Starting phenix.real_space_refine on Thu Sep 26 09:16:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/09_2024/6hjn_0234.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/09_2024/6hjn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/09_2024/6hjn_0234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/09_2024/6hjn_0234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/09_2024/6hjn_0234.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/09_2024/6hjn_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-5461/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: 10.47, per 1000 atoms: 0.85 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: 3.99 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: 1.70 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: 3.41 Time building geometry restraints manager: 4.41 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: 0.00 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: 11.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.910 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.750 ------------------------------------------------------------------------------- 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 12576 Z= 0.528 Angle : 1.231 11.639 17049 Z= 0.698 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 *********************** 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 fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.168 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: 0.3369 time to fit residues: 65.9405 Evaluate side-chains 64 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.6980 ------------------------------------------------------------------------------- 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 169 ASN C 184 HIS C 192 GLN C 286 HIS C 299 HIS E 130 HIS E 184 HIS E 286 HIS E 299 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12576 Z= 0.217 Angle : 0.758 11.140 17049 Z= 0.351 Chirality : 0.050 0.449 1971 Planarity : 0.004 0.033 2148 Dihedral : 12.992 78.606 2550 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.57 % Allowed : 7.55 % Favored : 89.88 % 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: -2.00 (0.20), residues: 1476 helix: 2.01 (0.28), residues: 351 sheet: -1.40 (0.31), residues: 219 loop : -2.90 (0.16), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 C 161 ARG 0.005 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 69 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.8780 (mmm) cc_final: 0.8511 (mmm) REVERT: D 59 MET cc_start: 0.8866 (mmm) cc_final: 0.8617 (mmm) REVERT: D 149 MET cc_start: 0.9422 (mmt) cc_final: 0.9199 (mmp) REVERT: F 59 MET cc_start: 0.8753 (mmm) cc_final: 0.8477 (mmm) REVERT: F 149 MET cc_start: 0.9411 (mmt) cc_final: 0.9199 (mmp) REVERT: C 115 PHE cc_start: 0.8233 (m-10) cc_final: 0.7922 (m-10) outliers start: 33 outliers final: 14 residues processed: 94 average time/residue: 0.3158 time to fit residues: 40.6509 Evaluate side-chains 71 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 B residue 140 PHE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain E residue 269 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS F 25 HIS C 184 HIS E 184 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12576 Z= 0.213 Angle : 0.660 9.834 17049 Z= 0.317 Chirality : 0.046 0.262 1971 Planarity : 0.004 0.030 2148 Dihedral : 10.905 64.443 2542 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.80 % Allowed : 7.55 % Favored : 89.64 % 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: -1.39 (0.21), residues: 1476 helix: 2.78 (0.27), residues: 351 sheet: -0.88 (0.33), residues: 219 loop : -2.67 (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 B 26 PHE 0.010 0.001 PHE D 9 TYR 0.014 0.001 TYR C 195 ARG 0.004 0.001 ARG E 211 *********************** 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 99 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 63 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9049 (tm) REVERT: C 7 ILE cc_start: 0.8951 (mp) cc_final: 0.8643 (tp) REVERT: C 115 PHE cc_start: 0.8111 (m-10) cc_final: 0.7833 (m-10) REVERT: E 7 ILE cc_start: 0.8735 (mp) cc_final: 0.8489 (tp) outliers start: 36 outliers final: 14 residues processed: 92 average time/residue: 0.2423 time to fit residues: 33.2378 Evaluate side-chains 71 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 231 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN C 130 HIS C 231 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12576 Z= 0.195 Angle : 0.643 9.625 17049 Z= 0.305 Chirality : 0.045 0.273 1971 Planarity : 0.003 0.026 2148 Dihedral : 9.862 58.805 2542 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.02 % Allowed : 9.19 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.99 (0.21), residues: 1476 helix: 3.09 (0.27), residues: 351 sheet: -0.48 (0.34), residues: 216 loop : -2.44 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 92 HIS 0.004 0.001 HIS D 26 PHE 0.010 0.001 PHE B 9 TYR 0.010 0.001 TYR A 195 ARG 0.006 0.001 ARG C 211 *********************** 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 89 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 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: symmetry clash REVERT: B 27 GLN cc_start: 0.9379 (tp-100) cc_final: 0.9157 (tp-100) REVERT: B 98 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9038 (tm) REVERT: C 7 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8673 (tp) REVERT: C 115 PHE cc_start: 0.8084 (m-10) cc_final: 0.7844 (m-10) REVERT: C 317 MET cc_start: 0.8854 (ttt) cc_final: 0.8610 (ttt) outliers start: 26 outliers final: 11 residues processed: 83 average time/residue: 0.2437 time to fit residues: 30.3097 Evaluate side-chains 71 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 105 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** E 231 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12576 Z= 0.198 Angle : 0.628 9.539 17049 Z= 0.299 Chirality : 0.045 0.255 1971 Planarity : 0.003 0.025 2148 Dihedral : 8.664 57.066 2542 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.57 % Allowed : 9.03 % Favored : 88.40 % 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: -0.70 (0.21), residues: 1476 helix: 3.36 (0.27), residues: 351 sheet: -0.22 (0.35), residues: 216 loop : -2.29 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 92 HIS 0.006 0.001 HIS D 142 PHE 0.011 0.001 PHE D 9 TYR 0.010 0.001 TYR E 102 ARG 0.004 0.000 ARG C 211 *********************** 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 101 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 68 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.7954 (p90) REVERT: B 27 GLN cc_start: 0.9336 (tp-100) cc_final: 0.9112 (tp-100) REVERT: B 98 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9047 (tm) REVERT: C 317 MET cc_start: 0.8918 (ttt) cc_final: 0.8683 (ttt) REVERT: E 184 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.6875 (p90) outliers start: 33 outliers final: 18 residues processed: 95 average time/residue: 0.2493 time to fit residues: 35.2202 Evaluate side-chains 75 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12576 Z= 0.257 Angle : 0.656 9.578 17049 Z= 0.314 Chirality : 0.046 0.247 1971 Planarity : 0.003 0.027 2148 Dihedral : 8.512 57.563 2542 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.26 % Allowed : 9.27 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.52 (0.21), residues: 1476 helix: 3.51 (0.27), residues: 351 sheet: -0.13 (0.35), residues: 216 loop : -2.16 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 92 HIS 0.003 0.001 HIS B 26 PHE 0.012 0.001 PHE D 9 TYR 0.010 0.001 TYR A 102 ARG 0.005 0.000 ARG D 127 *********************** 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 86 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 57 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7898 (p90) REVERT: A 196 GLN cc_start: 0.8275 (tt0) cc_final: 0.7827 (mp10) REVERT: B 98 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9055 (tm) REVERT: C 317 MET cc_start: 0.8927 (ttt) cc_final: 0.8680 (ttt) REVERT: E 184 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.6764 (p90) outliers start: 29 outliers final: 17 residues processed: 84 average time/residue: 0.2330 time to fit residues: 29.5970 Evaluate side-chains 74 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 0.0770 chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 119 optimal weight: 0.0050 chunk 79 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 0.0470 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 0.0670 overall best weight: 0.1788 ------------------------------------------------------------------------------- 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 E 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 12576 Z= 0.155 Angle : 0.622 9.610 17049 Z= 0.296 Chirality : 0.044 0.253 1971 Planarity : 0.003 0.024 2148 Dihedral : 8.087 56.630 2540 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.32 % Allowed : 10.28 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.29 (0.21), residues: 1476 helix: 3.71 (0.26), residues: 351 sheet: 0.00 (0.35), residues: 216 loop : -2.01 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 180 HIS 0.004 0.001 HIS C 276 PHE 0.010 0.001 PHE B 9 TYR 0.011 0.001 TYR E 195 ARG 0.005 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.7860 (p90) REVERT: B 98 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8938 (tm) REVERT: C 317 MET cc_start: 0.8907 (ttt) cc_final: 0.8661 (ttt) outliers start: 17 outliers final: 10 residues processed: 88 average time/residue: 0.2289 time to fit residues: 31.1879 Evaluate side-chains 76 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 98 LEU 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 D residue 103 GLU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12576 Z= 0.420 Angle : 0.717 9.598 17049 Z= 0.347 Chirality : 0.047 0.240 1971 Planarity : 0.003 0.025 2148 Dihedral : 8.368 58.149 2540 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.71 % Allowed : 10.59 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.37 (0.22), residues: 1476 helix: 3.60 (0.27), residues: 351 sheet: 0.01 (0.36), residues: 213 loop : -2.05 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.005 0.001 HIS E 184 PHE 0.015 0.002 PHE D 9 TYR 0.012 0.002 TYR A 102 ARG 0.003 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8062 (p90) REVERT: B 27 GLN cc_start: 0.9370 (tp-100) cc_final: 0.9148 (tp-100) REVERT: B 98 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9129 (tm) REVERT: C 317 MET cc_start: 0.8961 (ttt) cc_final: 0.8730 (ttt) REVERT: E 184 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.6796 (p90) outliers start: 22 outliers final: 14 residues processed: 83 average time/residue: 0.2575 time to fit residues: 31.3371 Evaluate side-chains 71 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN E 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12576 Z= 0.211 Angle : 0.650 9.952 17049 Z= 0.312 Chirality : 0.045 0.243 1971 Planarity : 0.003 0.024 2148 Dihedral : 8.168 56.780 2540 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.56 % Allowed : 11.37 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 3.69 (0.26), residues: 351 sheet: 0.15 (0.37), residues: 213 loop : -2.01 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.003 0.001 HIS C 276 PHE 0.011 0.001 PHE D 9 TYR 0.013 0.001 TYR E 195 ARG 0.005 0.000 ARG D 127 *********************** 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 78 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.7947 (p90) REVERT: B 27 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9057 (tp-100) REVERT: B 59 MET cc_start: 0.8853 (tpp) cc_final: 0.8607 (mmm) REVERT: B 98 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9070 (tm) REVERT: F 27 GLN cc_start: 0.9338 (tp-100) cc_final: 0.9052 (tp-100) REVERT: C 317 MET cc_start: 0.8920 (ttt) cc_final: 0.8692 (ttt) REVERT: E 184 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.6637 (p90) outliers start: 20 outliers final: 12 residues processed: 74 average time/residue: 0.2378 time to fit residues: 26.9615 Evaluate side-chains 69 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 19 ASP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 116 optimal weight: 0.0170 chunk 12 optimal weight: 0.0570 chunk 90 optimal weight: 0.0670 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.4274 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12576 Z= 0.169 Angle : 0.634 10.088 17049 Z= 0.302 Chirality : 0.045 0.245 1971 Planarity : 0.003 0.024 2148 Dihedral : 7.989 56.646 2540 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.17 % Allowed : 11.53 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.13 (0.22), residues: 1476 helix: 3.76 (0.26), residues: 351 sheet: 0.35 (0.37), residues: 213 loop : -1.93 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 92 HIS 0.004 0.001 HIS E 276 PHE 0.010 0.001 PHE D 9 TYR 0.014 0.001 TYR E 195 ARG 0.005 0.000 ARG D 127 ********************** 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 74 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.7854 (p90) REVERT: B 27 GLN cc_start: 0.9366 (tp-100) cc_final: 0.9086 (tp-100) REVERT: B 98 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9013 (tm) REVERT: F 27 GLN cc_start: 0.9356 (tp-100) cc_final: 0.9093 (tp-100) REVERT: C 317 MET cc_start: 0.8923 (ttt) cc_final: 0.8685 (ttt) REVERT: E 184 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.6729 (p90) outliers start: 15 outliers final: 10 residues processed: 74 average time/residue: 0.2284 time to fit residues: 26.1872 Evaluate side-chains 69 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU 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 98 LEU Chi-restraints excluded: chain F residue 103 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 102 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.044407 restraints weight = 34794.975| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 3.89 r_work: 0.2413 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12576 Z= 0.202 Angle : 0.639 9.912 17049 Z= 0.305 Chirality : 0.045 0.242 1971 Planarity : 0.003 0.024 2148 Dihedral : 7.972 56.783 2540 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.48 % Allowed : 11.60 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.07 (0.22), residues: 1476 helix: 3.78 (0.26), residues: 351 sheet: 0.42 (0.37), residues: 213 loop : -1.89 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 92 HIS 0.003 0.001 HIS A 276 PHE 0.012 0.001 PHE D 9 TYR 0.013 0.001 TYR E 195 ARG 0.005 0.000 ARG D 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.25 seconds wall clock time: 46 minutes 24.16 seconds (2784.16 seconds total)