Starting phenix.real_space_refine on Sat Apr 13 09:14:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/04_2024/8u7m_41986_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/04_2024/8u7m_41986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/04_2024/8u7m_41986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/04_2024/8u7m_41986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/04_2024/8u7m_41986_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/04_2024/8u7m_41986_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 176 5.16 5 C 17576 2.51 5 N 4832 2.21 5 O 5656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E GLU 487": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G GLU 487": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H GLU 487": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28336 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "B" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "C" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "D" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "E" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "F" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "H" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 15.33, per 1000 atoms: 0.54 Number of scatterers: 28336 At special positions: 0 Unit cell: (170.52, 170.52, 105.56, 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 176 16.00 P 96 15.00 O 5656 8.00 N 4832 7.00 C 17576 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: 12.03 Conformation dependent library (CDL) restraints added in 5.1 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 166 helices and 48 sheets defined 39.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.72 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.924A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) 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 76 through 84 Processing helix chain 'A' and resid 97 through 109 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 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 255 through 266 removed outlier: 4.154A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.687A pdb=" N GLN A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 4.109A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.913A 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: 4.000A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 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 26 removed outlier: 3.926A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) 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 76 through 84 Processing helix chain 'B' and resid 97 through 109 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 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 255 through 266 removed outlier: 4.132A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN B 265 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.726A pdb=" N GLN B 292 " --> pdb=" O HIS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 removed outlier: 4.104A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.911A 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: 4.000A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' 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 removed outlier: 3.648A pdb=" N ARG B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'C' and resid 20 through 26 removed outlier: 3.926A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) 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 76 through 84 Processing helix chain 'C' and resid 97 through 109 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 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 255 through 266 removed outlier: 4.139A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN C 265 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 3.712A pdb=" N GLN C 292 " --> pdb=" O HIS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 315 removed outlier: 4.134A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.918A 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: 4.002A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' 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 26 removed outlier: 3.902A pdb=" N SER D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) 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 76 through 84 Processing helix chain 'D' and resid 97 through 109 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 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 255 through 266 removed outlier: 4.130A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN D 265 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.727A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 315 removed outlier: 4.141A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.924A 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: 4.022A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' 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 removed outlier: 3.601A pdb=" N ARG D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'E' and resid 20 through 26 removed outlier: 3.923A pdb=" N SER E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) 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 76 through 84 Processing helix chain 'E' and resid 97 through 109 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 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 255 through 266 removed outlier: 4.154A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN E 265 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.689A pdb=" N GLN E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 315 removed outlier: 4.109A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.913A 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: 4.003A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 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 removed outlier: 3.558A pdb=" N ARG E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 500 Processing helix chain 'F' and resid 20 through 26 removed outlier: 3.925A pdb=" N SER F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) 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 76 through 84 Processing helix chain 'F' and resid 97 through 109 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 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 255 through 266 removed outlier: 4.131A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN F 265 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.730A pdb=" N GLN F 292 " --> pdb=" O HIS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 315 removed outlier: 4.085A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.892A 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: 4.002A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' 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 26 removed outlier: 3.918A pdb=" N SER G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) 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 76 through 84 Processing helix chain 'G' and resid 97 through 109 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 170 through 172 No H-bonds generated for 'chain 'G' and resid 170 through 172' Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 255 through 266 removed outlier: 4.141A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN G 265 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 3.711A pdb=" N GLN G 292 " --> pdb=" O HIS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 315 removed outlier: 4.119A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.922A 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: 4.018A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' 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 removed outlier: 3.601A pdb=" N ARG G 480 " --> pdb=" O LEU G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 500 Processing helix chain 'H' and resid 20 through 26 removed outlier: 3.921A pdb=" N SER H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) 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 76 through 84 Processing helix chain 'H' and resid 97 through 109 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 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 255 through 266 removed outlier: 4.130A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN H 265 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.728A pdb=" N GLN H 292 " --> pdb=" O HIS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 315 removed outlier: 4.139A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.925A 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: 4.021A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 388 through 390 No H-bonds generated for 'chain 'H' and resid 388 through 390' 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 removed outlier: 3.615A pdb=" N ARG H 480 " --> pdb=" O LEU H 476 " (cutoff:3.500A) 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: 6.455A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.952A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 187 through 189 removed outlier: 7.859A pdb=" N ALA A 188 " --> pdb=" O LYS A 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 222 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.485A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.503A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) 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: 6.524A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 142 through 144 removed outlier: 3.955A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 187 through 189 removed outlier: 7.876A pdb=" N ALA B 188 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 222 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.502A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.493A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) 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: 6.518A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.965A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 187 through 189 removed outlier: 7.846A pdb=" N ALA C 188 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 222 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.562A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) 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: 6.443A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.952A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 187 through 189 removed outlier: 7.859A pdb=" N ALA D 188 " --> pdb=" O LYS D 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 222 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.494A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.495A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) 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: 6.442A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 142 through 144 removed outlier: 3.959A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 187 through 189 removed outlier: 7.894A pdb=" N ALA E 188 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 222 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.494A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.502A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) 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: 6.482A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 142 through 144 removed outlier: 3.960A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 187 through 189 removed outlier: 7.849A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 222 " --> pdb=" O LEU F 209 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.502A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) 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: 6.499A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 142 through 144 removed outlier: 3.956A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 187 through 189 removed outlier: 7.902A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 222 " --> pdb=" O LEU G 209 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.561A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) 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: 6.503A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 142 through 144 removed outlier: 3.957A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 187 through 189 removed outlier: 8.029A pdb=" N ALA H 188 " --> pdb=" O LYS H 208 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE H 222 " --> pdb=" O LEU H 209 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.493A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.495A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2265 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: 10.47 Time building geometry restraints manager: 12.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4680 1.31 - 1.43: 6900 1.43 - 1.56: 16753 1.56 - 1.69: 171 1.69 - 1.81: 296 Bond restraints: 28800 Sorted by residual: bond pdb=" C5 IMP F 604 " pdb=" C6 IMP F 604 " ideal model delta sigma weight residual 1.390 1.532 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C5 IMP G 604 " pdb=" C6 IMP G 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C5 IMP D 604 " pdb=" C6 IMP D 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C5 IMP B 604 " pdb=" C6 IMP B 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C5 IMP H 604 " pdb=" C6 IMP H 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.98e+01 ... (remaining 28795 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.39: 777 105.39 - 112.42: 15218 112.42 - 119.45: 9456 119.45 - 126.49: 13318 126.49 - 133.52: 407 Bond angle restraints: 39176 Sorted by residual: angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 122.69 17.18 1.00e+00 1.00e+00 2.95e+02 angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 122.81 17.06 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.82e+02 ... (remaining 39171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 16912 35.57 - 71.14: 588 71.14 - 106.71: 97 106.71 - 142.28: 39 142.28 - 177.84: 12 Dihedral angle restraints: 17648 sinusoidal: 7488 harmonic: 10160 Sorted by residual: dihedral pdb=" C5' IMP A 604 " pdb=" O5' IMP A 604 " pdb=" P IMP A 604 " pdb=" O2P IMP A 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.09 177.84 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP D 604 " pdb=" O5' IMP D 604 " pdb=" P IMP D 604 " pdb=" O2P IMP D 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.31 177.62 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP B 604 " pdb=" O5' IMP B 604 " pdb=" P IMP B 604 " pdb=" O2P IMP B 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.43 177.50 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 17645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4568 0.340 - 0.680: 24 0.680 - 1.019: 0 1.019 - 1.359: 0 1.359 - 1.699: 8 Chirality restraints: 4600 Sorted by residual: chirality pdb=" C2' ATP A 603 " pdb=" C1' ATP A 603 " pdb=" C3' ATP A 603 " pdb=" O2' ATP A 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.21e+01 chirality pdb=" C2' ATP B 603 " pdb=" C1' ATP B 603 " pdb=" C3' ATP B 603 " pdb=" O2' ATP B 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.19e+01 chirality pdb=" C2' ATP C 603 " pdb=" C1' ATP C 603 " pdb=" C3' ATP C 603 " pdb=" O2' ATP C 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.19e+01 ... (remaining 4597 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 63 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 64 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " -0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO C 64 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 63 " 0.063 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO E 64 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " 0.052 5.00e-02 4.00e+02 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2990 2.74 - 3.28: 29610 3.28 - 3.82: 46510 3.82 - 4.36: 57635 4.36 - 4.90: 98592 Nonbonded interactions: 235337 Sorted by model distance: nonbonded pdb=" NZ LYS A 205 " pdb=" OG1 THR E 180 " model vdw 2.203 2.520 nonbonded pdb=" OG1 THR D 180 " pdb=" NZ LYS F 205 " model vdw 2.206 2.520 nonbonded pdb=" OG SER B 275 " pdb=" NE2 GLN B 283 " model vdw 2.209 2.520 nonbonded pdb=" OG SER F 275 " pdb=" NE2 GLN F 283 " model vdw 2.209 2.520 nonbonded pdb=" OG SER G 275 " pdb=" NE2 GLN G 283 " model vdw 2.211 2.520 ... (remaining 235332 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 14.810 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 77.360 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 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 : 0.007 0.142 28800 Z= 0.421 Angle : 1.128 19.362 39176 Z= 0.565 Chirality : 0.088 1.699 4600 Planarity : 0.006 0.104 4800 Dihedral : 20.220 177.844 11136 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.27 % Allowed : 14.96 % Favored : 84.77 % 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: 3528 helix: 0.12 (0.14), residues: 1344 sheet: -0.50 (0.29), residues: 280 loop : -1.42 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 372 PHE 0.013 0.002 PHE G 456 TYR 0.013 0.001 TYR E 459 ARG 0.009 0.001 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 505 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 507 average time/residue: 0.3746 time to fit residues: 310.7447 Evaluate side-chains 425 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.0770 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 326 optimal weight: 0.3980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN A 372 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 372 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 372 HIS C 469 GLN D 102 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 368 GLN D 372 HIS D 469 GLN E 102 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN E 372 HIS E 469 GLN F 102 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 372 HIS ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN G 372 HIS H 102 ASN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN H 372 HIS H 469 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28800 Z= 0.205 Angle : 0.633 7.373 39176 Z= 0.310 Chirality : 0.045 0.205 4600 Planarity : 0.005 0.064 4800 Dihedral : 20.811 154.287 4800 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.40 % Allowed : 16.87 % Favored : 81.73 % 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: -0.85 (0.14), residues: 3528 helix: 0.15 (0.14), residues: 1376 sheet: -0.30 (0.30), residues: 280 loop : -1.14 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 93 PHE 0.020 0.002 PHE F 456 TYR 0.011 0.001 TYR E 289 ARG 0.006 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 472 time to evaluate : 3.125 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.7430 (ptt) cc_final: 0.7074 (ptt) REVERT: A 182 ARG cc_start: 0.5597 (ttt-90) cc_final: 0.5349 (ttt-90) REVERT: A 198 ASN cc_start: 0.5554 (m-40) cc_final: 0.5262 (m-40) REVERT: A 208 LYS cc_start: 0.4307 (mmmt) cc_final: 0.3617 (mttm) REVERT: A 353 TYR cc_start: 0.7143 (t80) cc_final: 0.6884 (t80) REVERT: A 450 LYS cc_start: 0.7665 (ttmm) cc_final: 0.7218 (ttpt) REVERT: B 179 MET cc_start: 0.7517 (ptt) cc_final: 0.7030 (ptt) REVERT: B 208 LYS cc_start: 0.4528 (mmmt) cc_final: 0.3854 (mttm) REVERT: B 353 TYR cc_start: 0.7092 (t80) cc_final: 0.6809 (t80) REVERT: B 450 LYS cc_start: 0.7603 (ttmm) cc_final: 0.7359 (ttpt) REVERT: C 94 ASN cc_start: 0.6782 (OUTLIER) cc_final: 0.6523 (m-40) REVERT: C 179 MET cc_start: 0.7528 (ptt) cc_final: 0.7013 (ptt) REVERT: C 198 ASN cc_start: 0.5612 (m-40) cc_final: 0.5308 (m-40) REVERT: C 208 LYS cc_start: 0.4477 (mmmt) cc_final: 0.3813 (mttm) REVERT: C 353 TYR cc_start: 0.7164 (t80) cc_final: 0.6887 (t80) REVERT: C 450 LYS cc_start: 0.7641 (ttmm) cc_final: 0.7384 (ttpt) REVERT: D 179 MET cc_start: 0.7462 (ptt) cc_final: 0.6966 (ptt) REVERT: D 198 ASN cc_start: 0.5641 (m-40) cc_final: 0.5355 (m-40) REVERT: D 208 LYS cc_start: 0.4598 (mmmt) cc_final: 0.3803 (mttm) REVERT: D 353 TYR cc_start: 0.7130 (t80) cc_final: 0.6869 (t80) REVERT: E 179 MET cc_start: 0.7513 (ptt) cc_final: 0.6995 (ptt) REVERT: E 182 ARG cc_start: 0.5714 (ttt-90) cc_final: 0.5407 (ttt-90) REVERT: E 198 ASN cc_start: 0.5643 (m-40) cc_final: 0.5352 (m-40) REVERT: E 208 LYS cc_start: 0.4541 (mmmt) cc_final: 0.3757 (mttm) REVERT: E 353 TYR cc_start: 0.7147 (t80) cc_final: 0.6886 (t80) REVERT: E 450 LYS cc_start: 0.7719 (ttmm) cc_final: 0.7237 (ttpt) REVERT: F 179 MET cc_start: 0.7450 (ptt) cc_final: 0.7013 (ptt) REVERT: F 208 LYS cc_start: 0.4447 (mmmt) cc_final: 0.3782 (mttm) REVERT: F 353 TYR cc_start: 0.7144 (t80) cc_final: 0.6859 (t80) REVERT: F 450 LYS cc_start: 0.7587 (ttmm) cc_final: 0.7234 (ttpt) REVERT: G 94 ASN cc_start: 0.6776 (OUTLIER) cc_final: 0.6517 (m-40) REVERT: G 179 MET cc_start: 0.7492 (ptt) cc_final: 0.7045 (ptt) REVERT: G 198 ASN cc_start: 0.5648 (m-40) cc_final: 0.5360 (m-40) REVERT: G 353 TYR cc_start: 0.7099 (t80) cc_final: 0.6809 (t80) REVERT: G 450 LYS cc_start: 0.7590 (ttmm) cc_final: 0.7348 (ttpt) REVERT: H 179 MET cc_start: 0.7483 (ptt) cc_final: 0.7041 (ptt) REVERT: H 198 ASN cc_start: 0.5596 (m-40) cc_final: 0.5320 (m-40) REVERT: H 353 TYR cc_start: 0.7129 (t80) cc_final: 0.6867 (t80) REVERT: H 450 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7226 (ttpt) outliers start: 41 outliers final: 28 residues processed: 491 average time/residue: 0.3665 time to fit residues: 297.9322 Evaluate side-chains 453 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 423 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 90 optimal weight: 0.0020 chunk 327 optimal weight: 4.9990 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 28800 Z= 0.415 Angle : 0.740 6.698 39176 Z= 0.373 Chirality : 0.049 0.225 4600 Planarity : 0.006 0.049 4800 Dihedral : 19.531 151.418 4800 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.93 % Allowed : 16.91 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3528 helix: -0.43 (0.14), residues: 1320 sheet: -0.65 (0.28), residues: 264 loop : -1.38 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 93 PHE 0.024 0.003 PHE D 511 TYR 0.013 0.002 TYR H 459 ARG 0.005 0.001 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 443 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.7635 (ptt) cc_final: 0.7245 (ptt) REVERT: A 450 LYS cc_start: 0.7796 (ttmm) cc_final: 0.7498 (ttpt) REVERT: A 459 TYR cc_start: 0.6883 (t80) cc_final: 0.6450 (t80) REVERT: B 179 MET cc_start: 0.7722 (ptt) cc_final: 0.7272 (ptt) REVERT: B 254 GLU cc_start: 0.7245 (tp30) cc_final: 0.7045 (tp30) REVERT: B 459 TYR cc_start: 0.6858 (t80) cc_final: 0.6537 (t80) REVERT: C 179 MET cc_start: 0.7643 (ptt) cc_final: 0.7237 (ptt) REVERT: C 459 TYR cc_start: 0.6858 (t80) cc_final: 0.6568 (t80) REVERT: D 78 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7563 (ttm) REVERT: D 179 MET cc_start: 0.7641 (ptt) cc_final: 0.7231 (ptt) REVERT: D 450 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7406 (ttpt) REVERT: D 459 TYR cc_start: 0.6836 (t80) cc_final: 0.6517 (t80) REVERT: E 179 MET cc_start: 0.7633 (ptt) cc_final: 0.7208 (ptt) REVERT: E 450 LYS cc_start: 0.7824 (ttmm) cc_final: 0.7496 (ttpt) REVERT: E 459 TYR cc_start: 0.6865 (t80) cc_final: 0.6429 (t80) REVERT: F 179 MET cc_start: 0.7615 (ptt) cc_final: 0.7207 (ptt) REVERT: F 254 GLU cc_start: 0.7257 (tp30) cc_final: 0.7051 (tp30) REVERT: F 459 TYR cc_start: 0.6884 (t80) cc_final: 0.6571 (t80) REVERT: G 179 MET cc_start: 0.7681 (ptt) cc_final: 0.7251 (ptt) REVERT: G 459 TYR cc_start: 0.6855 (t80) cc_final: 0.6540 (t80) REVERT: H 179 MET cc_start: 0.7672 (ptt) cc_final: 0.7244 (ptt) REVERT: H 254 GLU cc_start: 0.7230 (tp30) cc_final: 0.7025 (tp30) outliers start: 115 outliers final: 67 residues processed: 536 average time/residue: 0.3779 time to fit residues: 334.1696 Evaluate side-chains 471 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 403 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 328 optimal weight: 0.9980 chunk 347 optimal weight: 0.0870 chunk 171 optimal weight: 0.8980 chunk 311 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28800 Z= 0.185 Angle : 0.572 7.135 39176 Z= 0.283 Chirality : 0.043 0.141 4600 Planarity : 0.004 0.052 4800 Dihedral : 18.665 162.429 4800 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.21 % Allowed : 18.65 % Favored : 78.14 % 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: -1.08 (0.14), residues: 3528 helix: -0.04 (0.14), residues: 1368 sheet: -0.41 (0.28), residues: 264 loop : -1.25 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 93 PHE 0.013 0.002 PHE C 456 TYR 0.011 0.001 TYR B 459 ARG 0.004 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 470 time to evaluate : 3.350 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.7432 (ptt) cc_final: 0.7226 (ptt) REVERT: A 208 LYS cc_start: 0.4772 (mmmt) cc_final: 0.3872 (mttm) REVERT: A 450 LYS cc_start: 0.7738 (ttmm) cc_final: 0.7489 (ttpt) REVERT: A 459 TYR cc_start: 0.6859 (t80) cc_final: 0.6582 (t80) REVERT: B 208 LYS cc_start: 0.4800 (mmmt) cc_final: 0.3863 (mttm) REVERT: B 450 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7433 (ttpt) REVERT: B 459 TYR cc_start: 0.6684 (t80) cc_final: 0.6390 (t80) REVERT: B 491 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6157 (tt0) REVERT: C 208 LYS cc_start: 0.4821 (mmmt) cc_final: 0.3911 (mttm) REVERT: C 450 LYS cc_start: 0.7582 (ttpt) cc_final: 0.7375 (ttpt) REVERT: C 459 TYR cc_start: 0.6769 (t80) cc_final: 0.6418 (t80) REVERT: D 208 LYS cc_start: 0.4946 (mmmt) cc_final: 0.3884 (mttm) REVERT: D 459 TYR cc_start: 0.6690 (t80) cc_final: 0.6321 (t80) REVERT: E 208 LYS cc_start: 0.4910 (mmmt) cc_final: 0.3847 (mttm) REVERT: E 450 LYS cc_start: 0.7729 (ttmm) cc_final: 0.7445 (ttpt) REVERT: E 459 TYR cc_start: 0.6823 (t80) cc_final: 0.6504 (t80) REVERT: F 208 LYS cc_start: 0.4796 (mmmt) cc_final: 0.3906 (mttm) REVERT: F 377 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7178 (mm) REVERT: F 450 LYS cc_start: 0.7788 (ttmm) cc_final: 0.7384 (ttpt) REVERT: F 459 TYR cc_start: 0.6851 (t80) cc_final: 0.6608 (t80) REVERT: G 459 TYR cc_start: 0.6758 (t80) cc_final: 0.6399 (t80) REVERT: H 136 ARG cc_start: 0.7083 (mmp-170) cc_final: 0.6874 (mmp-170) REVERT: H 450 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7330 (ttpt) outliers start: 94 outliers final: 64 residues processed: 547 average time/residue: 0.3947 time to fit residues: 347.3761 Evaluate side-chains 509 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 443 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 1.9990 chunk 197 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28800 Z= 0.259 Angle : 0.603 6.766 39176 Z= 0.300 Chirality : 0.044 0.144 4600 Planarity : 0.005 0.048 4800 Dihedral : 18.376 179.259 4800 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.27 % Allowed : 20.22 % 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: -1.21 (0.13), residues: 3528 helix: -0.16 (0.14), residues: 1368 sheet: -0.50 (0.27), residues: 264 loop : -1.33 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 93 PHE 0.020 0.002 PHE D 456 TYR 0.007 0.002 TYR G 348 ARG 0.004 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 454 time to evaluate : 3.358 Fit side-chains REVERT: A 254 GLU cc_start: 0.7225 (tp30) cc_final: 0.6907 (tp30) REVERT: A 450 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7465 (ttpt) REVERT: A 459 TYR cc_start: 0.6901 (t80) cc_final: 0.6553 (t80) REVERT: B 377 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7277 (mm) REVERT: B 459 TYR cc_start: 0.6793 (t80) cc_final: 0.6461 (t80) REVERT: B 491 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6187 (tt0) REVERT: C 450 LYS cc_start: 0.7689 (ttpt) cc_final: 0.7384 (ttpt) REVERT: C 459 TYR cc_start: 0.6903 (t80) cc_final: 0.6524 (t80) REVERT: D 208 LYS cc_start: 0.5056 (mmmt) cc_final: 0.3950 (mttm) REVERT: D 450 LYS cc_start: 0.7556 (ttpt) cc_final: 0.7323 (ttpt) REVERT: E 208 LYS cc_start: 0.4978 (mmmt) cc_final: 0.3876 (mttm) REVERT: E 254 GLU cc_start: 0.7051 (tp30) cc_final: 0.6771 (tp30) REVERT: E 450 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7505 (ttpt) REVERT: E 459 TYR cc_start: 0.6867 (t80) cc_final: 0.6536 (t80) REVERT: F 377 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7308 (mm) REVERT: F 450 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7542 (ttpt) REVERT: F 459 TYR cc_start: 0.6857 (t80) cc_final: 0.6545 (t80) REVERT: G 450 LYS cc_start: 0.7522 (ttpt) cc_final: 0.7275 (ttpt) REVERT: G 456 PHE cc_start: 0.7810 (t80) cc_final: 0.7555 (t80) REVERT: H 450 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7447 (ttpt) REVERT: H 459 TYR cc_start: 0.6794 (t80) cc_final: 0.6582 (t80) outliers start: 125 outliers final: 78 residues processed: 563 average time/residue: 0.3834 time to fit residues: 349.7445 Evaluate side-chains 520 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 439 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 367 ILE Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 chunk 68 optimal weight: 0.0270 chunk 204 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 348 optimal weight: 1.9990 chunk 289 optimal weight: 0.0050 chunk 161 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 0.3980 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28800 Z= 0.145 Angle : 0.548 6.834 39176 Z= 0.270 Chirality : 0.042 0.154 4600 Planarity : 0.004 0.054 4800 Dihedral : 17.607 176.052 4800 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.48 % Allowed : 22.51 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3528 helix: 0.12 (0.14), residues: 1416 sheet: -0.06 (0.28), residues: 264 loop : -1.14 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 92 PHE 0.022 0.001 PHE B 456 TYR 0.009 0.001 TYR A 282 ARG 0.004 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 464 time to evaluate : 3.284 Fit side-chains REVERT: A 217 GLU cc_start: 0.4619 (mp0) cc_final: 0.4320 (mp0) REVERT: A 254 GLU cc_start: 0.7150 (tp30) cc_final: 0.6907 (tp30) REVERT: A 450 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7523 (ttpt) REVERT: A 459 TYR cc_start: 0.7008 (t80) cc_final: 0.6687 (t80) REVERT: B 208 LYS cc_start: 0.4780 (mmmt) cc_final: 0.3806 (mttm) REVERT: B 377 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7142 (mm) REVERT: B 459 TYR cc_start: 0.6816 (t80) cc_final: 0.6526 (t80) REVERT: B 491 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6308 (tt0) REVERT: C 450 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7227 (ttpt) REVERT: C 459 TYR cc_start: 0.6817 (t80) cc_final: 0.6392 (t80) REVERT: D 78 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6487 (ttm) REVERT: D 208 LYS cc_start: 0.4828 (mmmt) cc_final: 0.3873 (mttm) REVERT: D 459 TYR cc_start: 0.6620 (t80) cc_final: 0.6257 (t80) REVERT: E 208 LYS cc_start: 0.4753 (mmmt) cc_final: 0.3850 (mttm) REVERT: E 254 GLU cc_start: 0.6917 (tp30) cc_final: 0.6697 (tp30) REVERT: E 450 LYS cc_start: 0.7713 (ttmm) cc_final: 0.7437 (ttpt) REVERT: E 459 TYR cc_start: 0.6975 (t80) cc_final: 0.6668 (t80) REVERT: F 377 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7183 (mm) REVERT: F 450 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7577 (ttpt) REVERT: F 459 TYR cc_start: 0.6843 (t80) cc_final: 0.6573 (t80) REVERT: G 459 TYR cc_start: 0.6658 (t80) cc_final: 0.6330 (t80) REVERT: H 450 LYS cc_start: 0.7633 (ttmm) cc_final: 0.7418 (ttpt) outliers start: 102 outliers final: 73 residues processed: 554 average time/residue: 0.3768 time to fit residues: 341.9638 Evaluate side-chains 512 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 435 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 211 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28800 Z= 0.312 Angle : 0.658 7.876 39176 Z= 0.327 Chirality : 0.046 0.186 4600 Planarity : 0.005 0.049 4800 Dihedral : 17.377 174.653 4800 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.83 % Allowed : 22.58 % Favored : 73.60 % 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: -1.36 (0.13), residues: 3528 helix: -0.41 (0.14), residues: 1416 sheet: -0.34 (0.26), residues: 272 loop : -1.36 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 372 PHE 0.020 0.002 PHE G 456 TYR 0.010 0.002 TYR G 348 ARG 0.006 0.001 ARG G 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 449 time to evaluate : 3.219 Fit side-chains REVERT: A 450 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7624 (ttpt) REVERT: A 491 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6253 (tt0) REVERT: B 377 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7296 (mm) REVERT: B 450 LYS cc_start: 0.7494 (ttpt) cc_final: 0.7246 (ttpt) REVERT: B 491 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6199 (tt0) REVERT: C 254 GLU cc_start: 0.7174 (tp30) cc_final: 0.6966 (tp30) REVERT: C 491 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6264 (tt0) REVERT: D 78 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7192 (ttm) REVERT: D 327 CYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7447 (p) REVERT: D 491 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6255 (tt0) REVERT: E 254 GLU cc_start: 0.7112 (tp30) cc_final: 0.6894 (tp30) REVERT: E 450 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7576 (ttpt) REVERT: F 377 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7324 (mm) REVERT: F 450 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7607 (ttpt) REVERT: G 254 GLU cc_start: 0.7167 (tp30) cc_final: 0.6959 (tp30) REVERT: G 327 CYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7540 (p) REVERT: G 459 TYR cc_start: 0.6983 (t80) cc_final: 0.6466 (t80) REVERT: G 491 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6231 (tt0) REVERT: H 450 LYS cc_start: 0.7785 (ttmm) cc_final: 0.7570 (ttpt) outliers start: 112 outliers final: 81 residues processed: 544 average time/residue: 0.3822 time to fit residues: 342.0746 Evaluate side-chains 528 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 437 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 272 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28800 Z= 0.214 Angle : 0.601 8.490 39176 Z= 0.294 Chirality : 0.044 0.175 4600 Planarity : 0.005 0.063 4800 Dihedral : 16.752 173.514 4800 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.00 % Allowed : 23.19 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3528 helix: -0.19 (0.14), residues: 1408 sheet: -0.41 (0.27), residues: 264 loop : -1.23 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 288 PHE 0.016 0.002 PHE G 456 TYR 0.007 0.001 TYR F 459 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 434 time to evaluate : 3.023 Fit side-chains REVERT: A 450 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7609 (ttpt) REVERT: B 377 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7239 (mm) REVERT: B 450 LYS cc_start: 0.7354 (ttpt) cc_final: 0.7102 (ttpt) REVERT: B 459 TYR cc_start: 0.6910 (t80) cc_final: 0.6397 (t80) REVERT: B 491 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: D 78 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6985 (ttm) REVERT: D 450 LYS cc_start: 0.7353 (ttpt) cc_final: 0.7064 (ttpt) REVERT: E 254 GLU cc_start: 0.7116 (tp30) cc_final: 0.6861 (tp30) REVERT: E 450 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7514 (ttpt) REVERT: F 377 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7252 (mm) REVERT: F 385 MET cc_start: 0.7390 (ttm) cc_final: 0.7185 (ttm) REVERT: F 450 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7560 (ttpt) REVERT: G 166 LEU cc_start: 0.6553 (mp) cc_final: 0.5575 (mp) REVERT: G 450 LYS cc_start: 0.7492 (ttpt) cc_final: 0.7205 (ttpt) REVERT: G 459 TYR cc_start: 0.6861 (t80) cc_final: 0.6407 (t80) REVERT: H 166 LEU cc_start: 0.6320 (mp) cc_final: 0.5323 (mp) REVERT: H 450 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7526 (ttpt) outliers start: 117 outliers final: 92 residues processed: 538 average time/residue: 0.3603 time to fit residues: 319.8649 Evaluate side-chains 522 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 426 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.0040 chunk 332 optimal weight: 0.7980 chunk 303 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 253 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 0.3980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 28800 Z= 0.158 Angle : 0.558 9.377 39176 Z= 0.273 Chirality : 0.042 0.146 4600 Planarity : 0.005 0.061 4800 Dihedral : 15.731 174.833 4800 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.24 % Allowed : 23.98 % Favored : 72.78 % 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: -0.76 (0.14), residues: 3528 helix: 0.14 (0.14), residues: 1408 sheet: -0.11 (0.28), residues: 264 loop : -1.04 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 171 PHE 0.021 0.001 PHE G 456 TYR 0.008 0.001 TYR D 289 ARG 0.002 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 447 time to evaluate : 3.207 Fit side-chains REVERT: A 166 LEU cc_start: 0.6213 (mp) cc_final: 0.5168 (mp) REVERT: A 450 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7548 (ttpt) REVERT: B 166 LEU cc_start: 0.6496 (mp) cc_final: 0.5498 (mp) REVERT: B 377 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7181 (mm) REVERT: B 491 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6322 (tt0) REVERT: C 103 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7273 (mm-30) REVERT: C 166 LEU cc_start: 0.6046 (mp) cc_final: 0.5070 (mp) REVERT: C 459 TYR cc_start: 0.6757 (t80) cc_final: 0.6157 (t80) REVERT: D 78 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.6594 (ttm) REVERT: D 166 LEU cc_start: 0.6219 (mp) cc_final: 0.5191 (mp) REVERT: D 491 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6277 (tt0) REVERT: E 254 GLU cc_start: 0.6918 (tp30) cc_final: 0.6597 (tp30) REVERT: E 450 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7479 (ttpt) REVERT: F 166 LEU cc_start: 0.6507 (mp) cc_final: 0.5507 (mp) REVERT: F 377 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7231 (mm) REVERT: F 450 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7559 (ttpt) REVERT: F 459 TYR cc_start: 0.6738 (t80) cc_final: 0.6199 (t80) REVERT: G 166 LEU cc_start: 0.6427 (mp) cc_final: 0.5513 (mp) REVERT: G 459 TYR cc_start: 0.6908 (t80) cc_final: 0.6489 (t80) REVERT: H 166 LEU cc_start: 0.6443 (mp) cc_final: 0.5532 (mp) REVERT: H 450 LYS cc_start: 0.7689 (ttmm) cc_final: 0.7420 (ttpt) outliers start: 95 outliers final: 82 residues processed: 526 average time/residue: 0.3693 time to fit residues: 320.3753 Evaluate side-chains 527 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 440 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.1980 chunk 341 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 358 optimal weight: 0.9990 chunk 330 optimal weight: 2.9990 chunk 285 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28800 Z= 0.189 Angle : 0.593 11.510 39176 Z= 0.287 Chirality : 0.043 0.182 4600 Planarity : 0.005 0.061 4800 Dihedral : 15.110 174.690 4800 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.07 % Allowed : 24.32 % Favored : 72.61 % 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: -0.87 (0.14), residues: 3528 helix: 0.05 (0.14), residues: 1408 sheet: -0.39 (0.29), residues: 224 loop : -1.06 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 288 PHE 0.017 0.001 PHE G 456 TYR 0.008 0.001 TYR D 258 ARG 0.003 0.000 ARG A 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 432 time to evaluate : 3.522 Fit side-chains REVERT: A 166 LEU cc_start: 0.6070 (mp) cc_final: 0.5035 (mp) REVERT: A 450 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7530 (ttpt) REVERT: B 166 LEU cc_start: 0.6493 (mp) cc_final: 0.5503 (mp) REVERT: B 377 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7257 (mm) REVERT: B 491 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6348 (tt0) REVERT: C 103 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 166 LEU cc_start: 0.5973 (mp) cc_final: 0.4996 (mp) REVERT: C 459 TYR cc_start: 0.6719 (t80) cc_final: 0.6248 (t80) REVERT: D 78 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6970 (ttm) REVERT: D 166 LEU cc_start: 0.6213 (mp) cc_final: 0.5183 (mp) REVERT: D 491 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6273 (tt0) REVERT: E 166 LEU cc_start: 0.6007 (mp) cc_final: 0.5012 (mp) REVERT: E 254 GLU cc_start: 0.6852 (tp30) cc_final: 0.6580 (tp30) REVERT: E 450 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7486 (ttpt) REVERT: F 166 LEU cc_start: 0.6486 (mp) cc_final: 0.5502 (mp) REVERT: F 377 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7300 (mm) REVERT: F 450 LYS cc_start: 0.7857 (ttmm) cc_final: 0.7559 (ttpt) REVERT: F 459 TYR cc_start: 0.6651 (t80) cc_final: 0.6216 (t80) REVERT: G 166 LEU cc_start: 0.6396 (mp) cc_final: 0.5493 (mp) REVERT: G 491 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6312 (tt0) REVERT: H 166 LEU cc_start: 0.6387 (mp) cc_final: 0.5518 (mp) REVERT: H 450 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7446 (ttpt) outliers start: 90 outliers final: 78 residues processed: 511 average time/residue: 0.3672 time to fit residues: 309.9543 Evaluate side-chains 511 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 427 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 293 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.188253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.160622 restraints weight = 32619.150| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.92 r_work: 0.4076 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28800 Z= 0.214 Angle : 0.606 11.252 39176 Z= 0.294 Chirality : 0.044 0.185 4600 Planarity : 0.005 0.060 4800 Dihedral : 14.914 175.384 4800 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.11 % Allowed : 24.45 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3528 helix: -0.02 (0.14), residues: 1400 sheet: -0.31 (0.28), residues: 232 loop : -1.18 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 288 PHE 0.020 0.002 PHE G 456 TYR 0.008 0.001 TYR H 258 ARG 0.003 0.000 ARG C 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7000.70 seconds wall clock time: 128 minutes 33.55 seconds (7713.55 seconds total)