Starting phenix.real_space_refine on Sun Apr 14 05:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7q_41989/04_2024/8u7q_41989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7q_41989/04_2024/8u7q_41989.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/8u7q_41989/04_2024/8u7q_41989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7q_41989/04_2024/8u7q_41989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7q_41989/04_2024/8u7q_41989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7q_41989/04_2024/8u7q_41989_updated.pdb" } 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= -0.001 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 184 5.16 5 C 18992 2.51 5 N 5192 2.21 5 O 6056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30520 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "D" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "E" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "F" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "G" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "H" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 15.12, per 1000 atoms: 0.50 Number of scatterers: 30520 At special positions: 0 Unit cell: (151.96, 151.96, 112.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 96 15.00 O 6056 8.00 N 5192 7.00 C 18992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 11.40 Conformation dependent library (CDL) restraints added in 5.1 seconds 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 56 sheets defined 35.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 85 removed outlier: 3.978A pdb=" N MET A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.136A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.327A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.978A pdb=" N MET B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.165A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.322A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 removed outlier: 3.978A pdb=" N MET C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 4.165A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.319A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 85 removed outlier: 4.038A pdb=" N MET D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 137 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.166A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.327A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'E' and resid 20 through 24 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 85 removed outlier: 3.971A pdb=" N MET E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 127 through 137 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 256 through 266 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 4.139A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.297A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 500 Processing helix chain 'F' and resid 20 through 24 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 85 removed outlier: 3.970A pdb=" N MET F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 127 through 137 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 256 through 266 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 4.138A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.296A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 500 Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 85 removed outlier: 3.934A pdb=" N MET G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 256 through 266 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 4.168A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.296A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 500 Processing helix chain 'H' and resid 20 through 24 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 removed outlier: 3.934A pdb=" N MET H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 256 through 266 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 4.168A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.341A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 500 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.747A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.682A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 409 through 412 Processing sheet with id= E, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 208 through 212 removed outlier: 3.759A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= I, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.749A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.682A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 409 through 412 Processing sheet with id= L, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.759A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= P, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.749A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.677A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 409 through 412 Processing sheet with id= S, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.566A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 208 through 212 removed outlier: 3.758A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= W, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.747A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.677A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 409 through 412 Processing sheet with id= Z, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.760A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.735A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.683A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'E' and resid 409 through 412 Processing sheet with id= AG, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.609A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.698A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AK, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.737A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.687A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'F' and resid 409 through 412 Processing sheet with id= AN, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.609A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 208 through 212 removed outlier: 3.698A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.747A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.679A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'G' and resid 409 through 412 Processing sheet with id= AU, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'G' and resid 208 through 212 removed outlier: 3.702A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AY, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.746A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.683A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'H' and resid 409 through 412 Processing sheet with id= BB, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'H' and resid 208 through 212 removed outlier: 3.702A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2484 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: 9.83 Time building geometry restraints manager: 12.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9523 1.34 - 1.45: 3862 1.45 - 1.57: 17231 1.57 - 1.69: 152 1.69 - 1.81: 312 Bond restraints: 31080 Sorted by residual: bond pdb=" N VAL C 350 " pdb=" CA VAL C 350 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.18e-02 7.18e+03 1.85e+01 bond pdb=" N VAL B 350 " pdb=" CA VAL B 350 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.18e-02 7.18e+03 1.83e+01 bond pdb=" N VAL A 350 " pdb=" CA VAL A 350 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.53e+01 bond pdb=" C2 IMP F 603 " pdb=" N3 IMP F 603 " ideal model delta sigma weight residual 1.380 1.305 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C2 IMP G 603 " pdb=" N3 IMP G 603 " ideal model delta sigma weight residual 1.380 1.305 0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 31075 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.49: 837 105.49 - 112.30: 15886 112.30 - 119.11: 9828 119.11 - 125.93: 15257 125.93 - 132.74: 480 Bond angle restraints: 42288 Sorted by residual: angle pdb=" PA ATP H 604 " pdb=" O3A ATP H 604 " pdb=" PB ATP H 604 " ideal model delta sigma weight residual 136.83 121.18 15.65 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP E 604 " pdb=" O3A ATP E 604 " pdb=" PB ATP E 604 " ideal model delta sigma weight residual 136.83 121.20 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP F 604 " pdb=" O3A ATP F 604 " pdb=" PB ATP F 604 " ideal model delta sigma weight residual 136.83 121.23 15.60 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP G 604 " pdb=" O3A ATP G 604 " pdb=" PB ATP G 604 " ideal model delta sigma weight residual 136.83 121.25 15.58 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 121.65 15.18 1.00e+00 1.00e+00 2.30e+02 ... (remaining 42283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 17840 33.95 - 67.89: 911 67.89 - 101.84: 169 101.84 - 135.79: 6 135.79 - 169.73: 26 Dihedral angle restraints: 18952 sinusoidal: 8008 harmonic: 10944 Sorted by residual: dihedral pdb=" O3B GTP F 601 " pdb=" O3A GTP F 601 " pdb=" PB GTP F 601 " pdb=" PA GTP F 601 " ideal model delta sinusoidal sigma weight residual -68.92 100.81 -169.73 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O3B GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PB GTP G 601 " pdb=" PA GTP G 601 " ideal model delta sinusoidal sigma weight residual -68.92 100.59 -169.51 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP B 601 " pdb=" C1' GTP B 601 " pdb=" N9 GTP B 601 " pdb=" O4' GTP B 601 " ideal model delta sinusoidal sigma weight residual 104.59 -59.17 163.76 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 18949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4308 0.077 - 0.154: 476 0.154 - 0.231: 37 0.231 - 0.308: 15 0.308 - 0.385: 60 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA PHE B 24 " pdb=" N PHE B 24 " pdb=" C PHE B 24 " pdb=" CB PHE B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE A 24 " pdb=" N PHE A 24 " pdb=" C PHE A 24 " pdb=" CB PHE A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA PHE H 24 " pdb=" N PHE H 24 " pdb=" C PHE H 24 " pdb=" CB PHE H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 4893 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO D 123 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 122 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO C 123 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 122 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 123 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.041 5.00e-02 4.00e+02 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10270 2.84 - 3.36: 29717 3.36 - 3.87: 49808 3.87 - 4.39: 60656 4.39 - 4.90: 104766 Nonbonded interactions: 255217 Sorted by model distance: nonbonded pdb=" O ASP E 170 " pdb=" OG1 THR E 173 " model vdw 2.325 2.440 nonbonded pdb=" O ASP G 170 " pdb=" OG1 THR G 173 " model vdw 2.326 2.440 nonbonded pdb=" O ASP F 170 " pdb=" OG1 THR F 173 " model vdw 2.326 2.440 nonbonded pdb=" O ASP H 170 " pdb=" OG1 THR H 173 " model vdw 2.326 2.440 nonbonded pdb=" O VAL G 73 " pdb=" OG1 THR G 74 " model vdw 2.345 2.440 ... (remaining 255212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 5.270 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: 0.030 Extract box with map and model: 15.180 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 76.260 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.006 0.075 31080 Z= 0.360 Angle : 1.092 15.647 42288 Z= 0.583 Chirality : 0.063 0.385 4896 Planarity : 0.005 0.073 5208 Dihedral : 20.740 169.733 11976 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % Rotamer: Outliers : 0.73 % Allowed : 15.98 % Favored : 83.29 % 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: -0.67 (0.14), residues: 3840 helix: -0.24 (0.14), residues: 1392 sheet: -1.25 (0.26), residues: 368 loop : -0.31 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 507 PHE 0.008 0.001 PHE G 41 TYR 0.010 0.001 TYR G 348 ARG 0.003 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 381 time to evaluate : 3.304 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 outliers start: 23 outliers final: 1 residues processed: 399 average time/residue: 0.4225 time to fit residues: 270.7862 Evaluate side-chains 347 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 346 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.7980 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 348 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN B 198 ASN C 198 ASN C 441 GLN D 198 ASN E 94 ASN E 498 GLN F 94 ASN F 171 HIS F 230 ASN G 94 ASN G 171 HIS G 198 ASN H 94 ASN H 171 HIS H 198 ASN H 498 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31080 Z= 0.283 Angle : 0.649 5.885 42288 Z= 0.323 Chirality : 0.047 0.183 4896 Planarity : 0.004 0.046 5208 Dihedral : 17.122 149.071 5138 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.83 % Favored : 95.96 % Rotamer: Outliers : 3.16 % Allowed : 18.04 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.42 (0.14), residues: 3840 helix: 0.07 (0.14), residues: 1408 sheet: -1.81 (0.23), residues: 416 loop : -0.03 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 507 PHE 0.012 0.002 PHE G 35 TYR 0.009 0.002 TYR D 459 ARG 0.002 0.000 ARG C 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 379 time to evaluate : 3.359 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: C 337 MET cc_start: 0.7429 (mpp) cc_final: 0.6873 (ptp) REVERT: E 337 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7439 (mpp) REVERT: F 337 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7445 (mpp) REVERT: H 337 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7444 (mpp) outliers start: 100 outliers final: 51 residues processed: 451 average time/residue: 0.4041 time to fit residues: 300.3425 Evaluate side-chains 368 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 314 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 290 optimal weight: 0.4980 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 chunk 346 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 230 ASN A 334 GLN B 22 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 230 ASN B 303 ASN B 334 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 230 ASN C 303 ASN C 334 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 230 ASN D 334 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 230 ASN E 303 ASN E 334 GLN F 303 ASN F 334 GLN G 230 ASN G 303 ASN G 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 334 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 31080 Z= 0.236 Angle : 0.580 5.987 42288 Z= 0.289 Chirality : 0.044 0.152 4896 Planarity : 0.004 0.039 5208 Dihedral : 16.092 147.335 5136 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.15 % Favored : 96.64 % Rotamer: Outliers : 4.53 % Allowed : 19.49 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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 (0.14), residues: 3840 helix: 0.21 (0.14), residues: 1424 sheet: -1.62 (0.22), residues: 416 loop : 0.05 (0.15), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 93 PHE 0.011 0.001 PHE F 35 TYR 0.009 0.001 TYR D 411 ARG 0.002 0.000 ARG E 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 355 time to evaluate : 3.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7852 (mpp) cc_final: 0.7506 (mpp) REVERT: B 337 MET cc_start: 0.7867 (mpp) cc_final: 0.7516 (mpp) REVERT: C 337 MET cc_start: 0.7550 (mpp) cc_final: 0.7289 (ptp) REVERT: D 325 MET cc_start: 0.8888 (ttt) cc_final: 0.8634 (ttt) REVERT: D 337 MET cc_start: 0.7906 (mpp) cc_final: 0.7551 (mpp) REVERT: E 136 ARG cc_start: 0.6612 (ttm-80) cc_final: 0.6319 (ttm110) REVERT: F 136 ARG cc_start: 0.6615 (ttm-80) cc_final: 0.6325 (ttm110) REVERT: G 136 ARG cc_start: 0.6613 (ttm-80) cc_final: 0.6322 (ttm110) REVERT: G 337 MET cc_start: 0.7679 (mpp) cc_final: 0.7392 (ptp) REVERT: G 384 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8689 (m) REVERT: H 136 ARG cc_start: 0.6606 (ttm-80) cc_final: 0.6316 (ttm110) REVERT: H 325 MET cc_start: 0.8912 (ttt) cc_final: 0.8650 (ttt) outliers start: 143 outliers final: 66 residues processed: 452 average time/residue: 0.4086 time to fit residues: 299.8636 Evaluate side-chains 382 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 315 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 1.9990 chunk 262 optimal weight: 0.0970 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 350 optimal weight: 8.9990 chunk 371 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 332 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN F 303 ASN G 303 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31080 Z= 0.206 Angle : 0.550 6.598 42288 Z= 0.271 Chirality : 0.043 0.149 4896 Planarity : 0.004 0.036 5208 Dihedral : 15.309 144.133 5136 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.89 % Favored : 96.90 % Rotamer: Outliers : 4.81 % Allowed : 18.86 % Favored : 76.33 % 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: -0.03 (0.14), residues: 3840 helix: 0.43 (0.15), residues: 1408 sheet: -1.47 (0.22), residues: 416 loop : 0.15 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 507 PHE 0.009 0.001 PHE G 35 TYR 0.009 0.001 TYR B 411 ARG 0.002 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 365 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8846 (m) REVERT: B 384 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8845 (m) REVERT: C 272 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8590 (p) REVERT: C 384 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8848 (m) REVERT: D 272 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8585 (p) REVERT: D 384 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8851 (m) REVERT: E 384 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8817 (m) REVERT: F 337 MET cc_start: 0.7774 (mpp) cc_final: 0.7421 (mpp) REVERT: F 384 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8809 (m) REVERT: G 384 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8801 (m) REVERT: H 384 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8812 (m) outliers start: 152 outliers final: 103 residues processed: 485 average time/residue: 0.4119 time to fit residues: 323.5989 Evaluate side-chains 412 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 299 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 334 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN B 303 ASN B 334 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN C 303 ASN C 334 GLN D 22 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN D 334 GLN D 507 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN E 303 ASN E 334 GLN E 507 HIS F 303 ASN F 334 GLN F 507 HIS G 303 ASN G 334 GLN G 507 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 GLN H 334 GLN H 507 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 31080 Z= 0.384 Angle : 0.644 5.952 42288 Z= 0.323 Chirality : 0.047 0.155 4896 Planarity : 0.004 0.034 5208 Dihedral : 15.980 144.323 5136 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.45 % Favored : 95.34 % Rotamer: Outliers : 5.57 % Allowed : 18.01 % Favored : 76.42 % 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: -0.50 (0.14), residues: 3840 helix: 0.03 (0.14), residues: 1408 sheet: -1.89 (0.23), residues: 368 loop : -0.14 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 507 PHE 0.016 0.002 PHE H 35 TYR 0.010 0.002 TYR E 459 ARG 0.002 0.000 ARG E 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 286 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7969 (ptt) REVERT: C 272 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8707 (p) REVERT: D 272 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8698 (p) REVERT: D 325 MET cc_start: 0.8967 (ttt) cc_final: 0.8703 (ttt) REVERT: D 384 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8962 (m) REVERT: G 384 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8941 (m) REVERT: H 384 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8950 (m) outliers start: 176 outliers final: 115 residues processed: 432 average time/residue: 0.4074 time to fit residues: 286.3911 Evaluate side-chains 389 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 268 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 1.9990 chunk 334 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 0.8980 chunk 308 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 0.0070 chunk 195 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31080 Z= 0.164 Angle : 0.537 7.039 42288 Z= 0.265 Chirality : 0.042 0.149 4896 Planarity : 0.003 0.036 5208 Dihedral : 15.139 145.498 5136 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.94 % Favored : 96.85 % Rotamer: Outliers : 4.75 % Allowed : 18.26 % Favored : 76.99 % 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: -0.12 (0.14), residues: 3840 helix: 0.44 (0.15), residues: 1408 sheet: -1.70 (0.23), residues: 392 loop : 0.04 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 507 PHE 0.008 0.001 PHE H 35 TYR 0.008 0.001 TYR B 411 ARG 0.001 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 304 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8365 (mmm) cc_final: 0.8088 (mmm) REVERT: B 85 MET cc_start: 0.8326 (mmm) cc_final: 0.8028 (mmm) REVERT: B 179 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7826 (ptt) REVERT: C 85 MET cc_start: 0.8335 (mmm) cc_final: 0.8054 (mmm) REVERT: C 179 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7882 (ptt) REVERT: C 272 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8643 (p) REVERT: D 85 MET cc_start: 0.8311 (mmm) cc_final: 0.8054 (mmm) REVERT: D 179 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7873 (ptt) REVERT: D 272 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8630 (p) REVERT: D 384 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8912 (m) REVERT: G 206 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7126 (ttmm) REVERT: H 206 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7131 (ttmm) outliers start: 150 outliers final: 97 residues processed: 424 average time/residue: 0.4176 time to fit residues: 286.4784 Evaluate side-chains 388 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 283 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 0.3980 chunk 312 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 370 optimal weight: 0.5980 chunk 231 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 HIS F 507 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 507 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31080 Z= 0.233 Angle : 0.560 7.415 42288 Z= 0.277 Chirality : 0.044 0.147 4896 Planarity : 0.004 0.032 5208 Dihedral : 15.050 145.271 5136 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.67 % Favored : 96.12 % Rotamer: Outliers : 4.68 % Allowed : 18.29 % Favored : 77.03 % 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: -0.05 (0.14), residues: 3840 helix: 0.44 (0.15), residues: 1408 sheet: -1.35 (0.27), residues: 312 loop : -0.02 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 507 PHE 0.011 0.001 PHE H 35 TYR 0.007 0.001 TYR G 32 ARG 0.001 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 281 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8384 (mmm) cc_final: 0.8143 (mmm) REVERT: A 179 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7859 (ptt) REVERT: B 85 MET cc_start: 0.8350 (mmm) cc_final: 0.8089 (mmm) REVERT: B 179 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7892 (ptt) REVERT: C 85 MET cc_start: 0.8356 (mmm) cc_final: 0.8106 (mmm) REVERT: C 179 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7898 (ptt) REVERT: C 272 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8693 (p) REVERT: D 85 MET cc_start: 0.8341 (mmm) cc_final: 0.8093 (mmm) REVERT: D 179 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7842 (ptt) REVERT: D 272 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8689 (p) REVERT: D 325 MET cc_start: 0.8880 (ttt) cc_final: 0.8678 (ttt) REVERT: E 179 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7898 (ptt) REVERT: E 206 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7128 (ttmm) REVERT: F 206 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7129 (ttmm) REVERT: G 206 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7122 (ttmm) REVERT: H 179 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7894 (ptt) REVERT: H 206 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7132 (ttmm) outliers start: 148 outliers final: 121 residues processed: 395 average time/residue: 0.4303 time to fit residues: 273.2008 Evaluate side-chains 409 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 276 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 34 optimal weight: 0.0060 chunk 290 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31080 Z= 0.200 Angle : 0.542 7.907 42288 Z= 0.267 Chirality : 0.043 0.144 4896 Planarity : 0.003 0.033 5208 Dihedral : 14.723 145.933 5136 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 4.68 % Allowed : 18.61 % Favored : 76.71 % 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: -0.06 (0.14), residues: 3840 helix: 0.54 (0.15), residues: 1416 sheet: -1.72 (0.23), residues: 392 loop : 0.04 (0.15), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 507 PHE 0.009 0.001 PHE F 35 TYR 0.006 0.001 TYR B 459 ARG 0.001 0.000 ARG F 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 294 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8349 (mmm) cc_final: 0.8114 (mmm) REVERT: A 179 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7793 (ptt) REVERT: A 337 MET cc_start: 0.7274 (mpp) cc_final: 0.7062 (mtt) REVERT: B 85 MET cc_start: 0.8336 (mmm) cc_final: 0.8091 (mmm) REVERT: B 179 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7789 (ptt) REVERT: C 85 MET cc_start: 0.8334 (mmm) cc_final: 0.8090 (mmm) REVERT: C 179 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7844 (ptt) REVERT: C 272 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8682 (p) REVERT: D 85 MET cc_start: 0.8315 (mmm) cc_final: 0.8064 (mmm) REVERT: D 179 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7782 (ptt) REVERT: D 272 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8689 (p) REVERT: E 206 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7162 (mmtp) REVERT: F 179 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7829 (ptt) REVERT: F 206 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7173 (mmtp) REVERT: G 179 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7816 (ptt) REVERT: G 206 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7088 (ttmm) REVERT: H 206 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7159 (mmtp) outliers start: 148 outliers final: 122 residues processed: 399 average time/residue: 0.4154 time to fit residues: 268.5306 Evaluate side-chains 412 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 278 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 503 VAL Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 3.9990 chunk 354 optimal weight: 0.0770 chunk 323 optimal weight: 1.9990 chunk 344 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 270 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 326 optimal weight: 6.9990 chunk 343 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN G 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31080 Z= 0.211 Angle : 0.551 8.121 42288 Z= 0.271 Chirality : 0.043 0.140 4896 Planarity : 0.003 0.031 5208 Dihedral : 14.610 145.745 5136 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.36 % Favored : 96.43 % Rotamer: Outliers : 4.30 % Allowed : 19.08 % Favored : 76.61 % 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: -0.00 (0.14), residues: 3840 helix: 0.55 (0.15), residues: 1416 sheet: -1.29 (0.27), residues: 312 loop : -0.06 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 507 PHE 0.010 0.001 PHE H 35 TYR 0.010 0.001 TYR F 411 ARG 0.001 0.000 ARG F 412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 282 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8356 (mmm) cc_final: 0.8100 (mmm) REVERT: A 179 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7804 (ptt) REVERT: B 85 MET cc_start: 0.8299 (mmm) cc_final: 0.8083 (mmm) REVERT: B 179 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7753 (ptt) REVERT: C 179 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7835 (ptt) REVERT: C 272 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8698 (p) REVERT: D 179 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7751 (ptt) REVERT: E 179 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7833 (ptt) REVERT: E 206 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7193 (mmtp) REVERT: F 85 MET cc_start: 0.8314 (mmm) cc_final: 0.8003 (mmm) REVERT: F 179 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7812 (ptt) REVERT: F 206 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7174 (mmtp) REVERT: F 337 MET cc_start: 0.7267 (mpp) cc_final: 0.7040 (mtt) REVERT: G 179 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7736 (ptt) REVERT: G 206 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7153 (mmtp) REVERT: H 179 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7826 (ptt) REVERT: H 206 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7154 (mmtp) outliers start: 136 outliers final: 118 residues processed: 384 average time/residue: 0.4243 time to fit residues: 263.1254 Evaluate side-chains 405 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 274 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.8980 chunk 364 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 253 optimal weight: 0.7980 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 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 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31080 Z= 0.191 Angle : 0.540 8.342 42288 Z= 0.265 Chirality : 0.043 0.135 4896 Planarity : 0.003 0.033 5208 Dihedral : 14.370 145.928 5136 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.88 % Rotamer: Outliers : 4.21 % Allowed : 19.27 % Favored : 76.52 % 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: 0.08 (0.14), residues: 3840 helix: 0.62 (0.15), residues: 1416 sheet: -1.23 (0.28), residues: 312 loop : -0.02 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 507 PHE 0.009 0.001 PHE F 35 TYR 0.009 0.001 TYR F 411 ARG 0.003 0.000 ARG C 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 293 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8349 (mmm) cc_final: 0.8091 (mmm) REVERT: A 179 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7764 (ptt) REVERT: B 85 MET cc_start: 0.8311 (mmm) cc_final: 0.8066 (mmm) REVERT: B 179 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7750 (ptt) REVERT: C 179 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7762 (ptt) REVERT: C 272 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8676 (p) REVERT: D 179 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7757 (ptt) REVERT: D 272 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8672 (p) REVERT: E 94 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8621 (t0) REVERT: E 179 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7768 (ptt) REVERT: E 206 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7146 (mmtp) REVERT: F 85 MET cc_start: 0.8287 (mmm) cc_final: 0.7999 (mmm) REVERT: F 179 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7752 (ptt) REVERT: F 206 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7154 (mmtp) REVERT: G 179 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7699 (ptt) REVERT: G 206 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7121 (mmtp) REVERT: H 179 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7754 (ptt) REVERT: H 206 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7122 (mmtp) outliers start: 133 outliers final: 113 residues processed: 386 average time/residue: 0.4190 time to fit residues: 264.1262 Evaluate side-chains 407 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 279 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 chunk 44 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 0.0870 chunk 56 optimal weight: 0.0770 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139170 restraints weight = 33202.877| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.19 r_work: 0.3496 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31080 Z= 0.144 Angle : 0.522 8.618 42288 Z= 0.254 Chirality : 0.042 0.135 4896 Planarity : 0.003 0.035 5208 Dihedral : 13.958 146.572 5136 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.89 % Favored : 96.90 % Rotamer: Outliers : 4.05 % Allowed : 19.94 % Favored : 76.01 % 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: 0.21 (0.14), residues: 3840 helix: 0.82 (0.15), residues: 1416 sheet: -1.50 (0.24), residues: 392 loop : 0.13 (0.15), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS E 93 PHE 0.006 0.001 PHE F 35 TYR 0.010 0.001 TYR G 411 ARG 0.001 0.000 ARG H 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6487.56 seconds wall clock time: 120 minutes 8.54 seconds (7208.54 seconds total)