Starting phenix.real_space_refine on Sun Feb 18 08:04:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/02_2024/7zpr_14862_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/02_2024/7zpr_14862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/02_2024/7zpr_14862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/02_2024/7zpr_14862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/02_2024/7zpr_14862_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/02_2024/7zpr_14862_updated.pdb" } resolution = 3.56 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= 0.004 sd= 0.009 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 Mg 8 5.21 5 S 140 5.16 5 C 13782 2.51 5 N 3576 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 23": "OE1" <-> "OE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "I GLU 24": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "M GLU 24": "OE1" <-> "OE2" Residue "M GLU 149": "OE1" <-> "OE2" Residue "M GLU 260": "OE1" <-> "OE2" Residue "M GLU 393": "OE1" <-> "OE2" Residue "M GLU 413": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 393": "OE1" <-> "OE2" Residue "G GLU 413": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21350 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "I" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "J" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "L" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "M" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "C" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "G" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.28, per 1000 atoms: 0.67 Number of scatterers: 21350 At special positions: 0 Unit cell: (95.9651, 110.921, 173.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 140 16.00 P 16 15.00 Mg 8 11.99 O 3824 8.00 N 3576 7.00 C 13782 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: 8.27 Conformation dependent library (CDL) restraints added in 4.9 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 10 sheets defined 60.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'H' and resid 15 through 27 removed outlier: 3.520A pdb=" N SER H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.713A pdb=" N GLY H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 65 Processing helix chain 'H' and resid 81 through 93 Processing helix chain 'H' and resid 106 through 115 Processing helix chain 'H' and resid 123 through 136 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 123 through 136 Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 123 through 136 Processing helix chain 'F' and resid 15 through 27 Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 67 through 69 No H-bonds generated for 'chain 'F' and resid 67 through 69' Processing helix chain 'F' and resid 81 through 94 Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 123 through 136 Processing helix chain 'I' and resid 24 through 43 removed outlier: 3.527A pdb=" N PHE I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 35 " --> pdb=" O SER I 31 " (cutoff:3.500A) Proline residue: I 38 - end of helix Processing helix chain 'I' and resid 55 through 66 Processing helix chain 'I' and resid 76 through 79 No H-bonds generated for 'chain 'I' and resid 76 through 79' Processing helix chain 'I' and resid 82 through 121 Processing helix chain 'I' and resid 134 through 164 removed outlier: 3.710A pdb=" N ARG I 159 " --> pdb=" O PHE I 155 " (cutoff:3.500A) Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 168 through 181 Processing helix chain 'I' and resid 200 through 213 Processing helix chain 'I' and resid 217 through 226 Processing helix chain 'I' and resid 231 through 233 No H-bonds generated for 'chain 'I' and resid 231 through 233' Processing helix chain 'I' and resid 236 through 260 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 272 through 285 Processing helix chain 'I' and resid 301 through 313 Processing helix chain 'I' and resid 326 through 340 Processing helix chain 'I' and resid 355 through 382 Processing helix chain 'I' and resid 387 through 399 Processing helix chain 'I' and resid 408 through 410 No H-bonds generated for 'chain 'I' and resid 408 through 410' Processing helix chain 'I' and resid 413 through 438 Proline residue: I 430 - end of helix Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.842A pdb=" N GLU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 38 through 46 removed outlier: 3.684A pdb=" N GLY B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'J' and resid 15 through 26 Processing helix chain 'J' and resid 38 through 45 Processing helix chain 'J' and resid 59 through 64 Processing helix chain 'J' and resid 81 through 93 Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 123 through 136 Processing helix chain 'L' and resid 15 through 27 removed outlier: 3.618A pdb=" N SER L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 45 Processing helix chain 'L' and resid 59 through 65 Processing helix chain 'L' and resid 67 through 69 No H-bonds generated for 'chain 'L' and resid 67 through 69' Processing helix chain 'L' and resid 81 through 93 Processing helix chain 'L' and resid 106 through 115 Processing helix chain 'L' and resid 123 through 136 Processing helix chain 'M' and resid 24 through 44 Proline residue: M 38 - end of helix removed outlier: 3.770A pdb=" N THR M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 66 Processing helix chain 'M' and resid 76 through 79 No H-bonds generated for 'chain 'M' and resid 76 through 79' Processing helix chain 'M' and resid 82 through 121 removed outlier: 3.582A pdb=" N GLN M 99 " --> pdb=" O GLY M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 164 removed outlier: 3.846A pdb=" N ARG M 159 " --> pdb=" O PHE M 155 " (cutoff:3.500A) Proline residue: M 162 - end of helix Processing helix chain 'M' and resid 166 through 181 removed outlier: 3.594A pdb=" N PHE M 171 " --> pdb=" O GLN M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 213 Processing helix chain 'M' and resid 217 through 226 Processing helix chain 'M' and resid 231 through 233 No H-bonds generated for 'chain 'M' and resid 231 through 233' Processing helix chain 'M' and resid 236 through 260 Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 272 through 285 Processing helix chain 'M' and resid 301 through 313 Processing helix chain 'M' and resid 326 through 341 Processing helix chain 'M' and resid 355 through 382 Processing helix chain 'M' and resid 387 through 399 Processing helix chain 'M' and resid 413 through 438 removed outlier: 3.536A pdb=" N TYR M 417 " --> pdb=" O GLU M 413 " (cutoff:3.500A) Proline residue: M 430 - end of helix Processing helix chain 'C' and resid 24 through 43 removed outlier: 3.525A pdb=" N PHE C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Proline residue: C 38 - end of helix Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 76 through 79 No H-bonds generated for 'chain 'C' and resid 76 through 79' Processing helix chain 'C' and resid 82 through 121 Processing helix chain 'C' and resid 134 through 164 removed outlier: 3.711A pdb=" N ARG C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 236 through 260 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 272 through 285 Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 355 through 382 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 413 through 438 Proline residue: C 430 - end of helix Processing helix chain 'G' and resid 24 through 44 Proline residue: G 38 - end of helix removed outlier: 3.770A pdb=" N THR G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 Processing helix chain 'G' and resid 76 through 79 No H-bonds generated for 'chain 'G' and resid 76 through 79' Processing helix chain 'G' and resid 82 through 121 removed outlier: 3.581A pdb=" N GLN G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 164 removed outlier: 3.846A pdb=" N ARG G 159 " --> pdb=" O PHE G 155 " (cutoff:3.500A) Proline residue: G 162 - end of helix Processing helix chain 'G' and resid 166 through 181 removed outlier: 3.593A pdb=" N PHE G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 213 Processing helix chain 'G' and resid 217 through 226 Processing helix chain 'G' and resid 231 through 233 No H-bonds generated for 'chain 'G' and resid 231 through 233' Processing helix chain 'G' and resid 236 through 260 Proline residue: G 246 - end of helix Processing helix chain 'G' and resid 272 through 285 Processing helix chain 'G' and resid 301 through 313 Processing helix chain 'G' and resid 326 through 341 Processing helix chain 'G' and resid 355 through 382 Processing helix chain 'G' and resid 387 through 399 Processing helix chain 'G' and resid 413 through 438 removed outlier: 3.537A pdb=" N TYR G 417 " --> pdb=" O GLU G 413 " (cutoff:3.500A) Proline residue: G 430 - end of helix Processing sheet with id= A, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.836A pdb=" N MET H 72 " --> pdb=" O GLN H 7 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN H 30 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL H 10 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU H 32 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN H 50 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASP H 35 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE H 52 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.998A pdb=" N MET D 72 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN D 30 " --> pdb=" O PHE D 8 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL D 10 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 32 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN D 50 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASP D 35 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE D 52 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 119 through 121 removed outlier: 6.200A pdb=" N VAL E 73 " --> pdb=" O TRP E 100 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS E 102 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE E 75 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN E 30 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL E 10 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU E 32 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN E 50 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ASP E 35 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE E 52 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 119 through 121 removed outlier: 6.222A pdb=" N VAL F 73 " --> pdb=" O TRP F 100 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LYS F 102 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE F 75 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN F 30 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL F 10 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU F 32 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN F 50 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ASP F 35 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE F 52 " --> pdb=" O ASP F 35 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.828A pdb=" N MET A 72 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN A 30 " --> pdb=" O PHE A 8 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL A 10 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU A 32 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN A 50 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ASP A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 52 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 119 through 122 removed outlier: 4.125A pdb=" N MET B 72 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN B 30 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL B 10 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 32 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN B 50 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ASP B 35 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 52 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 119 through 121 removed outlier: 6.184A pdb=" N VAL J 73 " --> pdb=" O TRP J 100 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS J 102 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE J 75 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET J 72 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN J 30 " --> pdb=" O PHE J 8 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL J 10 " --> pdb=" O GLN J 30 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU J 32 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN J 50 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASP J 35 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE J 52 " --> pdb=" O ASP J 35 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 119 through 121 removed outlier: 3.511A pdb=" N VAL L 73 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET L 72 " --> pdb=" O GLN L 7 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN L 30 " --> pdb=" O PHE L 8 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL L 10 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU L 32 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN L 50 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ASP L 35 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE L 52 " --> pdb=" O ASP L 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 346 through 348 removed outlier: 4.421A pdb=" N VAL M 346 " --> pdb=" O VAL M 353 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 346 through 348 removed outlier: 4.420A pdb=" N VAL G 346 " --> pdb=" O VAL G 353 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3621 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: 6.37 Time building geometry restraints manager: 8.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4195 1.33 - 1.45: 4835 1.45 - 1.57: 12413 1.57 - 1.69: 24 1.69 - 1.82: 261 Bond restraints: 21728 Sorted by residual: bond pdb=" N PRO H 123 " pdb=" CD PRO H 123 " ideal model delta sigma weight residual 1.473 1.729 -0.256 1.40e-02 5.10e+03 3.35e+02 bond pdb=" C4 ADP J 301 " pdb=" C5 ADP J 301 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N PRO A 123 " pdb=" CD PRO A 123 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C5 ADP A1002 " pdb=" C6 ADP A1002 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 21723 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.51: 385 105.51 - 113.22: 12482 113.22 - 120.93: 11159 120.93 - 128.64: 5263 128.64 - 136.35: 169 Bond angle restraints: 29458 Sorted by residual: angle pdb=" C THR G 288 " pdb=" CA THR G 288 " pdb=" CB THR G 288 " ideal model delta sigma weight residual 110.42 119.31 -8.89 1.99e+00 2.53e-01 2.00e+01 angle pdb=" C THR M 288 " pdb=" CA THR M 288 " pdb=" CB THR M 288 " ideal model delta sigma weight residual 110.42 119.28 -8.86 1.99e+00 2.53e-01 1.98e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" C LEU G 296 " ideal model delta sigma weight residual 112.89 107.50 5.39 1.24e+00 6.50e-01 1.89e+01 angle pdb=" N LEU M 296 " pdb=" CA LEU M 296 " pdb=" C LEU M 296 " ideal model delta sigma weight residual 112.89 107.58 5.31 1.24e+00 6.50e-01 1.84e+01 angle pdb=" N LEU C 296 " pdb=" CA LEU C 296 " pdb=" C LEU C 296 " ideal model delta sigma weight residual 112.89 107.71 5.18 1.24e+00 6.50e-01 1.75e+01 ... (remaining 29453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 12514 33.64 - 67.28: 281 67.28 - 100.92: 16 100.92 - 134.56: 5 134.56 - 168.20: 6 Dihedral angle restraints: 12822 sinusoidal: 4956 harmonic: 7866 Sorted by residual: dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual 300.00 131.80 168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP A1002 " pdb=" O5' ADP A1002 " pdb=" PA ADP A1002 " pdb=" O2A ADP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 100.80 -160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP L 301 " pdb=" O5' ADP L 301 " pdb=" PA ADP L 301 " pdb=" O2A ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 100.02 -160.01 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 12819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3354 0.108 - 0.215: 188 0.215 - 0.322: 2 0.322 - 0.430: 0 0.430 - 0.537: 4 Chirality restraints: 3548 Sorted by residual: chirality pdb=" CA THR G 288 " pdb=" N THR G 288 " pdb=" C THR G 288 " pdb=" CB THR G 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" CA THR M 288 " pdb=" N THR M 288 " pdb=" C THR M 288 " pdb=" CB THR M 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" CA THR C 288 " pdb=" N THR C 288 " pdb=" C THR C 288 " pdb=" CB THR C 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.09e+00 ... (remaining 3545 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 92 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C MET M 92 " 0.041 2.00e-02 2.50e+03 pdb=" O MET M 92 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN M 93 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 92 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET G 92 " -0.041 2.00e-02 2.50e+03 pdb=" O MET G 92 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN G 93 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 122 " 0.032 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 123 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.026 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 141 2.56 - 3.21: 20011 3.21 - 3.85: 43485 3.85 - 4.50: 61509 4.50 - 5.14: 95538 Nonbonded interactions: 220684 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O3B ADP A1002 " model vdw 1.919 2.170 nonbonded pdb=" OD1 ASN H 82 " pdb=" ND2 ASN B 82 " model vdw 1.954 2.520 nonbonded pdb=" O2B ADP L 301 " pdb="MG MG L 302 " model vdw 1.977 2.170 nonbonded pdb=" O3B ADP B1001 " pdb="MG MG B1002 " model vdw 1.984 2.170 nonbonded pdb=" O3B ADP E 301 " pdb="MG MG E 302 " model vdw 1.988 2.170 ... (remaining 220679 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' and resid 6 through 137) selection = (chain 'B' and resid 6 through 137) selection = (chain 'D' and resid 6 through 137) selection = (chain 'E' and resid 6 through 137) selection = (chain 'F' and resid 6 through 137) selection = (chain 'H' and resid 6 through 137) selection = (chain 'J' and resid 6 through 137) selection = (chain 'L' and resid 6 through 137) } ncs_group { reference = (chain 'C' and (resid 21 through 350 or resid 352 through 455 or resid 601)) selection = (chain 'G' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 455 or resid 501)) selection = (chain 'I' and (resid 21 through 350 or resid 352 through 455 or resid 601)) selection = (chain 'M' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 455 or resid 501)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.120 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 60.960 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.005 0.256 21728 Z= 0.363 Angle : 0.800 10.803 29458 Z= 0.497 Chirality : 0.053 0.537 3548 Planarity : 0.004 0.047 3608 Dihedral : 14.454 168.201 7742 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.27 % Favored : 97.51 % Rotamer: Outliers : 0.89 % Allowed : 1.16 % Favored : 97.95 % Cbeta Deviations : 0.16 % 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: 1.50 (0.15), residues: 2736 helix: 1.46 (0.12), residues: 1760 sheet: 1.61 (0.28), residues: 282 loop : -0.34 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 337 HIS 0.005 0.001 HIS G 345 PHE 0.026 0.001 PHE I 210 TYR 0.014 0.002 TYR F 70 ARG 0.005 0.000 ARG J 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 772 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7987 (tp30) cc_final: 0.7136 (tp30) REVERT: H 127 MET cc_start: 0.8929 (tpt) cc_final: 0.8175 (tpp) REVERT: D 23 GLU cc_start: 0.7866 (tp30) cc_final: 0.7666 (tp30) REVERT: D 110 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8190 (mtm180) REVERT: D 133 ARG cc_start: 0.7368 (mtt90) cc_final: 0.7025 (mtm-85) REVERT: E 29 SER cc_start: 0.7901 (m) cc_final: 0.7690 (p) REVERT: E 96 VAL cc_start: 0.8462 (t) cc_final: 0.8256 (t) REVERT: E 127 MET cc_start: 0.8340 (mmm) cc_final: 0.8095 (mmm) REVERT: I 92 MET cc_start: 0.7593 (ptt) cc_final: 0.7332 (ptt) REVERT: I 387 PHE cc_start: 0.7513 (t80) cc_final: 0.7042 (t80) REVERT: I 389 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7597 (ttmt) REVERT: I 420 ILE cc_start: 0.7474 (mt) cc_final: 0.7060 (mt) REVERT: I 447 TYR cc_start: 0.8776 (m-80) cc_final: 0.8502 (m-80) REVERT: A 23 GLU cc_start: 0.7777 (tp30) cc_final: 0.7219 (tp30) REVERT: A 133 ARG cc_start: 0.7424 (mtt90) cc_final: 0.7215 (mtm180) REVERT: B 23 GLU cc_start: 0.7382 (tp30) cc_final: 0.7021 (tp30) REVERT: B 127 MET cc_start: 0.9040 (tpt) cc_final: 0.8791 (tpp) REVERT: B 133 ARG cc_start: 0.7327 (mtt90) cc_final: 0.7040 (mtm-85) REVERT: J 122 MET cc_start: 0.7679 (mtp) cc_final: 0.6736 (mtm) REVERT: J 126 ASP cc_start: 0.7860 (m-30) cc_final: 0.7548 (m-30) REVERT: L 98 SER cc_start: 0.7307 (p) cc_final: 0.6760 (p) REVERT: L 122 MET cc_start: 0.7622 (mtp) cc_final: 0.6897 (mtm) REVERT: M 76 THR cc_start: 0.7360 (m) cc_final: 0.7095 (m) REVERT: M 93 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6901 (tp-100) REVERT: M 298 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: M 420 ILE cc_start: 0.7844 (mt) cc_final: 0.7505 (mt) REVERT: M 447 TYR cc_start: 0.8739 (m-80) cc_final: 0.8474 (m-80) REVERT: C 92 MET cc_start: 0.7635 (ptt) cc_final: 0.7375 (ptt) REVERT: C 93 GLN cc_start: 0.7529 (tp-100) cc_final: 0.7235 (tp-100) REVERT: C 108 TYR cc_start: 0.7607 (t80) cc_final: 0.7366 (t80) REVERT: C 136 ARG cc_start: 0.5225 (ttt180) cc_final: 0.4998 (tpt170) REVERT: C 387 PHE cc_start: 0.7615 (t80) cc_final: 0.7195 (t80) REVERT: C 389 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7639 (ttmt) REVERT: C 420 ILE cc_start: 0.7642 (mt) cc_final: 0.7243 (mt) REVERT: C 447 TYR cc_start: 0.8841 (m-80) cc_final: 0.8597 (m-80) REVERT: C 449 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6444 (mt-10) REVERT: G 93 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6857 (tp-100) REVERT: G 277 LEU cc_start: 0.8276 (tp) cc_final: 0.7858 (tt) REVERT: G 298 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: G 400 THR cc_start: 0.8878 (m) cc_final: 0.8576 (m) REVERT: G 420 ILE cc_start: 0.7862 (mt) cc_final: 0.7609 (mt) REVERT: G 447 TYR cc_start: 0.8782 (m-80) cc_final: 0.8549 (m-80) outliers start: 20 outliers final: 2 residues processed: 782 average time/residue: 0.3515 time to fit residues: 409.9004 Evaluate side-chains 481 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 475 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 GLN D 50 GLN I 78 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN I 301 GLN A 50 GLN J 30 GLN J 108 GLN J 113 GLN M 262 HIS C 78 GLN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN C 301 GLN G 345 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21728 Z= 0.274 Angle : 0.660 7.231 29458 Z= 0.323 Chirality : 0.045 0.158 3548 Planarity : 0.004 0.036 3608 Dihedral : 9.435 176.839 3010 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.89 % Allowed : 11.26 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2736 helix: 2.05 (0.12), residues: 1756 sheet: 2.02 (0.28), residues: 282 loop : -0.33 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 257 HIS 0.009 0.002 HIS C 79 PHE 0.039 0.002 PHE C 210 TYR 0.011 0.002 TYR G 447 ARG 0.005 0.001 ARG I 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 532 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7887 (tp30) cc_final: 0.7044 (tp30) REVERT: H 134 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8232 (mtpt) REVERT: D 23 GLU cc_start: 0.7888 (tp30) cc_final: 0.7263 (tp30) REVERT: D 127 MET cc_start: 0.8853 (mmm) cc_final: 0.8546 (tpp) REVERT: D 133 ARG cc_start: 0.7383 (mtt90) cc_final: 0.7120 (mtm-85) REVERT: E 71 ASP cc_start: 0.7406 (m-30) cc_final: 0.6716 (m-30) REVERT: E 72 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6225 (mmm) REVERT: F 59 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7061 (mt-10) REVERT: F 126 ASP cc_start: 0.7672 (m-30) cc_final: 0.7389 (m-30) REVERT: I 139 LYS cc_start: 0.7216 (ttpp) cc_final: 0.6757 (ttmt) REVERT: I 241 MET cc_start: 0.7956 (mmt) cc_final: 0.7624 (mmt) REVERT: I 389 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7552 (ttmt) REVERT: I 420 ILE cc_start: 0.8279 (mt) cc_final: 0.7864 (mt) REVERT: I 447 TYR cc_start: 0.8890 (m-80) cc_final: 0.8676 (m-80) REVERT: A 23 GLU cc_start: 0.7837 (tp30) cc_final: 0.7114 (tp30) REVERT: A 93 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 133 ARG cc_start: 0.7462 (mtt90) cc_final: 0.7017 (mmm-85) REVERT: B 23 GLU cc_start: 0.7699 (tp30) cc_final: 0.7112 (tp30) REVERT: B 127 MET cc_start: 0.8956 (tpt) cc_final: 0.8720 (tpp) REVERT: B 133 ARG cc_start: 0.7350 (mtt90) cc_final: 0.7065 (mtm-85) REVERT: L 122 MET cc_start: 0.7648 (mtp) cc_final: 0.7339 (mtm) REVERT: M 99 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: M 241 MET cc_start: 0.7959 (mmt) cc_final: 0.7653 (mmt) REVERT: M 265 ASN cc_start: 0.7690 (t0) cc_final: 0.7048 (t0) REVERT: M 298 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6638 (mt0) REVERT: M 420 ILE cc_start: 0.8475 (mt) cc_final: 0.8252 (mt) REVERT: C 193 MET cc_start: 0.7914 (mmt) cc_final: 0.7699 (mmt) REVERT: C 241 MET cc_start: 0.7979 (mmt) cc_final: 0.7722 (mmt) REVERT: C 292 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6870 (p0) REVERT: C 389 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7493 (ttmt) REVERT: C 420 ILE cc_start: 0.8363 (mt) cc_final: 0.7987 (mt) REVERT: G 99 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: G 193 MET cc_start: 0.8062 (mmt) cc_final: 0.7831 (mmt) REVERT: G 241 MET cc_start: 0.7872 (mmt) cc_final: 0.7616 (mmt) REVERT: G 292 ASN cc_start: 0.7085 (p0) cc_final: 0.6727 (p0) REVERT: G 420 ILE cc_start: 0.8531 (mt) cc_final: 0.8330 (mt) outliers start: 65 outliers final: 43 residues processed: 573 average time/residue: 0.3155 time to fit residues: 283.2341 Evaluate side-chains 506 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 458 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 428 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 267 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN M 93 GLN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN G 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21728 Z= 0.240 Angle : 0.612 8.073 29458 Z= 0.296 Chirality : 0.043 0.152 3548 Planarity : 0.003 0.040 3608 Dihedral : 8.694 178.269 3001 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.47 % Allowed : 14.02 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.16), residues: 2736 helix: 2.32 (0.12), residues: 1738 sheet: 2.02 (0.29), residues: 282 loop : -0.43 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 166 HIS 0.005 0.001 HIS G 79 PHE 0.034 0.002 PHE C 210 TYR 0.018 0.001 TYR C 158 ARG 0.005 0.000 ARG M 427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 512 time to evaluate : 2.497 Fit side-chains REVERT: H 23 GLU cc_start: 0.7919 (tp30) cc_final: 0.7231 (tp30) REVERT: H 134 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8248 (mtpt) REVERT: D 23 GLU cc_start: 0.7934 (tp30) cc_final: 0.7281 (tp30) REVERT: D 127 MET cc_start: 0.8845 (mmm) cc_final: 0.8479 (tpp) REVERT: D 133 ARG cc_start: 0.7312 (mtt90) cc_final: 0.7048 (mtm-85) REVERT: E 23 GLU cc_start: 0.7724 (tp30) cc_final: 0.7484 (tp30) REVERT: E 72 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6515 (mmm) REVERT: E 98 SER cc_start: 0.7945 (p) cc_final: 0.7710 (p) REVERT: E 126 ASP cc_start: 0.7939 (m-30) cc_final: 0.7546 (m-30) REVERT: F 59 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7186 (mt-10) REVERT: F 126 ASP cc_start: 0.8004 (m-30) cc_final: 0.7682 (m-30) REVERT: I 139 LYS cc_start: 0.7128 (ttpp) cc_final: 0.6812 (ttmt) REVERT: I 241 MET cc_start: 0.8045 (mmt) cc_final: 0.7749 (mmt) REVERT: I 389 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7469 (ttmt) REVERT: I 420 ILE cc_start: 0.8382 (mt) cc_final: 0.8035 (mt) REVERT: A 23 GLU cc_start: 0.7830 (tp30) cc_final: 0.7170 (tp30) REVERT: A 42 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8076 (mtmt) REVERT: A 133 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7030 (mmm-85) REVERT: B 23 GLU cc_start: 0.7833 (tp30) cc_final: 0.7191 (tp30) REVERT: B 127 MET cc_start: 0.8951 (tpt) cc_final: 0.8710 (tpp) REVERT: J 126 ASP cc_start: 0.7983 (m-30) cc_final: 0.7691 (m-30) REVERT: L 23 GLU cc_start: 0.7827 (tp30) cc_final: 0.7557 (tp30) REVERT: L 72 MET cc_start: 0.6923 (mmm) cc_final: 0.6616 (mmp) REVERT: M 93 GLN cc_start: 0.8242 (tp40) cc_final: 0.8007 (tp40) REVERT: M 241 MET cc_start: 0.7992 (mmt) cc_final: 0.7724 (mmt) REVERT: M 292 ASN cc_start: 0.6988 (p0) cc_final: 0.6631 (p0) REVERT: M 376 MET cc_start: 0.7500 (mtm) cc_final: 0.7297 (mtm) REVERT: M 410 GLU cc_start: 0.7229 (pp20) cc_final: 0.6715 (pt0) REVERT: M 423 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7118 (mtm) REVERT: C 241 MET cc_start: 0.8028 (mmt) cc_final: 0.7761 (mmt) REVERT: C 389 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7506 (ttmt) REVERT: C 420 ILE cc_start: 0.8519 (mt) cc_final: 0.8197 (mt) REVERT: G 241 MET cc_start: 0.8007 (mmt) cc_final: 0.7693 (mmt) REVERT: G 292 ASN cc_start: 0.6773 (p0) cc_final: 0.6549 (p0) REVERT: G 410 GLU cc_start: 0.6980 (pp20) cc_final: 0.6691 (pt0) REVERT: G 423 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7139 (mtm) REVERT: G 427 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.7577 (tpt170) outliers start: 78 outliers final: 52 residues processed: 563 average time/residue: 0.3065 time to fit residues: 271.6801 Evaluate side-chains 534 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 479 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 396 SER Chi-restraints excluded: chain G residue 423 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 128 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21728 Z= 0.170 Angle : 0.570 8.208 29458 Z= 0.272 Chirality : 0.041 0.151 3548 Planarity : 0.003 0.047 3608 Dihedral : 7.955 177.319 2998 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.40 % Allowed : 16.38 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.16), residues: 2736 helix: 2.48 (0.12), residues: 1738 sheet: 2.14 (0.29), residues: 282 loop : -0.47 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 166 HIS 0.004 0.001 HIS G 79 PHE 0.034 0.002 PHE C 210 TYR 0.011 0.001 TYR C 158 ARG 0.006 0.000 ARG M 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 507 time to evaluate : 2.240 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7860 (tp30) cc_final: 0.7263 (tp30) REVERT: H 134 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8280 (mtpt) REVERT: D 23 GLU cc_start: 0.7918 (tp30) cc_final: 0.7313 (tp30) REVERT: D 127 MET cc_start: 0.8754 (mmm) cc_final: 0.8524 (tpp) REVERT: D 133 ARG cc_start: 0.7286 (mtt90) cc_final: 0.6954 (mtm-85) REVERT: E 59 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7329 (mt-10) REVERT: E 126 ASP cc_start: 0.7958 (m-30) cc_final: 0.7635 (m-30) REVERT: F 59 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7257 (mt-10) REVERT: F 113 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7294 (tm-30) REVERT: F 114 LYS cc_start: 0.8527 (mttm) cc_final: 0.8180 (mttm) REVERT: F 126 ASP cc_start: 0.7761 (m-30) cc_final: 0.7477 (m-30) REVERT: I 241 MET cc_start: 0.8181 (mmt) cc_final: 0.7876 (mmt) REVERT: I 292 ASN cc_start: 0.6927 (p0) cc_final: 0.6527 (p0) REVERT: I 389 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7232 (mtmt) REVERT: I 420 ILE cc_start: 0.8403 (mt) cc_final: 0.8070 (mt) REVERT: A 23 GLU cc_start: 0.7816 (tp30) cc_final: 0.7185 (tp30) REVERT: A 42 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7937 (mtpt) REVERT: A 133 ARG cc_start: 0.7334 (mtt90) cc_final: 0.6935 (mmm-85) REVERT: B 23 GLU cc_start: 0.7838 (tp30) cc_final: 0.7242 (tp30) REVERT: B 127 MET cc_start: 0.8926 (tpt) cc_final: 0.8685 (tpp) REVERT: J 126 ASP cc_start: 0.7948 (m-30) cc_final: 0.7659 (m-30) REVERT: L 23 GLU cc_start: 0.7801 (tp30) cc_final: 0.7511 (tp30) REVERT: L 72 MET cc_start: 0.6827 (mmm) cc_final: 0.6540 (mmp) REVERT: M 241 MET cc_start: 0.7892 (mmt) cc_final: 0.7647 (mmt) REVERT: M 292 ASN cc_start: 0.6921 (p0) cc_final: 0.6334 (p0) REVERT: M 376 MET cc_start: 0.7685 (mtm) cc_final: 0.7476 (mtm) REVERT: M 410 GLU cc_start: 0.7019 (pp20) cc_final: 0.6771 (pt0) REVERT: M 423 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7145 (mtm) REVERT: C 241 MET cc_start: 0.8173 (mmt) cc_final: 0.7900 (mmt) REVERT: C 292 ASN cc_start: 0.7065 (p0) cc_final: 0.6727 (p0) REVERT: C 388 ASP cc_start: 0.7190 (p0) cc_final: 0.6923 (p0) REVERT: C 389 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7207 (mtmt) REVERT: C 420 ILE cc_start: 0.8448 (mt) cc_final: 0.8111 (mt) REVERT: G 241 MET cc_start: 0.7901 (mmt) cc_final: 0.7677 (mmt) REVERT: G 292 ASN cc_start: 0.6905 (p0) cc_final: 0.6432 (p0) REVERT: G 423 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7084 (mtm) outliers start: 54 outliers final: 38 residues processed: 540 average time/residue: 0.2957 time to fit residues: 254.0630 Evaluate side-chains 512 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 472 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 HIS ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 345 HIS ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN C 345 HIS ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 21728 Z= 0.379 Angle : 0.695 8.015 29458 Z= 0.341 Chirality : 0.046 0.159 3548 Planarity : 0.004 0.051 3608 Dihedral : 7.980 167.933 2998 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.10 % Allowed : 16.38 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.16), residues: 2736 helix: 2.07 (0.12), residues: 1736 sheet: 1.51 (0.29), residues: 286 loop : -0.52 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 276 HIS 0.006 0.002 HIS C 79 PHE 0.036 0.002 PHE C 210 TYR 0.025 0.002 TYR C 158 ARG 0.011 0.001 ARG M 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 489 time to evaluate : 2.612 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7971 (tp30) cc_final: 0.7352 (tp30) REVERT: H 74 MET cc_start: 0.7946 (tpp) cc_final: 0.7733 (tpp) REVERT: H 134 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8323 (mtpt) REVERT: D 23 GLU cc_start: 0.7977 (tp30) cc_final: 0.7421 (tp30) REVERT: D 127 MET cc_start: 0.8879 (mmm) cc_final: 0.8559 (tpp) REVERT: D 133 ARG cc_start: 0.7379 (mtt90) cc_final: 0.7031 (mtm-85) REVERT: E 126 ASP cc_start: 0.8108 (m-30) cc_final: 0.7686 (m-30) REVERT: F 58 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.7245 (t70) REVERT: F 59 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7228 (mt-10) REVERT: F 126 ASP cc_start: 0.8155 (m-30) cc_final: 0.7886 (m-30) REVERT: I 121 LEU cc_start: 0.7022 (mt) cc_final: 0.6795 (mp) REVERT: I 241 MET cc_start: 0.8260 (mmt) cc_final: 0.7897 (mmt) REVERT: I 292 ASN cc_start: 0.7412 (p0) cc_final: 0.7080 (p0) REVERT: I 299 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: I 304 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8626 (mp) REVERT: I 389 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7455 (ptpt) REVERT: A 23 GLU cc_start: 0.7939 (tp30) cc_final: 0.7243 (tp30) REVERT: A 133 ARG cc_start: 0.7386 (mtt90) cc_final: 0.6964 (mmm-85) REVERT: B 23 GLU cc_start: 0.7925 (tp30) cc_final: 0.7251 (tp30) REVERT: L 23 GLU cc_start: 0.7794 (tp30) cc_final: 0.7554 (tp30) REVERT: L 126 ASP cc_start: 0.7893 (m-30) cc_final: 0.7535 (m-30) REVERT: L 127 MET cc_start: 0.8673 (tpp) cc_final: 0.7918 (tpt) REVERT: M 194 MET cc_start: 0.7426 (mmm) cc_final: 0.7148 (mmm) REVERT: M 241 MET cc_start: 0.8111 (mmt) cc_final: 0.7823 (mmt) REVERT: M 292 ASN cc_start: 0.7047 (p0) cc_final: 0.6652 (p0) REVERT: M 343 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8479 (mtpt) REVERT: M 401 VAL cc_start: 0.9040 (t) cc_final: 0.8702 (t) REVERT: C 121 LEU cc_start: 0.7033 (mt) cc_final: 0.6803 (mp) REVERT: C 241 MET cc_start: 0.8258 (mmt) cc_final: 0.7913 (mmt) REVERT: C 292 ASN cc_start: 0.7319 (p0) cc_final: 0.6984 (p0) REVERT: C 389 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7366 (ptpt) REVERT: G 241 MET cc_start: 0.8133 (mmt) cc_final: 0.7818 (mmt) REVERT: G 292 ASN cc_start: 0.7062 (p0) cc_final: 0.6697 (p0) REVERT: G 343 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8490 (mtpt) outliers start: 92 outliers final: 76 residues processed: 556 average time/residue: 0.3182 time to fit residues: 277.2479 Evaluate side-chains 535 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 456 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 344 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 ASN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21728 Z= 0.171 Angle : 0.581 7.865 29458 Z= 0.278 Chirality : 0.042 0.148 3548 Planarity : 0.003 0.039 3608 Dihedral : 7.404 165.086 2998 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.27 % Allowed : 19.72 % Favored : 78.01 % 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: 2.38 (0.16), residues: 2736 helix: 2.36 (0.12), residues: 1734 sheet: 2.02 (0.30), residues: 274 loop : -0.60 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 276 HIS 0.004 0.001 HIS G 79 PHE 0.033 0.001 PHE C 210 TYR 0.009 0.001 TYR C 447 ARG 0.007 0.000 ARG J 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 519 time to evaluate : 2.489 Fit side-chains REVERT: H 23 GLU cc_start: 0.7913 (tp30) cc_final: 0.7532 (tp30) REVERT: H 74 MET cc_start: 0.7825 (tpp) cc_final: 0.7545 (tpp) REVERT: H 134 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8366 (mtpt) REVERT: D 23 GLU cc_start: 0.7863 (tp30) cc_final: 0.7423 (tp30) REVERT: D 133 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7043 (mtm-85) REVERT: E 50 GLN cc_start: 0.8027 (tt0) cc_final: 0.7770 (tt0) REVERT: E 126 ASP cc_start: 0.8004 (m-30) cc_final: 0.7662 (m-30) REVERT: F 59 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7232 (mt-10) REVERT: F 113 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7334 (tm-30) REVERT: F 126 ASP cc_start: 0.8053 (m-30) cc_final: 0.7583 (m-30) REVERT: I 241 MET cc_start: 0.8190 (mmt) cc_final: 0.7854 (mmt) REVERT: I 265 ASN cc_start: 0.8113 (t0) cc_final: 0.7823 (t0) REVERT: I 292 ASN cc_start: 0.7306 (p0) cc_final: 0.7074 (p0) REVERT: I 304 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8520 (mp) REVERT: I 389 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7373 (ptpt) REVERT: I 404 THR cc_start: 0.7915 (m) cc_final: 0.7711 (m) REVERT: A 23 GLU cc_start: 0.7848 (tp30) cc_final: 0.7325 (tp30) REVERT: A 133 ARG cc_start: 0.7225 (mtt90) cc_final: 0.6830 (mmm-85) REVERT: B 23 GLU cc_start: 0.7881 (tp30) cc_final: 0.7445 (tp30) REVERT: J 113 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7292 (tm-30) REVERT: J 126 ASP cc_start: 0.8013 (m-30) cc_final: 0.7581 (m-30) REVERT: L 23 GLU cc_start: 0.7757 (tp30) cc_final: 0.7492 (tp30) REVERT: L 50 GLN cc_start: 0.7895 (tt0) cc_final: 0.7685 (tt0) REVERT: L 126 ASP cc_start: 0.7694 (m-30) cc_final: 0.7329 (m-30) REVERT: L 127 MET cc_start: 0.8443 (tpp) cc_final: 0.7895 (tpt) REVERT: M 35 VAL cc_start: 0.7765 (m) cc_final: 0.7526 (p) REVERT: M 194 MET cc_start: 0.7259 (mmm) cc_final: 0.6987 (mmt) REVERT: M 241 MET cc_start: 0.7981 (mmt) cc_final: 0.7657 (mmt) REVERT: M 292 ASN cc_start: 0.6743 (p0) cc_final: 0.6446 (p0) REVERT: M 311 MET cc_start: 0.8530 (ttm) cc_final: 0.8289 (ttm) REVERT: C 241 MET cc_start: 0.8133 (mmt) cc_final: 0.7830 (mmt) REVERT: C 292 ASN cc_start: 0.7179 (p0) cc_final: 0.6881 (p0) REVERT: C 388 ASP cc_start: 0.7171 (p0) cc_final: 0.6889 (p0) REVERT: C 389 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7553 (ptpt) REVERT: C 392 PHE cc_start: 0.7920 (t80) cc_final: 0.7658 (t80) REVERT: G 35 VAL cc_start: 0.7785 (m) cc_final: 0.7554 (p) REVERT: G 241 MET cc_start: 0.8068 (mmt) cc_final: 0.7762 (mmt) REVERT: G 292 ASN cc_start: 0.6710 (p0) cc_final: 0.6407 (p0) outliers start: 51 outliers final: 39 residues processed: 556 average time/residue: 0.3190 time to fit residues: 283.7661 Evaluate side-chains 511 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 471 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 159 optimal weight: 0.4980 chunk 121 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21728 Z= 0.174 Angle : 0.576 8.132 29458 Z= 0.276 Chirality : 0.042 0.146 3548 Planarity : 0.003 0.037 3608 Dihedral : 7.033 167.675 2998 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.45 % Allowed : 21.15 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.16), residues: 2736 helix: 2.42 (0.12), residues: 1734 sheet: 2.15 (0.30), residues: 274 loop : -0.68 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 227 HIS 0.004 0.001 HIS M 176 PHE 0.032 0.001 PHE C 210 TYR 0.012 0.001 TYR G 447 ARG 0.007 0.000 ARG J 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 486 time to evaluate : 2.422 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7929 (tp30) cc_final: 0.7551 (tp30) REVERT: H 74 MET cc_start: 0.7844 (tpp) cc_final: 0.7506 (tpp) REVERT: H 134 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8371 (mtpt) REVERT: D 23 GLU cc_start: 0.7851 (tp30) cc_final: 0.7419 (tp30) REVERT: D 133 ARG cc_start: 0.7329 (mtt90) cc_final: 0.6982 (mtm-85) REVERT: E 126 ASP cc_start: 0.8095 (m-30) cc_final: 0.7407 (m-30) REVERT: E 127 MET cc_start: 0.8431 (mmm) cc_final: 0.7911 (tpt) REVERT: F 59 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7266 (mt-10) REVERT: F 82 ASN cc_start: 0.8504 (t0) cc_final: 0.7609 (m-40) REVERT: F 113 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7314 (tm-30) REVERT: F 126 ASP cc_start: 0.8024 (m-30) cc_final: 0.7537 (m-30) REVERT: I 241 MET cc_start: 0.8098 (mmt) cc_final: 0.7800 (mmt) REVERT: I 292 ASN cc_start: 0.7304 (p0) cc_final: 0.7088 (p0) REVERT: I 389 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7556 (ptpt) REVERT: A 23 GLU cc_start: 0.7899 (tp30) cc_final: 0.7339 (tp30) REVERT: A 133 ARG cc_start: 0.7235 (mtt90) cc_final: 0.6786 (mmm-85) REVERT: B 23 GLU cc_start: 0.7896 (tp30) cc_final: 0.7450 (tp30) REVERT: J 113 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7257 (tm-30) REVERT: J 126 ASP cc_start: 0.7999 (m-30) cc_final: 0.7575 (m-30) REVERT: L 23 GLU cc_start: 0.7729 (tp30) cc_final: 0.7478 (tp30) REVERT: L 126 ASP cc_start: 0.7781 (m-30) cc_final: 0.7359 (m-30) REVERT: M 241 MET cc_start: 0.7902 (mmt) cc_final: 0.7587 (mmt) REVERT: M 292 ASN cc_start: 0.6690 (p0) cc_final: 0.6426 (p0) REVERT: M 311 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8253 (ttm) REVERT: C 241 MET cc_start: 0.8100 (mmt) cc_final: 0.7815 (mmt) REVERT: C 292 ASN cc_start: 0.7076 (p0) cc_final: 0.6727 (p0) REVERT: C 389 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7539 (ptpt) REVERT: G 117 ARG cc_start: 0.7513 (tpp80) cc_final: 0.6943 (mtp85) REVERT: G 241 MET cc_start: 0.8125 (mmt) cc_final: 0.7791 (mmt) REVERT: G 292 ASN cc_start: 0.6663 (p0) cc_final: 0.6398 (p0) REVERT: G 387 PHE cc_start: 0.7451 (t80) cc_final: 0.7238 (t80) outliers start: 55 outliers final: 45 residues processed: 526 average time/residue: 0.2856 time to fit residues: 241.6023 Evaluate side-chains 511 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 465 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 311 MET Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 381 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.2980 chunk 104 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN L 50 GLN ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21728 Z= 0.159 Angle : 0.576 7.848 29458 Z= 0.273 Chirality : 0.042 0.222 3548 Planarity : 0.003 0.036 3608 Dihedral : 6.790 167.722 2998 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.36 % Allowed : 21.06 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.16), residues: 2736 helix: 2.47 (0.12), residues: 1734 sheet: 2.17 (0.30), residues: 286 loop : -0.67 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 227 HIS 0.003 0.001 HIS G 79 PHE 0.032 0.001 PHE C 210 TYR 0.025 0.001 TYR C 158 ARG 0.008 0.000 ARG G 427 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 488 time to evaluate : 2.380 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7910 (tp30) cc_final: 0.7543 (tp30) REVERT: H 74 MET cc_start: 0.7877 (tpp) cc_final: 0.7546 (tpp) REVERT: H 110 ARG cc_start: 0.8738 (mtm110) cc_final: 0.8148 (mtm110) REVERT: H 134 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8368 (mtpt) REVERT: D 23 GLU cc_start: 0.7815 (tp30) cc_final: 0.7428 (tp30) REVERT: D 127 MET cc_start: 0.8836 (tpt) cc_final: 0.8604 (tpp) REVERT: D 133 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6940 (mtm-85) REVERT: E 50 GLN cc_start: 0.8144 (tt0) cc_final: 0.7755 (tt0) REVERT: E 126 ASP cc_start: 0.8039 (m-30) cc_final: 0.7531 (m-30) REVERT: F 50 GLN cc_start: 0.8079 (tt0) cc_final: 0.7641 (tt0) REVERT: F 82 ASN cc_start: 0.8498 (t0) cc_final: 0.7626 (m-40) REVERT: F 126 ASP cc_start: 0.7818 (m-30) cc_final: 0.7349 (m-30) REVERT: I 241 MET cc_start: 0.8049 (mmt) cc_final: 0.7772 (mmt) REVERT: I 389 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7583 (ptpt) REVERT: A 23 GLU cc_start: 0.7875 (tp30) cc_final: 0.7392 (tp30) REVERT: B 23 GLU cc_start: 0.7868 (tp30) cc_final: 0.7398 (tp30) REVERT: B 93 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7938 (mt-10) REVERT: J 113 GLN cc_start: 0.7513 (tm-30) cc_final: 0.7274 (tm-30) REVERT: J 126 ASP cc_start: 0.7886 (m-30) cc_final: 0.7484 (m-30) REVERT: L 23 GLU cc_start: 0.7798 (tp30) cc_final: 0.7541 (tp30) REVERT: L 50 GLN cc_start: 0.8022 (tt0) cc_final: 0.7699 (tt0) REVERT: L 126 ASP cc_start: 0.7723 (m-30) cc_final: 0.7344 (m-30) REVERT: M 241 MET cc_start: 0.7830 (mmt) cc_final: 0.7568 (mmt) REVERT: M 311 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8216 (ttm) REVERT: C 241 MET cc_start: 0.8003 (mmt) cc_final: 0.7692 (mmt) REVERT: C 292 ASN cc_start: 0.7004 (p0) cc_final: 0.6681 (p0) REVERT: C 389 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7466 (ptpt) REVERT: G 117 ARG cc_start: 0.7352 (tpp80) cc_final: 0.6787 (mtp85) REVERT: G 241 MET cc_start: 0.8080 (mmt) cc_final: 0.7728 (mmt) REVERT: G 292 ASN cc_start: 0.6858 (p0) cc_final: 0.6606 (p0) REVERT: G 410 GLU cc_start: 0.6496 (pt0) cc_final: 0.6248 (pt0) outliers start: 53 outliers final: 43 residues processed: 524 average time/residue: 0.2971 time to fit residues: 248.1687 Evaluate side-chains 520 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 476 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 311 MET Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 381 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 231 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 ASN ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 ASN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21728 Z= 0.195 Angle : 0.594 7.374 29458 Z= 0.284 Chirality : 0.042 0.175 3548 Planarity : 0.003 0.035 3608 Dihedral : 6.679 163.605 2998 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.45 % Allowed : 21.24 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.16), residues: 2736 helix: 2.50 (0.12), residues: 1730 sheet: 2.12 (0.31), residues: 286 loop : -0.71 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 227 HIS 0.003 0.001 HIS M 176 PHE 0.032 0.001 PHE C 210 TYR 0.009 0.001 TYR C 447 ARG 0.008 0.000 ARG G 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 458 time to evaluate : 2.630 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7937 (tp30) cc_final: 0.7579 (tp30) REVERT: H 110 ARG cc_start: 0.8735 (mtm110) cc_final: 0.8072 (mtm110) REVERT: H 134 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8270 (mtpt) REVERT: D 23 GLU cc_start: 0.7825 (tp30) cc_final: 0.7420 (tp30) REVERT: D 127 MET cc_start: 0.8905 (tpt) cc_final: 0.8704 (tpp) REVERT: D 133 ARG cc_start: 0.7316 (mtt90) cc_final: 0.6868 (mtm-85) REVERT: E 50 GLN cc_start: 0.8157 (tt0) cc_final: 0.7749 (tt0) REVERT: F 50 GLN cc_start: 0.8070 (tt0) cc_final: 0.7628 (tt0) REVERT: F 126 ASP cc_start: 0.7985 (m-30) cc_final: 0.7516 (m-30) REVERT: I 24 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: I 241 MET cc_start: 0.8068 (mmt) cc_final: 0.7768 (mmt) REVERT: I 304 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8508 (mp) REVERT: I 389 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7557 (ptpt) REVERT: A 23 GLU cc_start: 0.7898 (tp30) cc_final: 0.7418 (tp30) REVERT: B 23 GLU cc_start: 0.7897 (tp30) cc_final: 0.7478 (tp30) REVERT: J 126 ASP cc_start: 0.7918 (m-30) cc_final: 0.7613 (m-30) REVERT: L 50 GLN cc_start: 0.7987 (tt0) cc_final: 0.7607 (tt0) REVERT: L 126 ASP cc_start: 0.7748 (m-30) cc_final: 0.7282 (m-30) REVERT: M 241 MET cc_start: 0.7950 (mmt) cc_final: 0.7636 (mmt) REVERT: C 24 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: C 30 LEU cc_start: 0.8194 (mm) cc_final: 0.7936 (pp) REVERT: C 241 MET cc_start: 0.8017 (mmt) cc_final: 0.7721 (mmt) REVERT: C 292 ASN cc_start: 0.7063 (p0) cc_final: 0.6812 (p0) REVERT: C 389 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7518 (ptpt) REVERT: C 420 ILE cc_start: 0.8997 (mt) cc_final: 0.8762 (mt) REVERT: G 48 PHE cc_start: 0.6737 (m-80) cc_final: 0.6531 (m-80) REVERT: G 117 ARG cc_start: 0.7372 (tpp80) cc_final: 0.6813 (mtp85) REVERT: G 241 MET cc_start: 0.8107 (mmt) cc_final: 0.7761 (mmt) REVERT: G 292 ASN cc_start: 0.7065 (p0) cc_final: 0.6756 (p0) REVERT: G 410 GLU cc_start: 0.6538 (pt0) cc_final: 0.6279 (pt0) outliers start: 55 outliers final: 46 residues processed: 502 average time/residue: 0.3243 time to fit residues: 258.3636 Evaluate side-chains 497 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 448 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 292 ASN Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 348 MET Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 381 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 8.9990 chunk 258 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 270 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 ASN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21728 Z= 0.191 Angle : 0.593 9.778 29458 Z= 0.283 Chirality : 0.042 0.161 3548 Planarity : 0.003 0.036 3608 Dihedral : 6.658 159.976 2998 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.27 % Allowed : 21.64 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.16), residues: 2736 helix: 2.50 (0.12), residues: 1728 sheet: 2.09 (0.31), residues: 286 loop : -0.72 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 227 HIS 0.003 0.001 HIS G 79 PHE 0.032 0.001 PHE C 210 TYR 0.024 0.001 TYR G 158 ARG 0.007 0.000 ARG G 427 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 455 time to evaluate : 2.310 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7930 (tp30) cc_final: 0.7579 (tp30) REVERT: H 110 ARG cc_start: 0.8744 (mtm110) cc_final: 0.8072 (mtm110) REVERT: H 127 MET cc_start: 0.8685 (tpp) cc_final: 0.8483 (tpp) REVERT: H 134 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8267 (mtpt) REVERT: D 23 GLU cc_start: 0.7827 (tp30) cc_final: 0.7560 (tp30) REVERT: D 127 MET cc_start: 0.8928 (tpt) cc_final: 0.8715 (tpp) REVERT: D 133 ARG cc_start: 0.7326 (mtt90) cc_final: 0.6847 (mtm-85) REVERT: E 50 GLN cc_start: 0.8161 (tt0) cc_final: 0.7758 (tt0) REVERT: E 126 ASP cc_start: 0.8054 (m-30) cc_final: 0.7587 (m-30) REVERT: F 50 GLN cc_start: 0.8075 (tt0) cc_final: 0.7625 (tt0) REVERT: F 126 ASP cc_start: 0.7969 (m-30) cc_final: 0.7387 (m-30) REVERT: I 24 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: I 30 LEU cc_start: 0.8178 (mm) cc_final: 0.7955 (pp) REVERT: I 241 MET cc_start: 0.8012 (mmt) cc_final: 0.7697 (mmt) REVERT: I 304 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8514 (mp) REVERT: I 389 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7543 (ptpt) REVERT: A 23 GLU cc_start: 0.7904 (tp30) cc_final: 0.7437 (tp30) REVERT: A 133 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6826 (mmm-85) REVERT: B 23 GLU cc_start: 0.7896 (tp30) cc_final: 0.7434 (tp30) REVERT: B 25 GLN cc_start: 0.8579 (tp40) cc_final: 0.8114 (tp40) REVERT: L 50 GLN cc_start: 0.7943 (tt0) cc_final: 0.7594 (tt0) REVERT: M 139 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7378 (ttmt) REVERT: M 241 MET cc_start: 0.7940 (mmt) cc_final: 0.7619 (mmt) REVERT: C 241 MET cc_start: 0.8044 (mmt) cc_final: 0.7754 (mmt) REVERT: C 292 ASN cc_start: 0.7047 (p0) cc_final: 0.6822 (p0) REVERT: C 389 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7501 (ptpt) REVERT: C 419 MET cc_start: 0.8784 (tpp) cc_final: 0.8555 (tpt) REVERT: G 48 PHE cc_start: 0.6603 (m-80) cc_final: 0.6395 (m-80) REVERT: G 241 MET cc_start: 0.8118 (mmt) cc_final: 0.7771 (mmt) REVERT: G 292 ASN cc_start: 0.7038 (p0) cc_final: 0.6763 (p0) outliers start: 51 outliers final: 47 residues processed: 495 average time/residue: 0.2935 time to fit residues: 231.9453 Evaluate side-chains 493 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 444 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 292 ASN Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 381 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 198 optimal weight: 0.0970 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 216 optimal weight: 0.0020 chunk 90 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 27 optimal weight: 0.0050 chunk 39 optimal weight: 10.0000 overall best weight: 1.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 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 = 0.3663 r_free = 0.3663 target = 0.147294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125344 restraints weight = 35919.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130102 restraints weight = 16507.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133178 restraints weight = 9632.396| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21728 Z= 0.198 Angle : 0.596 9.509 29458 Z= 0.283 Chirality : 0.042 0.164 3548 Planarity : 0.003 0.035 3608 Dihedral : 6.537 155.967 2995 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.18 % Allowed : 21.46 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.16), residues: 2736 helix: 2.51 (0.12), residues: 1728 sheet: 2.14 (0.31), residues: 274 loop : -0.80 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 227 HIS 0.003 0.001 HIS I 176 PHE 0.032 0.001 PHE C 210 TYR 0.010 0.001 TYR G 447 ARG 0.007 0.000 ARG G 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5125.78 seconds wall clock time: 93 minutes 19.05 seconds (5599.05 seconds total)