0.9358 (ttt) cc_final: 0.9142 (ttt) REVERT: E 7 ILE cc_start: 0.8767 (mp) cc_final: 0.8545 (tp) REVERT: E 184 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.6560 (p90) REVERT: E 239 GLN cc_start: 0.9202 (mp10) cc_final: 0.8838 (mp10) outliers start: 31 outliers final: 14 residues processed: 99 average time/residue: 0.1122 time to fit residues: 16.7516 Evaluate side-chains 76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 45 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 140 PHE 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 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 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 31 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 89 optimal weight: 0.0010 chunk 133 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 196 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.044530 restraints weight = 35257.375| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 3.89 r_work: 0.2416 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12639 Z= 0.130 Angle : 0.667 9.944 17220 Z= 0.311 Chirality : 0.045 0.250 1971 Planarity : 0.003 0.024 2148 Dihedral : 8.291 56.793 2542 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.02 % Allowed : 9.97 % Favored : 88.01 % 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 aren not related in a simple way. whole: -0.38 (0.21), residues: 1476 helix: 3.62 (0.26), residues: 351 sheet: -0.07 (0.35), residues: 216 loop : -2.06 (0.18), residues: 909 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 0.010 0.001 PHE D 9 TRP 0.006 0.001 TRP D 92 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00267 (12576) covalent geometry : angle 0.63769 (17049) SS BOND : bond 0.00327 ( 18) SS BOND : angle 2.22322 ( 36) hydrogen bonds : bond 0.06013 ( 403) hydrogen bonds : angle 3.88949 ( 1101) link_ALPHA1-3 : bond 0.03324 ( 3) link_ALPHA1-3 : angle 3.44684 ( 9) link_ALPHA1-6 : bond 0.00845 ( 3) link_ALPHA1-6 : angle 1.24846 ( 9) link_BETA1-4 : bond 0.00554 ( 21) link_BETA1-4 : angle 1.42906 ( 63) link_BETA1-6 : bond 0.00577 ( 3) link_BETA1-6 : angle 1.08452 ( 9) link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 2.57226 ( 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 88 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7607 (p90) REVERT: A 239 GLN cc_start: 0.9304 (mp10) cc_final: 0.9020 (mp10) REVERT: B 2 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8762 (tm) REVERT: B 27 GLN cc_start: 0.9317 (tp-100) cc_final: 0.9047 (tp-100) REVERT: B 59 MET cc_start: 0.8792 (mmm) cc_final: 0.8566 (mmm) REVERT: F 2 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8575 (tm) REVERT: F 59 MET cc_start: 0.8751 (mmm) cc_final: 0.8511 (mmm) REVERT: C 7 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8418 (mp) REVERT: C 317 MET cc_start: 0.9342 (ttt) cc_final: 0.9108 (ttt) REVERT: E 47 CYS cc_start: 0.4946 (OUTLIER) cc_final: 0.4644 (p) REVERT: E 184 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.6516 (p90) outliers start: 26 outliers final: 11 residues processed: 85 average time/residue: 0.1221 time to fit residues: 15.3720 Evaluate side-chains 74 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 B residue 140 PHE 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 7 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 0.0000 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 196 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.044143 restraints weight = 35267.362| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 3.89 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: 0.8801 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12639 Z= 0.146 Angle : 0.675 10.270 17220 Z= 0.315 Chirality : 0.045 0.243 1971 Planarity : 0.003 0.024 2148 Dihedral : 8.187 56.943 2542 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.87 % Allowed : 10.20 % Favored : 87.93 % 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 aren not related in a simple way. whole: -0.30 (0.22), residues: 1476 helix: 3.69 (0.26), residues: 351 sheet: -0.16 (0.35), residues: 225 loop : -1.98 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 127 TYR 0.009 0.001 TYR A 102 PHE 0.011 0.001 PHE D 9 TRP 0.006 0.001 TRP F 92 HIS 0.004 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00317 (12576) covalent geometry : angle 0.64359 (17049) SS BOND : bond 0.00294 ( 18) SS BOND : angle 2.56360 ( 36) hydrogen bonds : bond 0.06082 ( 403) hydrogen bonds : angle 3.88686 ( 1101) link_ALPHA1-3 : bond 0.03292 ( 3) link_ALPHA1-3 : angle 3.51018 ( 9) link_ALPHA1-6 : bond 0.00786 ( 3) link_ALPHA1-6 : angle 1.21898 ( 9) link_BETA1-4 : bond 0.00536 ( 21) link_BETA1-4 : angle 1.40701 ( 63) link_BETA1-6 : bond 0.00568 ( 3) link_BETA1-6 : angle 1.10884 ( 9) link_NAG-ASN : bond 0.00183 ( 15) link_NAG-ASN : angle 2.49448 ( 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 84 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7530 (p90) REVERT: A 239 GLN cc_start: 0.9293 (mp10) cc_final: 0.9002 (mp10) REVERT: B 2 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8708 (tm) REVERT: B 27 GLN cc_start: 0.9298 (tp-100) cc_final: 0.9048 (tp-100) REVERT: B 59 MET cc_start: 0.8781 (mmm) cc_final: 0.8532 (mmm) REVERT: F 2 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8473 (tm) REVERT: F 59 MET cc_start: 0.8723 (mmm) cc_final: 0.8504 (mmm) REVERT: C 7 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8367 (mp) REVERT: C 239 GLN cc_start: 0.9133 (mp10) cc_final: 0.8909 (mp10) REVERT: C 317 MET cc_start: 0.9351 (ttt) cc_final: 0.9120 (ttt) REVERT: E 184 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.6417 (p90) outliers start: 24 outliers final: 13 residues processed: 82 average time/residue: 0.1199 time to fit residues: 14.6552 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 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 B residue 140 PHE 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 98 LEU 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 184 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS E 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.044143 restraints weight = 35125.588| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 3.88 r_work: 0.2407 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12639 Z= 0.146 Angle : 0.680 12.435 17220 Z= 0.317 Chirality : 0.045 0.240 1971 Planarity : 0.003 0.024 2148 Dihedral : 8.117 56.839 2542 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.79 % Allowed : 10.51 % Favored : 87.69 % 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 aren not related in a simple way. whole: -0.24 (0.22), residues: 1476 helix: 3.73 (0.26), residues: 351 sheet: -0.11 (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 0.009 0.001 TYR C 102 PHE 0.011 0.001 PHE D 9 TRP 0.007 0.001 TRP F 92 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00317 (12576) covalent geometry : angle 0.65050 (17049) SS BOND : bond 0.00346 ( 18) SS BOND : angle 2.62851 ( 36) hydrogen bonds : bond 0.06081 ( 403) hydrogen bonds : angle 3.93454 ( 1101) link_ALPHA1-3 : bond 0.03141 ( 3) link_ALPHA1-3 : angle 3.47952 ( 9) link_ALPHA1-6 : bond 0.00739 ( 3) link_ALPHA1-6 : angle 1.21340 ( 9) link_BETA1-4 : bond 0.00570 ( 21) link_BETA1-4 : angle 1.35967 ( 63) link_BETA1-6 : bond 0.00566 ( 3) link_BETA1-6 : angle 1.11772 ( 9) link_NAG-ASN : bond 0.00174 ( 15) link_NAG-ASN : angle 2.38313 ( 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 79 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7541 (p90) REVERT: B 2 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8690 (tm) REVERT: B 27 GLN cc_start: 0.9291 (tp-100) cc_final: 0.9069 (tp-100) REVERT: B 59 MET cc_start: 0.8785 (mmm) cc_final: 0.8528 (mmm) REVERT: F 2 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8466 (tm) REVERT: F 27 GLN cc_start: 0.9415 (tp-100) cc_final: 0.9164 (tp-100) REVERT: F 59 MET cc_start: 0.8735 (mmm) cc_final: 0.8517 (mmm) REVERT: C 7 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 115 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: C 317 MET cc_start: 0.9365 (ttt) cc_final: 0.9130 (ttt) REVERT: E 184 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.6429 (p90) REVERT: E 268 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9029 (mm) outliers start: 23 outliers final: 13 residues processed: 76 average time/residue: 0.1160 time to fit residues: 13.5281 Evaluate side-chains 74 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 B residue 140 PHE 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 98 LEU 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 115 PHE 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 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 32 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.0270 chunk 137 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 196 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 = 0.2942 r_free = 0.2942 target = 0.058962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.044390 restraints weight = 35287.783| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 3.86 r_work: 0.2416 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12639 Z= 0.139 Angle : 0.663 12.282 17220 Z= 0.309 Chirality : 0.045 0.250 1971 Planarity : 0.003 0.024 2148 Dihedral : 8.017 56.764 2542 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.64 % Allowed : 10.67 % Favored : 87.69 % 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 aren not related in a simple way. whole: -0.17 (0.22), residues: 1476 helix: 3.77 (0.26), residues: 351 sheet: -0.04 (0.35), residues: 225 loop : -1.90 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 127 TYR 0.009 0.001 TYR E 195 PHE 0.011 0.001 PHE B 9 TRP 0.006 0.001 TRP F 92 HIS 0.005 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00299 (12576) covalent geometry : angle 0.63567 (17049) SS BOND : bond 0.00337 ( 18) SS BOND : angle 2.36182 ( 36) hydrogen bonds : bond 0.05984 ( 403) hydrogen bonds : angle 3.85891 ( 1101) link_ALPHA1-3 : bond 0.03174 ( 3) link_ALPHA1-3 : angle 3.55943 ( 9) link_ALPHA1-6 : bond 0.00714 ( 3) link_ALPHA1-6 : angle 1.21992 ( 9) link_BETA1-4 : bond 0.00534 ( 21) link_BETA1-4 : angle 1.31950 ( 63) link_BETA1-6 : bond 0.00553 ( 3) link_BETA1-6 : angle 1.10819 ( 9) link_NAG-ASN : bond 0.00158 ( 15) link_NAG-ASN : angle 2.25466 ( 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 82 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.7544 (p90) REVERT: B 2 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8665 (tm) REVERT: B 27 GLN cc_start: 0.9324 (tp-100) cc_final: 0.9067 (tp-100) REVERT: B 59 MET cc_start: 0.8783 (mmm) cc_final: 0.8530 (mmm) REVERT: F 2 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8487 (tm) REVERT: F 27 GLN cc_start: 0.9456 (tp-100) cc_final: 0.9208 (tp-100) REVERT: F 59 MET cc_start: 0.8740 (mmm) cc_final: 0.8538 (mmm) REVERT: C 7 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 317 MET cc_start: 0.9362 (ttt) cc_final: 0.9133 (ttt) REVERT: E 184 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.6411 (p90) REVERT: E 268 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9032 (mm) outliers start: 21 outliers final: 13 residues processed: 80 average time/residue: 0.1242 time to fit residues: 14.7706 Evaluate side-chains 73 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 B residue 140 PHE 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 98 LEU 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 184 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 196 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.058484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.043874 restraints weight = 35225.667| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 3.86 r_work: 0.2396 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2926 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= 0.161 Angle : 0.680 12.418 17220 Z= 0.318 Chirality : 0.045 0.241 1971 Planarity : 0.003 0.024 2148 Dihedral : 8.036 56.915 2542 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.95 % Allowed : 10.67 % 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 aren not related in a simple way. whole: -0.14 (0.22), residues: 1476 helix: 3.80 (0.26), residues: 351 sheet: -0.02 (0.35), residues: 225 loop : -1.88 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 127 TYR 0.009 0.001 TYR C 102 PHE 0.012 0.001 PHE D 9 TRP 0.007 0.001 TRP F 92 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00359 (12576) covalent geometry : angle 0.65163 (17049) SS BOND : bond 0.00361 ( 18) SS BOND : angle 2.61748 ( 36) hydrogen bonds : bond 0.06149 ( 403) hydrogen bonds : angle 3.92919 ( 1101) link_ALPHA1-3 : bond 0.03104 ( 3) link_ALPHA1-3 : angle 3.51856 ( 9) link_ALPHA1-6 : bond 0.00750 ( 3) link_ALPHA1-6 : angle 1.23247 ( 9) link_BETA1-4 : bond 0.00513 ( 21) link_BETA1-4 : angle 1.32139 ( 63) link_BETA1-6 : bond 0.00533 ( 3) link_BETA1-6 : angle 1.12607 ( 9) link_NAG-ASN : bond 0.00179 ( 15) link_NAG-ASN : angle 2.26251 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.10 seconds wall clock time: 44 minutes 13.94 seconds (2653.94 seconds total)