Starting phenix.real_space_refine on Wed Jul 30 20:16:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hjn_0234/07_2025/6hjn_0234.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjn_0234/07_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_0234/07_2025/6hjn_0234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjn_0234/07_2025/6hjn_0234.map" model { file = "/net/cci-nas-00/data/ceres_data/6hjn_0234/07_2025/6hjn_0234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjn_0234/07_2025/6hjn_0234.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.84, per 1000 atoms: 0.80 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: 3.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.57 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: 3.42 Time building geometry restraints manager: 4.01 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: 0.05 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: 57.120 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.930 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.004 TRP C 153 HIS 0.004 0.002 HIS C 276 PHE 0.013 0.003 PHE B 140 TYR 0.016 0.003 TYR D 157 ARG 0.007 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.01015 ( 15) link_NAG-ASN : angle 9.12498 ( 45) 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_ALPHA1-3 : bond 0.03367 ( 3) link_ALPHA1-3 : angle 8.09519 ( 9) hydrogen bonds : bond 0.17725 ( 403) hydrogen bonds : angle 6.17035 ( 1101) link_BETA1-6 : bond 0.00125 ( 3) link_BETA1-6 : angle 1.74271 ( 9) SS BOND : bond 0.00877 ( 18) SS BOND : angle 1.62224 ( 36) covalent geometry : bond 0.00814 (12576) covalent geometry : angle 1.23077 (17049) *********************** 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 : 1.282 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: 0.3359 time to fit residues: 65.9624 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 : 1.499 ------------------------------------------------------------------------------- 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 124 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 192 GLN A 286 HIS A 299 HIS B 169 ASN D 169 ASN F 25 HIS F 169 ASN C 184 HIS C 192 GLN C 286 HIS C 299 HIS E 184 HIS E 286 HIS E 299 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.044338 restraints weight = 35004.048| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 3.86 r_work: 0.2402 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12639 Z= 0.170 Angle : 0.834 16.175 17220 Z= 0.373 Chirality : 0.051 0.451 1971 Planarity : 0.004 0.034 2148 Dihedral : 13.266 80.574 2550 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.49 % Allowed : 7.48 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1476 helix: 1.94 (0.28), residues: 351 sheet: -1.35 (0.32), residues: 213 loop : -2.92 (0.16), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 255 HIS 0.003 0.001 HIS D 142 PHE 0.011 0.001 PHE B 140 TYR 0.017 0.001 TYR A 161 ARG 0.005 0.001 ARG D 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 15) link_NAG-ASN : angle 5.21888 ( 45) link_ALPHA1-6 : bond 0.00301 ( 3) link_ALPHA1-6 : angle 1.52438 ( 9) link_BETA1-4 : bond 0.00871 ( 21) link_BETA1-4 : angle 2.38594 ( 63) link_ALPHA1-3 : bond 0.04191 ( 3) link_ALPHA1-3 : angle 4.90592 ( 9) hydrogen bonds : bond 0.07403 ( 403) hydrogen bonds : angle 4.53317 ( 1101) link_BETA1-6 : bond 0.00679 ( 3) link_BETA1-6 : angle 1.13724 ( 9) SS BOND : bond 0.00576 ( 18) SS BOND : angle 0.87848 ( 36) covalent geometry : bond 0.00353 (12576) covalent geometry : angle 0.77033 (17049) *********************** 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 100 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.9046 (tt0) cc_final: 0.8678 (pt0) REVERT: B 59 MET cc_start: 0.8761 (mmm) cc_final: 0.8486 (mmm) REVERT: D 59 MET cc_start: 0.8901 (mmm) cc_final: 0.8641 (mmm) REVERT: D 149 MET cc_start: 0.9195 (mmt) cc_final: 0.8952 (mmp) REVERT: F 59 MET cc_start: 0.8794 (mmm) cc_final: 0.8541 (mmm) REVERT: F 149 MET cc_start: 0.9215 (mmt) cc_final: 0.8962 (mmp) REVERT: C 115 PHE cc_start: 0.8467 (m-10) cc_final: 0.8158 (m-10) outliers start: 32 outliers final: 11 residues processed: 93 average time/residue: 0.3283 time to fit residues: 41.5919 Evaluate side-chains 69 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 184 HIS E 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.058190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.043598 restraints weight = 35380.485| |-----------------------------------------------------------------------------| r_work (start): 0.2537 rms_B_bonded: 3.87 r_work: 0.2377 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12639 Z= 0.179 Angle : 0.719 11.245 17220 Z= 0.335 Chirality : 0.047 0.279 1971 Planarity : 0.004 0.030 2148 Dihedral : 11.255 67.728 2542 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.73 % Allowed : 7.55 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1476 helix: 2.70 (0.27), residues: 351 sheet: -0.92 (0.33), residues: 219 loop : -2.69 (0.16), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 92 HIS 0.004 0.001 HIS A 276 PHE 0.011 0.001 PHE D 9 TYR 0.013 0.001 TYR A 195 ARG 0.004 0.001 ARG D 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 15) link_NAG-ASN : angle 3.92152 ( 45) link_ALPHA1-6 : bond 0.00306 ( 3) link_ALPHA1-6 : angle 1.65380 ( 9) link_BETA1-4 : bond 0.00744 ( 21) link_BETA1-4 : angle 2.03596 ( 63) link_ALPHA1-3 : bond 0.03764 ( 3) link_ALPHA1-3 : angle 4.13240 ( 9) hydrogen bonds : bond 0.06991 ( 403) hydrogen bonds : angle 4.10954 ( 1101) link_BETA1-6 : bond 0.00561 ( 3) link_BETA1-6 : angle 1.13233 ( 9) SS BOND : bond 0.00569 ( 18) SS BOND : angle 0.94657 ( 36) covalent geometry : bond 0.00391 (12576) covalent geometry : angle 0.67354 (17049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.9061 (tt0) cc_final: 0.8653 (pt0) REVERT: B 149 MET cc_start: 0.9201 (mmp) cc_final: 0.8993 (mmp) REVERT: C 7 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8614 (tp) REVERT: C 115 PHE cc_start: 0.8414 (m-10) cc_final: 0.8131 (m-10) REVERT: C 196 GLN cc_start: 0.8442 (tt0) cc_final: 0.8229 (mt0) REVERT: C 296 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8805 (tm-30) REVERT: E 7 ILE cc_start: 0.8815 (mp) cc_final: 0.8511 (tp) outliers start: 35 outliers final: 13 residues processed: 89 average time/residue: 0.2541 time to fit residues: 33.6927 Evaluate side-chains 73 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 296 GLN Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN F 62 GLN C 231 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS E 130 HIS E 231 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS E 296 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.040773 restraints weight = 35919.804| |-----------------------------------------------------------------------------| r_work (start): 0.2464 rms_B_bonded: 3.92 r_work: 0.2304 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12639 Z= 0.268 Angle : 0.768 10.225 17220 Z= 0.364 Chirality : 0.047 0.257 1971 Planarity : 0.004 0.033 2148 Dihedral : 10.098 59.935 2542 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.73 % Allowed : 8.57 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.21), residues: 1476 helix: 2.82 (0.27), residues: 351 sheet: -0.46 (0.35), residues: 216 loop : -2.50 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 92 HIS 0.007 0.002 HIS E 184 PHE 0.017 0.002 PHE D 110 TYR 0.015 0.002 TYR A 102 ARG 0.004 0.001 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 15) link_NAG-ASN : angle 3.46399 ( 45) link_ALPHA1-6 : bond 0.00515 ( 3) link_ALPHA1-6 : angle 1.68448 ( 9) link_BETA1-4 : bond 0.00521 ( 21) link_BETA1-4 : angle 1.75224 ( 63) link_ALPHA1-3 : bond 0.03414 ( 3) link_ALPHA1-3 : angle 3.56907 ( 9) hydrogen bonds : bond 0.07585 ( 403) hydrogen bonds : angle 4.21875 ( 1101) link_BETA1-6 : bond 0.00566 ( 3) link_BETA1-6 : angle 1.18227 ( 9) SS BOND : bond 0.00554 ( 18) SS BOND : angle 1.50729 ( 36) covalent geometry : bond 0.00618 (12576) covalent geometry : angle 0.73445 (17049) *********************** 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 93 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8905 (mp) cc_final: 0.8577 (tp) REVERT: A 184 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.7760 (p90) REVERT: B 2 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8816 (tm) REVERT: B 27 GLN cc_start: 0.9377 (tp-100) cc_final: 0.9103 (tp-100) REVERT: D 140 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: F 2 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8789 (tm) REVERT: C 7 ILE cc_start: 0.8981 (mp) cc_final: 0.8645 (tp) REVERT: C 184 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8136 (p90) REVERT: E 7 ILE cc_start: 0.8805 (mp) cc_final: 0.8560 (tp) REVERT: E 184 HIS cc_start: 0.8792 (OUTLIER) cc_final: 0.6687 (p90) REVERT: E 296 GLN cc_start: 0.9405 (OUTLIER) cc_final: 0.8921 (pp30) outliers start: 35 outliers final: 17 residues processed: 87 average time/residue: 0.2533 time to fit residues: 32.5873 Evaluate side-chains 77 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 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 98 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 140 PHE 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 E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.042324 restraints weight = 35244.566| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 3.89 r_work: 0.2347 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12639 Z= 0.158 Angle : 0.692 9.563 17220 Z= 0.325 Chirality : 0.045 0.258 1971 Planarity : 0.003 0.028 2148 Dihedral : 9.210 57.781 2542 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.26 % Allowed : 9.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1476 helix: 3.21 (0.27), residues: 351 sheet: -0.26 (0.35), residues: 216 loop : -2.34 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 92 HIS 0.003 0.001 HIS E 276 PHE 0.012 0.001 PHE B 9 TYR 0.011 0.001 TYR A 195 ARG 0.002 0.000 ARG D 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 15) link_NAG-ASN : angle 3.01550 ( 45) link_ALPHA1-6 : bond 0.00663 ( 3) link_ALPHA1-6 : angle 1.71478 ( 9) link_BETA1-4 : bond 0.00617 ( 21) link_BETA1-4 : angle 1.54454 ( 63) link_ALPHA1-3 : bond 0.03472 ( 3) link_ALPHA1-3 : angle 3.40559 ( 9) hydrogen bonds : bond 0.06894 ( 403) hydrogen bonds : angle 4.03742 ( 1101) link_BETA1-6 : bond 0.00645 ( 3) link_BETA1-6 : angle 1.16117 ( 9) SS BOND : bond 0.00418 ( 18) SS BOND : angle 1.89679 ( 36) covalent geometry : bond 0.00335 (12576) covalent geometry : angle 0.65940 (17049) *********************** 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 91 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: A 184 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.7542 (p90) REVERT: B 2 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8775 (tm) REVERT: B 27 GLN cc_start: 0.9317 (tp-100) cc_final: 0.9096 (tp-100) REVERT: F 2 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8687 (tm) REVERT: E 115 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8176 (m-10) REVERT: E 196 GLN cc_start: 0.8337 (tt0) cc_final: 0.8102 (mt0) REVERT: E 296 GLN cc_start: 0.9500 (OUTLIER) cc_final: 0.9112 (pp30) outliers start: 29 outliers final: 13 residues processed: 88 average time/residue: 0.3179 time to fit residues: 43.2275 Evaluate side-chains 74 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 PHE 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 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 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 71 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 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 = 0.2900 r_free = 0.2900 target = 0.057304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.042565 restraints weight = 35802.541| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 3.94 r_work: 0.2354 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12639 Z= 0.163 Angle : 0.695 9.573 17220 Z= 0.326 Chirality : 0.045 0.251 1971 Planarity : 0.003 0.029 2148 Dihedral : 8.698 57.204 2542 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.57 % Allowed : 9.19 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1476 helix: 3.38 (0.27), residues: 351 sheet: -0.16 (0.36), residues: 216 loop : -2.23 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 92 HIS 0.004 0.001 HIS E 184 PHE 0.012 0.001 PHE D 9 TYR 0.010 0.001 TYR A 102 ARG 0.006 0.000 ARG D 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 15) link_NAG-ASN : angle 2.83508 ( 45) link_ALPHA1-6 : bond 0.00826 ( 3) link_ALPHA1-6 : angle 1.44152 ( 9) link_BETA1-4 : bond 0.00549 ( 21) link_BETA1-4 : angle 1.51077 ( 63) link_ALPHA1-3 : bond 0.03327 ( 3) link_ALPHA1-3 : angle 3.36220 ( 9) hydrogen bonds : bond 0.06725 ( 403) hydrogen bonds : angle 4.03204 ( 1101) link_BETA1-6 : bond 0.00577 ( 3) link_BETA1-6 : angle 1.12125 ( 9) SS BOND : bond 0.00352 ( 18) SS BOND : angle 2.47182 ( 36) covalent geometry : bond 0.00357 (12576) covalent geometry : angle 0.66184 (17049) *********************** 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 91 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8212 (m-10) REVERT: A 184 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.7477 (p90) REVERT: B 2 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8777 (tm) REVERT: B 27 GLN cc_start: 0.9302 (tp-100) cc_final: 0.9069 (tp-100) REVERT: F 2 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8617 (tm) REVERT: C 239 GLN cc_start: 0.9052 (mp10) cc_final: 0.8729 (mp10) REVERT: E 115 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8137 (m-10) REVERT: E 184 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.6389 (p90) REVERT: E 196 GLN cc_start: 0.8312 (tt0) cc_final: 0.8075 (mt0) REVERT: E 296 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9125 (pp30) outliers start: 33 outliers final: 16 residues processed: 89 average time/residue: 0.2361 time to fit residues: 31.4858 Evaluate side-chains 76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 PHE 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 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 32 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2845 r_free = 0.2845 target = 0.054970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.040315 restraints weight = 36468.013| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 3.91 r_work: 0.2291 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 12639 Z= 0.337 Angle : 0.797 10.259 17220 Z= 0.381 Chirality : 0.049 0.240 1971 Planarity : 0.004 0.032 2148 Dihedral : 8.760 58.499 2542 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 2.41 % Allowed : 9.66 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1476 helix: 3.24 (0.27), residues: 351 sheet: -0.23 (0.36), residues: 216 loop : -2.25 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 64 HIS 0.006 0.002 HIS E 184 PHE 0.018 0.002 PHE D 9 TYR 0.018 0.002 TYR A 102 ARG 0.005 0.001 ARG D 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 15) link_NAG-ASN : angle 3.04262 ( 45) link_ALPHA1-6 : bond 0.00880 ( 3) link_ALPHA1-6 : angle 1.20799 ( 9) link_BETA1-4 : bond 0.00490 ( 21) link_BETA1-4 : angle 1.56319 ( 63) link_ALPHA1-3 : bond 0.03133 ( 3) link_ALPHA1-3 : angle 3.22435 ( 9) hydrogen bonds : bond 0.07584 ( 403) hydrogen bonds : angle 4.33723 ( 1101) link_BETA1-6 : bond 0.00502 ( 3) link_BETA1-6 : angle 1.25088 ( 9) SS BOND : bond 0.00610 ( 18) SS BOND : angle 3.09526 ( 36) covalent geometry : bond 0.00789 (12576) covalent geometry : angle 0.76242 (17049) *********************** 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 87 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.7819 (p90) REVERT: B 2 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8837 (tm) REVERT: B 27 GLN cc_start: 0.9322 (tp-100) cc_final: 0.9079 (tp-100) REVERT: F 2 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8659 (tm) REVERT: F 27 GLN cc_start: 0.9383 (tp-100) cc_final: 0.9076 (tp-100) REVERT: C 115 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8337 (m-10) REVERT: E 184 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.6567 (p90) REVERT: E 296 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8723 (pp30) outliers start: 31 outliers final: 19 residues processed: 83 average time/residue: 0.2548 time to fit residues: 31.1842 Evaluate side-chains 77 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU 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 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 115 PHE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.056749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.042037 restraints weight = 35733.255| |-----------------------------------------------------------------------------| r_work (start): 0.2500 rms_B_bonded: 3.90 r_work: 0.2339 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12639 Z= 0.158 Angle : 0.710 10.817 17220 Z= 0.335 Chirality : 0.046 0.246 1971 Planarity : 0.003 0.029 2148 Dihedral : 8.390 56.981 2542 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.02 % Allowed : 10.36 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1476 helix: 3.52 (0.27), residues: 351 sheet: -0.01 (0.36), residues: 216 loop : -2.19 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 92 HIS 0.003 0.001 HIS E 184 PHE 0.012 0.001 PHE D 140 TYR 0.010 0.001 TYR E 195 ARG 0.007 0.000 ARG F 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 15) link_NAG-ASN : angle 2.68695 ( 45) link_ALPHA1-6 : bond 0.00814 ( 3) link_ALPHA1-6 : angle 1.19809 ( 9) link_BETA1-4 : bond 0.00556 ( 21) link_BETA1-4 : angle 1.38477 ( 63) link_ALPHA1-3 : bond 0.03258 ( 3) link_ALPHA1-3 : angle 3.35882 ( 9) hydrogen bonds : bond 0.06894 ( 403) hydrogen bonds : angle 4.11441 ( 1101) link_BETA1-6 : bond 0.00569 ( 3) link_BETA1-6 : angle 1.13792 ( 9) SS BOND : bond 0.00499 ( 18) SS BOND : angle 3.26731 ( 36) covalent geometry : bond 0.00343 (12576) covalent geometry : angle 0.67355 (17049) *********************** 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 82 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.7663 (p90) REVERT: A 305 GLU cc_start: 0.9077 (tt0) cc_final: 0.8659 (pt0) REVERT: B 2 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8825 (tm) REVERT: B 27 GLN cc_start: 0.9280 (tp-100) cc_final: 0.9001 (tp-100) REVERT: F 2 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8633 (tm) REVERT: F 27 GLN cc_start: 0.9387 (tp-100) cc_final: 0.9062 (tp-100) REVERT: C 115 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8344 (m-10) REVERT: C 230 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8824 (mtm) REVERT: C 239 GLN cc_start: 0.9047 (mp10) cc_final: 0.8757 (mp10) REVERT: E 184 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.6303 (p90) REVERT: E 239 GLN cc_start: 0.9140 (mp10) cc_final: 0.8821 (mp10) REVERT: E 296 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.8917 (pp30) outliers start: 26 outliers final: 16 residues processed: 80 average time/residue: 0.2459 time to fit residues: 29.5701 Evaluate side-chains 76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 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 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 115 PHE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 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 32 HIS ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2902 r_free = 0.2902 target = 0.057318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.042647 restraints weight = 35564.470| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 3.91 r_work: 0.2357 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12639 Z= 0.146 Angle : 0.690 11.091 17220 Z= 0.325 Chirality : 0.045 0.245 1971 Planarity : 0.003 0.028 2148 Dihedral : 8.216 56.986 2542 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.95 % Allowed : 10.75 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1476 helix: 3.68 (0.26), residues: 351 sheet: 0.13 (0.36), residues: 216 loop : -2.12 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 92 HIS 0.003 0.001 HIS E 276 PHE 0.013 0.001 PHE D 140 TYR 0.010 0.001 TYR E 195 ARG 0.007 0.000 ARG F 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 15) link_NAG-ASN : angle 2.53068 ( 45) link_ALPHA1-6 : bond 0.00795 ( 3) link_ALPHA1-6 : angle 1.20234 ( 9) link_BETA1-4 : bond 0.00543 ( 21) link_BETA1-4 : angle 1.37644 ( 63) link_ALPHA1-3 : bond 0.03278 ( 3) link_ALPHA1-3 : angle 3.46673 ( 9) hydrogen bonds : bond 0.06593 ( 403) hydrogen bonds : angle 3.99644 ( 1101) link_BETA1-6 : bond 0.00577 ( 3) link_BETA1-6 : angle 1.10356 ( 9) SS BOND : bond 0.00387 ( 18) SS BOND : angle 3.04102 ( 36) covalent geometry : bond 0.00312 (12576) covalent geometry : angle 0.65560 (17049) *********************** 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 85 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8125 (m-10) REVERT: A 184 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.7664 (p90) REVERT: B 2 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8749 (tm) REVERT: B 27 GLN cc_start: 0.9305 (tp-100) cc_final: 0.9037 (tp-100) REVERT: B 59 MET cc_start: 0.8831 (tpp) cc_final: 0.8479 (mmt) REVERT: F 2 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8572 (tm) REVERT: F 27 GLN cc_start: 0.9413 (tp-100) cc_final: 0.9077 (tp-100) REVERT: C 7 ILE cc_start: 0.8755 (mp) cc_final: 0.8522 (tp) REVERT: C 115 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: C 239 GLN cc_start: 0.9039 (mp10) cc_final: 0.8691 (mp10) REVERT: E 184 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.6388 (p90) REVERT: E 239 GLN cc_start: 0.9179 (mp10) cc_final: 0.8824 (mp10) REVERT: E 296 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8969 (pp30) outliers start: 25 outliers final: 15 residues processed: 83 average time/residue: 0.2346 time to fit residues: 29.5247 Evaluate side-chains 76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 PHE 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 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 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 115 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 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 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.043116 restraints weight = 35430.474| |-----------------------------------------------------------------------------| r_work (start): 0.2530 rms_B_bonded: 3.89 r_work: 0.2370 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12639 Z= 0.140 Angle : 0.689 11.633 17220 Z= 0.324 Chirality : 0.045 0.244 1971 Planarity : 0.003 0.027 2148 Dihedral : 8.104 56.894 2542 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.02 % Allowed : 10.98 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1476 helix: 3.75 (0.26), residues: 351 sheet: 0.20 (0.36), residues: 216 loop : -2.06 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 92 HIS 0.003 0.001 HIS A 276 PHE 0.013 0.001 PHE D 140 TYR 0.012 0.001 TYR E 195 ARG 0.006 0.000 ARG F 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 15) link_NAG-ASN : angle 2.39762 ( 45) link_ALPHA1-6 : bond 0.00758 ( 3) link_ALPHA1-6 : angle 1.21003 ( 9) link_BETA1-4 : bond 0.00537 ( 21) link_BETA1-4 : angle 1.35029 ( 63) link_ALPHA1-3 : bond 0.03165 ( 3) link_ALPHA1-3 : angle 3.46208 ( 9) hydrogen bonds : bond 0.06389 ( 403) hydrogen bonds : angle 3.95764 ( 1101) link_BETA1-6 : bond 0.00575 ( 3) link_BETA1-6 : angle 1.09647 ( 9) SS BOND : bond 0.00499 ( 18) SS BOND : angle 3.24214 ( 36) covalent geometry : bond 0.00297 (12576) covalent geometry : angle 0.65383 (17049) ********************** 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: 26 poor density : 56 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: A 184 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.7660 (p90) REVERT: B 2 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8743 (tm) REVERT: B 27 GLN cc_start: 0.9276 (tp-100) cc_final: 0.9035 (tp-100) REVERT: B 59 MET cc_start: 0.8831 (tpp) cc_final: 0.8468 (mmt) REVERT: F 2 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8551 (tm) REVERT: F 27 GLN cc_start: 0.9433 (tp-100) cc_final: 0.9097 (tp-100) REVERT: C 115 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8194 (m-10) REVERT: C 239 GLN cc_start: 0.9041 (mp10) cc_final: 0.8708 (mp10) REVERT: E 115 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: E 184 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.6317 (p90) REVERT: E 296 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.9042 (pp30) outliers start: 26 outliers final: 13 residues processed: 78 average time/residue: 0.2977 time to fit residues: 35.1864 Evaluate side-chains 74 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 296 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 32 HIS ** 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 = 0.2907 r_free = 0.2907 target = 0.057520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.042905 restraints weight = 35347.496| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 3.87 r_work: 0.2364 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12639 Z= 0.158 Angle : 0.688 10.954 17220 Z= 0.323 Chirality : 0.045 0.243 1971 Planarity : 0.003 0.027 2148 Dihedral : 8.080 56.999 2542 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.10 % Allowed : 10.90 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1476 helix: 3.76 (0.26), residues: 351 sheet: 0.02 (0.35), residues: 225 loop : -2.01 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 92 HIS 0.003 0.001 HIS C 276 PHE 0.018 0.001 PHE D 140 TYR 0.010 0.001 TYR E 195 ARG 0.006 0.000 ARG F 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 15) link_NAG-ASN : angle 2.36436 ( 45) link_ALPHA1-6 : bond 0.00758 ( 3) link_ALPHA1-6 : angle 1.20650 ( 9) link_BETA1-4 : bond 0.00521 ( 21) link_BETA1-4 : angle 1.34552 ( 63) link_ALPHA1-3 : bond 0.03170 ( 3) link_ALPHA1-3 : angle 3.48517 ( 9) hydrogen bonds : bond 0.06414 ( 403) hydrogen bonds : angle 3.91656 ( 1101) link_BETA1-6 : bond 0.00553 ( 3) link_BETA1-6 : angle 1.11679 ( 9) SS BOND : bond 0.00368 ( 18) SS BOND : angle 2.87672 ( 36) covalent geometry : bond 0.00350 (12576) covalent geometry : angle 0.65650 (17049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6892.87 seconds wall clock time: 125 minutes 33.44 seconds (7533.44 seconds total)