Starting phenix.real_space_refine on Wed Feb 21 08:47:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/02_2024/8u8o_42026_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/02_2024/8u8o_42026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/02_2024/8u8o_42026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/02_2024/8u8o_42026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/02_2024/8u8o_42026_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/02_2024/8u8o_42026_updated.pdb" } resolution = 2.4 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= 0.008 sd= 0.074 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 72 5.49 5 S 192 5.16 5 C 18760 2.51 5 N 5136 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 43": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 477": "OD1" <-> "OD2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 477": "OD1" <-> "OD2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 477": "OD1" <-> "OD2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H ASP 77": "OD1" <-> "OD2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ASP 232": "OD1" <-> "OD2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 477": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "B" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "C" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "D" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "E" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "F" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "G" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "H" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 15.01, per 1000 atoms: 0.50 Number of scatterers: 30080 At special positions: 0 Unit cell: (159.327, 159.327, 134.037, 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 192 16.00 P 72 15.00 O 5920 8.00 N 5136 7.00 C 18760 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: 10.82 Conformation dependent library (CDL) restraints added in 5.3 seconds 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 48 sheets defined 34.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.52 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 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 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' 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 229 removed outlier: 3.630A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.736A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.386A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.537A 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 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' 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 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 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' 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 229 removed outlier: 3.638A pdb=" N LYS B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.737A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.387A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.539A 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 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' 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 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 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' 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 229 removed outlier: 3.633A pdb=" N LYS C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.738A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.386A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.539A 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 418 through 420 No H-bonds generated for 'chain 'C' and resid 418 through 420' 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 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 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' 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 229 removed outlier: 3.629A pdb=" N LYS D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) 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: 3.737A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.382A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.534A 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 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' 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 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' 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 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 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' 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 229 removed outlier: 3.638A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.736A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.387A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.538A 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 418 through 420 No H-bonds generated for 'chain 'E' and resid 418 through 420' 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 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' 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 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 163 No H-bonds generated for 'chain 'F' and resid 160 through 163' 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 229 removed outlier: 3.636A pdb=" N LYS F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.737A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.386A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.538A 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 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' 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 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' 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 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 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' 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 229 removed outlier: 3.634A pdb=" N LYS G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.736A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.387A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.539A 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 418 through 420 No H-bonds generated for 'chain 'G' and resid 418 through 420' 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 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' 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 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 163 No H-bonds generated for 'chain 'H' and resid 160 through 163' 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 229 removed outlier: 3.634A pdb=" N LYS H 229 " --> pdb=" O THR H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.736A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.383A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.533A 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 418 through 420 No H-bonds generated for 'chain 'H' and resid 418 through 420' 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: 6.590A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 120 through 122 Processing sheet with id= D, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.725A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 408 through 412 Processing sheet with id= F, first strand: chain 'A' and resid 208 through 212 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.598A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 120 through 122 Processing sheet with id= J, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.725A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.036A 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 408 through 412 Processing sheet with id= L, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.595A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 120 through 122 Processing sheet with id= P, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.727A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 408 through 412 Processing sheet with id= R, first strand: chain 'C' and resid 208 through 212 Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.587A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 120 through 122 Processing sheet with id= V, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.794A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 408 through 412 Processing sheet with id= X, first strand: chain 'D' and resid 208 through 212 Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.586A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 120 through 122 Processing sheet with id= AB, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.726A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 408 through 412 Processing sheet with id= AD, first strand: chain 'E' and resid 208 through 212 Processing sheet with id= AE, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.595A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 120 through 122 Processing sheet with id= AH, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.724A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 408 through 412 Processing sheet with id= AJ, first strand: chain 'F' and resid 208 through 212 Processing sheet with id= AK, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.592A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= AN, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.722A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'G' and resid 408 through 412 Processing sheet with id= AP, first strand: chain 'G' and resid 208 through 212 Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.592A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 120 through 122 Processing sheet with id= AT, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.726A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'H' and resid 408 through 412 Processing sheet with id= AV, first strand: chain 'H' and resid 208 through 212 833 hydrogen bonds defined for protein. 2451 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: 9.29 Time building geometry restraints manager: 11.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4969 1.30 - 1.43: 7402 1.43 - 1.56: 17765 1.56 - 1.69: 128 1.69 - 1.82: 328 Bond restraints: 30592 Sorted by residual: bond pdb=" C5 IMP A 603 " pdb=" C6 IMP A 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 IMP H 603 " pdb=" C6 IMP H 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 IMP D 603 " pdb=" C6 IMP D 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C5 IMP E 603 " pdb=" C6 IMP E 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C5 IMP G 603 " pdb=" C6 IMP G 603 " ideal model delta sigma weight residual 1.390 1.533 -0.143 2.00e-02 2.50e+03 5.15e+01 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 99.83 - 107.51: 1277 107.51 - 115.20: 18786 115.20 - 122.89: 18820 122.89 - 130.57: 2485 130.57 - 138.26: 168 Bond angle restraints: 41536 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 130.93 8.94 1.00e+00 1.00e+00 7.99e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 131.00 8.87 1.00e+00 1.00e+00 7.86e+01 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 131.03 8.84 1.00e+00 1.00e+00 7.81e+01 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 131.06 8.81 1.00e+00 1.00e+00 7.77e+01 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 131.87 8.00 1.00e+00 1.00e+00 6.40e+01 ... (remaining 41531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 17766 31.18 - 62.37: 1042 62.37 - 93.55: 92 93.55 - 124.73: 0 124.73 - 155.92: 4 Dihedral angle restraints: 18904 sinusoidal: 8016 harmonic: 10888 Sorted by residual: dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.15 -155.92 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.17 -155.90 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' IMP E 603 " pdb=" O5' IMP E 603 " pdb=" P IMP E 603 " pdb=" O2P IMP E 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.27 -155.80 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 18901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2650 0.030 - 0.060: 1280 0.060 - 0.090: 539 0.090 - 0.119: 291 0.119 - 0.149: 80 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ILE C 439 " pdb=" N ILE C 439 " pdb=" C ILE C 439 " pdb=" CB ILE C 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE D 439 " pdb=" N ILE D 439 " pdb=" C ILE D 439 " pdb=" CB ILE D 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE F 439 " pdb=" N ILE F 439 " pdb=" C ILE F 439 " pdb=" CB ILE F 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 4837 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 63 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO G 64 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 64 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 63 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO D 64 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.027 5.00e-02 4.00e+02 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6226 2.79 - 3.31: 28489 3.31 - 3.84: 52351 3.84 - 4.37: 64398 4.37 - 4.90: 102817 Nonbonded interactions: 254281 Sorted by model distance: nonbonded pdb=" O ALA G 396 " pdb=" NZ LYS G 409 " model vdw 2.256 2.520 nonbonded pdb=" O ALA F 396 " pdb=" NZ LYS F 409 " model vdw 2.261 2.520 nonbonded pdb=" O ALA E 396 " pdb=" NZ LYS E 409 " model vdw 2.264 2.520 nonbonded pdb=" O ALA B 396 " pdb=" NZ LYS B 409 " model vdw 2.264 2.520 nonbonded pdb=" O ALA C 396 " pdb=" NZ LYS C 409 " model vdw 2.265 2.520 ... (remaining 254276 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: 4.050 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: 0.020 Extract box with map and model: 14.660 Check model and map are aligned: 0.480 Set scattering table: 0.310 Process input model: 74.970 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.200 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:10.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 0.144 30592 Z= 0.414 Angle : 0.776 8.941 41536 Z= 0.441 Chirality : 0.046 0.149 4840 Planarity : 0.005 0.049 5160 Dihedral : 18.028 155.916 11960 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.24 % Allowed : 12.15 % Favored : 86.61 % 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: 0.12 (0.13), residues: 3808 helix: 0.80 (0.13), residues: 1464 sheet: 0.15 (0.25), residues: 448 loop : -0.44 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 92 PHE 0.014 0.002 PHE C 357 TYR 0.012 0.002 TYR H 353 ARG 0.004 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 855 time to evaluate : 3.345 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 11 residues processed: 875 average time/residue: 1.5337 time to fit residues: 1552.4483 Evaluate side-chains 664 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 653 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.8980 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 348 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30592 Z= 0.297 Angle : 0.578 6.455 41536 Z= 0.302 Chirality : 0.044 0.151 4840 Planarity : 0.004 0.040 5160 Dihedral : 12.457 165.113 5178 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.74 % Allowed : 16.45 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.13), residues: 3808 helix: 1.33 (0.14), residues: 1400 sheet: 0.61 (0.24), residues: 488 loop : -0.18 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 92 PHE 0.013 0.002 PHE D 114 TYR 0.012 0.002 TYR A 233 ARG 0.010 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 674 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 487 GLU cc_start: 0.5869 (mm-30) cc_final: 0.5630 (mm-30) REVERT: F 487 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5582 (mm-30) REVERT: H 487 GLU cc_start: 0.5840 (mm-30) cc_final: 0.5578 (mm-30) outliers start: 86 outliers final: 32 residues processed: 719 average time/residue: 1.5967 time to fit residues: 1320.6912 Evaluate side-chains 673 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 641 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 418 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 290 optimal weight: 0.4980 chunk 237 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 349 optimal weight: 1.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 346 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 280 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN H 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30592 Z= 0.281 Angle : 0.539 7.314 41536 Z= 0.285 Chirality : 0.043 0.155 4840 Planarity : 0.004 0.057 5160 Dihedral : 12.316 175.465 5160 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.97 % Allowed : 17.79 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.13), residues: 3808 helix: 1.42 (0.14), residues: 1408 sheet: 1.08 (0.28), residues: 368 loop : -0.19 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 92 PHE 0.011 0.002 PHE D 114 TYR 0.011 0.001 TYR F 233 ARG 0.011 0.001 ARG H 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 665 time to evaluate : 3.261 Fit side-chains revert: symmetry clash REVERT: B 136 ARG cc_start: 0.5274 (ttp80) cc_final: 0.5013 (mtm110) REVERT: E 203 ARG cc_start: 0.6293 (mtm-85) cc_final: 0.5873 (mtm110) REVERT: E 487 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5265 (mm-30) REVERT: F 203 ARG cc_start: 0.6264 (mtm-85) cc_final: 0.5890 (mtm110) REVERT: F 487 GLU cc_start: 0.6119 (mm-30) cc_final: 0.4039 (mm-30) REVERT: G 487 GLU cc_start: 0.6208 (mm-30) cc_final: 0.4130 (mm-30) REVERT: H 487 GLU cc_start: 0.5823 (mm-30) cc_final: 0.3731 (mm-30) outliers start: 93 outliers final: 44 residues processed: 721 average time/residue: 1.5544 time to fit residues: 1295.9562 Evaluate side-chains 687 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 643 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 166 optimal weight: 0.2980 chunk 234 optimal weight: 2.9990 chunk 350 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30592 Z= 0.168 Angle : 0.505 6.780 41536 Z= 0.264 Chirality : 0.041 0.153 4840 Planarity : 0.004 0.042 5160 Dihedral : 11.670 167.675 5160 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.55 % Allowed : 19.23 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3808 helix: 1.73 (0.14), residues: 1408 sheet: 1.34 (0.29), residues: 352 loop : -0.14 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 92 PHE 0.006 0.001 PHE E 99 TYR 0.011 0.001 TYR B 353 ARG 0.008 0.001 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 664 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.4180 (tm-30) cc_final: 0.3707 (tm-30) REVERT: D 132 GLU cc_start: 0.4124 (tm-30) cc_final: 0.3785 (tm-30) REVERT: E 487 GLU cc_start: 0.5781 (mm-30) cc_final: 0.3969 (mm-30) REVERT: F 487 GLU cc_start: 0.5846 (mm-30) cc_final: 0.3847 (mm-30) REVERT: G 487 GLU cc_start: 0.6007 (mm-30) cc_final: 0.4038 (mm-30) REVERT: H 487 GLU cc_start: 0.5694 (mm-30) cc_final: 0.3770 (mm-30) outliers start: 80 outliers final: 33 residues processed: 704 average time/residue: 1.5546 time to fit residues: 1263.6274 Evaluate side-chains 665 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 632 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 276 optimal weight: 0.0970 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN H 441 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 30592 Z= 0.252 Angle : 0.545 7.003 41536 Z= 0.284 Chirality : 0.043 0.156 4840 Planarity : 0.004 0.042 5160 Dihedral : 11.328 130.544 5160 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.90 % Allowed : 20.15 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.13), residues: 3808 helix: 1.69 (0.14), residues: 1400 sheet: 1.16 (0.28), residues: 368 loop : -0.15 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 92 PHE 0.010 0.002 PHE F 114 TYR 0.011 0.001 TYR A 353 ARG 0.010 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 647 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 GLU cc_start: 0.4144 (tm-30) cc_final: 0.3761 (tm-30) REVERT: E 487 GLU cc_start: 0.5851 (mm-30) cc_final: 0.4048 (mm-30) REVERT: F 487 GLU cc_start: 0.5929 (mm-30) cc_final: 0.3849 (mm-30) REVERT: G 487 GLU cc_start: 0.6100 (mm-30) cc_final: 0.4094 (mm-30) REVERT: H 487 GLU cc_start: 0.5766 (mm-30) cc_final: 0.3734 (mm-30) outliers start: 91 outliers final: 43 residues processed: 699 average time/residue: 1.5591 time to fit residues: 1261.1922 Evaluate side-chains 673 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 630 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 371 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 195 optimal weight: 0.0030 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 30592 Z= 0.296 Angle : 0.573 9.598 41536 Z= 0.298 Chirality : 0.044 0.161 4840 Planarity : 0.004 0.045 5160 Dihedral : 11.259 96.010 5160 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 20.92 % Favored : 76.08 % 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: 0.89 (0.13), residues: 3808 helix: 1.54 (0.14), residues: 1400 sheet: 1.46 (0.31), residues: 288 loop : -0.14 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 92 PHE 0.012 0.002 PHE E 110 TYR 0.011 0.001 TYR H 353 ARG 0.012 0.001 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 632 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 153 LYS cc_start: 0.5712 (tppt) cc_final: 0.5379 (tppt) REVERT: E 487 GLU cc_start: 0.5977 (mm-30) cc_final: 0.4047 (mm-30) REVERT: F 132 GLU cc_start: 0.4140 (tm-30) cc_final: 0.3769 (tm-30) REVERT: F 487 GLU cc_start: 0.6059 (mm-30) cc_final: 0.3972 (mm-30) REVERT: G 487 GLU cc_start: 0.6195 (mm-30) cc_final: 0.4237 (mm-30) REVERT: H 487 GLU cc_start: 0.5905 (mm-30) cc_final: 0.3914 (mm-30) outliers start: 94 outliers final: 48 residues processed: 685 average time/residue: 1.5404 time to fit residues: 1219.8783 Evaluate side-chains 650 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 602 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 312 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 370 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30592 Z= 0.203 Angle : 0.560 8.642 41536 Z= 0.288 Chirality : 0.042 0.150 4840 Planarity : 0.004 0.053 5160 Dihedral : 11.003 88.294 5160 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.01 % Allowed : 22.35 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.14), residues: 3808 helix: 1.69 (0.14), residues: 1400 sheet: 1.81 (0.32), residues: 272 loop : -0.08 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 92 PHE 0.007 0.001 PHE A 99 TYR 0.010 0.001 TYR C 353 ARG 0.013 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 620 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 487 GLU cc_start: 0.5876 (mm-30) cc_final: 0.3812 (mm-30) REVERT: F 487 GLU cc_start: 0.5961 (mm-30) cc_final: 0.3945 (mm-30) REVERT: G 487 GLU cc_start: 0.6105 (mm-30) cc_final: 0.4405 (mm-30) REVERT: H 487 GLU cc_start: 0.5817 (mm-30) cc_final: 0.3740 (mm-30) outliers start: 63 outliers final: 35 residues processed: 660 average time/residue: 1.5643 time to fit residues: 1202.7069 Evaluate side-chains 640 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 605 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 252 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 34 optimal weight: 0.0040 chunk 290 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30592 Z= 0.175 Angle : 0.558 11.027 41536 Z= 0.286 Chirality : 0.041 0.150 4840 Planarity : 0.004 0.059 5160 Dihedral : 10.669 89.349 5160 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.04 % Allowed : 22.45 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3808 helix: 1.76 (0.15), residues: 1408 sheet: 1.86 (0.32), residues: 272 loop : -0.06 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 92 PHE 0.005 0.001 PHE E 99 TYR 0.008 0.001 TYR B 353 ARG 0.013 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 628 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 487 GLU cc_start: 0.5781 (mm-30) cc_final: 0.3848 (mm-30) REVERT: F 487 GLU cc_start: 0.5825 (mm-30) cc_final: 0.3814 (mm-30) REVERT: G 487 GLU cc_start: 0.6055 (mm-30) cc_final: 0.4226 (mm-30) REVERT: H 132 GLU cc_start: 0.4016 (tp30) cc_final: 0.3809 (tp30) REVERT: H 487 GLU cc_start: 0.5710 (mm-30) cc_final: 0.3844 (mm-30) outliers start: 64 outliers final: 27 residues processed: 671 average time/residue: 1.5139 time to fit residues: 1176.3793 Evaluate side-chains 641 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 614 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.6980 chunk 354 optimal weight: 2.9990 chunk 323 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 311 optimal weight: 4.9990 chunk 326 optimal weight: 5.9990 chunk 343 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN F 448 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30592 Z= 0.221 Angle : 0.591 12.649 41536 Z= 0.301 Chirality : 0.042 0.151 4840 Planarity : 0.005 0.064 5160 Dihedral : 10.687 88.947 5160 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.69 % Allowed : 23.15 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3808 helix: 1.76 (0.15), residues: 1400 sheet: 1.85 (0.31), residues: 272 loop : -0.07 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 92 PHE 0.008 0.001 PHE E 99 TYR 0.010 0.001 TYR E 353 ARG 0.014 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 615 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 487 GLU cc_start: 0.5841 (mm-30) cc_final: 0.3931 (mm-30) REVERT: F 487 GLU cc_start: 0.5945 (mm-30) cc_final: 0.3904 (mm-30) REVERT: G 487 GLU cc_start: 0.6108 (mm-30) cc_final: 0.4189 (mm-30) REVERT: H 487 GLU cc_start: 0.5778 (mm-30) cc_final: 0.3953 (mm-30) outliers start: 53 outliers final: 34 residues processed: 644 average time/residue: 1.5478 time to fit residues: 1152.2279 Evaluate side-chains 637 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 603 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 437 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: 3.9990 chunk 173 optimal weight: 1.9990 chunk 253 optimal weight: 0.2980 chunk 382 optimal weight: 3.9990 chunk 352 optimal weight: 0.0670 chunk 304 optimal weight: 0.0000 chunk 31 optimal weight: 0.5980 chunk 235 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 368 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN F 448 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30592 Z= 0.168 Angle : 0.585 12.055 41536 Z= 0.297 Chirality : 0.040 0.149 4840 Planarity : 0.005 0.064 5160 Dihedral : 10.167 89.280 5160 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.89 % Allowed : 24.04 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 3808 helix: 1.89 (0.15), residues: 1400 sheet: 1.91 (0.31), residues: 272 loop : -0.00 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS C 137 PHE 0.006 0.001 PHE C 401 TYR 0.008 0.001 TYR A 353 ARG 0.018 0.001 ARG H 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 637 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.4107 (tp30) cc_final: 0.3313 (tp30) REVERT: B 132 GLU cc_start: 0.4037 (tp30) cc_final: 0.3452 (tp30) REVERT: C 150 MET cc_start: 0.6398 (mmt) cc_final: 0.6165 (mtt) REVERT: D 132 GLU cc_start: 0.4058 (tp30) cc_final: 0.3212 (tp30) REVERT: E 487 GLU cc_start: 0.5794 (mm-30) cc_final: 0.3886 (mm-30) REVERT: F 487 GLU cc_start: 0.5785 (mm-30) cc_final: 0.3762 (mm-30) REVERT: G 487 GLU cc_start: 0.5980 (mm-30) cc_final: 0.4185 (mm-30) REVERT: H 132 GLU cc_start: 0.4051 (tp30) cc_final: 0.3477 (tp30) REVERT: H 337 MET cc_start: 0.6745 (mmp) cc_final: 0.6255 (mmm) REVERT: H 487 GLU cc_start: 0.5600 (mm-30) cc_final: 0.3918 (mm-30) outliers start: 28 outliers final: 20 residues processed: 659 average time/residue: 1.5240 time to fit residues: 1162.5746 Evaluate side-chains 636 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 616 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 437 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: 4.9990 chunk 93 optimal weight: 0.9990 chunk 280 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 313 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN F 448 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 441 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077466 restraints weight = 54791.289| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.96 r_work: 0.3074 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30592 Z= 0.251 Angle : 0.635 12.233 41536 Z= 0.324 Chirality : 0.042 0.151 4840 Planarity : 0.005 0.075 5160 Dihedral : 10.445 89.733 5160 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.08 % Allowed : 24.23 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3808 helix: 1.78 (0.15), residues: 1392 sheet: 1.33 (0.27), residues: 368 loop : -0.12 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 137 PHE 0.008 0.001 PHE F 110 TYR 0.011 0.001 TYR D 353 ARG 0.017 0.001 ARG H 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16429.58 seconds wall clock time: 290 minutes 36.78 seconds (17436.78 seconds total)