Starting phenix.real_space_refine on Sun Feb 18 22:35:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/02_2024/7zp9_14851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/02_2024/7zp9_14851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/02_2024/7zp9_14851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/02_2024/7zp9_14851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/02_2024/7zp9_14851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/02_2024/7zp9_14851_updated.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 14942 2.51 5 N 3628 2.21 5 O 4359 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23097 Number of models: 1 Model: "" Number of chains: 34 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: 3347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 bond proxies already assigned to first conformer: 3407 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: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3344 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 3347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 bond proxies already assigned to first conformer: 3407 Chain: "G" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3344 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 2 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 316 Unusual residues: {' K': 1, 'LMT': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 15.10, per 1000 atoms: 0.65 Number of scatterers: 23097 At special positions: 0 Unit cell: (93.903, 115.509, 172.017, 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 4359 8.00 N 3628 7.00 C 14942 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: 9.22 Conformation dependent library (CDL) restraints added in 5.4 seconds 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 10 sheets defined 59.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 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: 3.550A 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: 3.711A 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: 3.841A 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: 3.619A 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: 3.771A 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: 3.845A 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: 3.593A 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: 3.537A 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: 3.527A 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: 3.771A 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: 3.845A 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: 6.446A pdb=" N GLN H 30 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 7.670A 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: 6.340A pdb=" N GLN D 30 " --> pdb=" O PHE D 8 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL D 10 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 6.180A 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: 8.484A pdb=" N ASP D 35 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.355A 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: 7.198A pdb=" N ILE E 75 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.078A 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: 6.094A 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: 8.246A 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: 6.221A pdb=" N VAL F 73 " --> pdb=" O TRP F 100 " (cutoff:3.500A) removed outlier: 7.791A 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: 6.267A pdb=" N GLN F 30 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL F 10 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 6.156A 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: 6.498A pdb=" N GLN A 30 " --> pdb=" O PHE A 8 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 10 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.132A 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: 6.405A 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: 7.747A 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: 6.361A 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: 6.183A 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: 7.130A pdb=" N ILE J 75 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET J 72 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN J 30 " --> pdb=" O PHE J 8 " (cutoff:3.500A) removed outlier: 7.457A 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: 6.482A 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: 6.471A 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: 7.482A 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: 4.421A 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: 8.05 Time building geometry restraints manager: 9.98 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: 4052 1.33 - 1.45: 5708 1.45 - 1.57: 13429 1.57 - 1.69: 28 1.69 - 1.81: 261 Bond restraints: 23478 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 3.34e+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 3.09e+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 3.00e+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 23473 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.51: 451 105.51 - 113.21: 14187 113.21 - 120.91: 11528 120.91 - 128.61: 5415 128.61 - 136.30: 171 Bond angle restraints: 31752 Sorted by residual: angle pdb=" N GLU F 93 " pdb=" CA GLU F 93 " pdb=" C GLU F 93 " ideal model delta sigma weight residual 111.69 105.83 5.86 1.23e+00 6.61e-01 2.27e+01 angle pdb=" C THR M 288 " pdb=" CA THR M 288 " pdb=" CB THR M 288 " ideal model delta sigma weight residual 110.42 119.37 -8.95 1.99e+00 2.53e-01 2.02e+01 angle pdb=" C THR G 288 " pdb=" CA THR G 288 " pdb=" CB THR G 288 " ideal model delta sigma weight residual 110.42 119.33 -8.91 1.99e+00 2.53e-01 2.01e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" C LEU G 296 " ideal model delta sigma weight residual 112.89 107.54 5.35 1.24e+00 6.50e-01 1.86e+01 angle pdb=" N LEU M 296 " pdb=" CA LEU M 296 " pdb=" C LEU M 296 " ideal model delta sigma weight residual 112.89 107.54 5.35 1.24e+00 6.50e-01 1.86e+01 ... (remaining 31747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 14553 33.64 - 67.27: 580 67.27 - 100.91: 106 100.91 - 134.54: 187 134.54 - 168.18: 6 Dihedral angle restraints: 15432 sinusoidal: 7468 harmonic: 7964 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 300.00 131.82 168.18 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 -60.00 100.86 -160.86 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 -60.00 100.11 -160.11 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 15429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3651 0.107 - 0.213: 285 0.213 - 0.320: 42 0.320 - 0.426: 0 0.426 - 0.533: 8 Chirality restraints: 3986 Sorted by residual: 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 0.53 2.00e-01 2.50e+01 7.10e+00 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 0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA THR I 288 " pdb=" N THR I 288 " pdb=" C THR I 288 " pdb=" CB THR I 288 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 7.00e+00 ... (remaining 3983 not shown) Planarity restraints: 3662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 92 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C MET M 92 " 0.040 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 2.34e-02 5.47e+00 pdb=" C MET G 92 " -0.040 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=" CA LEU F 86 " -0.010 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C LEU F 86 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU F 86 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA F 87 " -0.013 2.00e-02 2.50e+03 ... (remaining 3659 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.04: 20 2.04 - 2.82: 6284 2.82 - 3.59: 38896 3.59 - 4.37: 71510 4.37 - 5.14: 123126 Nonbonded interactions: 239836 Sorted by model distance: nonbonded pdb=" OE1 GLU F 64 " pdb=" CA GLY C 8 " model vdw 1.266 3.440 nonbonded pdb=" OE1 GLU L 64 " pdb=" CA GLY G 8 " model vdw 1.404 3.440 nonbonded pdb=" OE2 GLU L 64 " pdb=" N GLY G 8 " model vdw 1.471 2.520 nonbonded pdb=" OE2 GLU F 64 " pdb=" N GLY C 8 " model vdw 1.577 2.520 nonbonded pdb=" OE1 GLU L 38 " pdb=" OH TYR G 11 " model vdw 1.778 2.440 ... (remaining 239831 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 7 through 15 or resid 21 through 350 or resid 352 through \ 455 or resid 503 through 510)) selection = (chain 'G' and (resid 7 through 15 or resid 21 through 122 or resid 132 through \ 350 or resid 352 through 455 or resid 503 through 510)) selection = (chain 'I' and (resid 7 through 15 or resid 21 through 350 or resid 352 through \ 455 or resid 503 through 510)) selection = (chain 'M' and (resid 7 through 15 or resid 21 through 122 or resid 132 through \ 350 or resid 352 through 455 or resid 503 through 510)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.260 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 67.870 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.170 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.256 23478 Z= 0.515 Angle : 1.130 10.792 31752 Z= 0.557 Chirality : 0.065 0.533 3986 Planarity : 0.004 0.047 3662 Dihedral : 23.096 168.179 10292 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.21 % Favored : 97.58 % Rotamer: Outliers : 0.88 % Allowed : 1.14 % Favored : 97.98 % 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: 2766 helix: 1.44 (0.12), residues: 1760 sheet: 1.61 (0.28), residues: 282 loop : -0.26 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 337 HIS 0.005 0.001 HIS G 345 PHE 0.026 0.001 PHE I 210 TYR 0.014 0.001 TYR F 70 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 516 time to evaluate : 2.456 Fit side-chains revert: symmetry clash REVERT: H 59 GLU cc_start: 0.8137 (pt0) cc_final: 0.7850 (pt0) REVERT: F 130 ARG cc_start: 0.6899 (ttt90) cc_final: 0.6655 (ttt90) REVERT: I 139 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7499 (tptp) REVERT: I 299 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: I 354 ASN cc_start: 0.8260 (p0) cc_final: 0.7879 (p0) REVERT: A 22 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7894 (tptp) REVERT: M 139 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7288 (tptp) REVERT: M 296 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8238 (mt) REVERT: M 299 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: C 139 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7493 (tptp) REVERT: C 299 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: C 354 ASN cc_start: 0.8247 (p0) cc_final: 0.7855 (p0) REVERT: G 139 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7284 (tptp) REVERT: G 296 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (mt) REVERT: G 299 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7995 (m-80) outliers start: 20 outliers final: 4 residues processed: 532 average time/residue: 1.6341 time to fit residues: 970.2303 Evaluate side-chains 434 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 424 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 4.9990 chunk 209 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 250 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN H 50 GLN D 37 ASN D 50 GLN D 113 GLN F 108 GLN I 119 GLN I 263 ASN I 342 GLN A 37 ASN A 113 GLN B 30 GLN B 37 ASN B 50 GLN B 113 GLN J 108 GLN M 93 GLN M 263 ASN M 301 GLN M 342 GLN C 119 GLN C 263 ASN C 342 GLN G 93 GLN G 263 ASN G 301 GLN G 342 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23478 Z= 0.177 Angle : 0.736 10.405 31752 Z= 0.315 Chirality : 0.047 0.377 3986 Planarity : 0.004 0.037 3662 Dihedral : 18.603 179.135 5494 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.02 % Allowed : 8.66 % Favored : 89.32 % 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: 2.39 (0.16), residues: 2766 helix: 2.22 (0.12), residues: 1762 sheet: 2.10 (0.28), residues: 270 loop : -0.20 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 337 HIS 0.004 0.001 HIS I 176 PHE 0.036 0.002 PHE I 210 TYR 0.012 0.001 TYR F 70 ARG 0.005 0.000 ARG C 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 455 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 GLU cc_start: 0.7409 (mp0) cc_final: 0.7179 (mp0) REVERT: H 130 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7309 (mmm160) REVERT: I 26 ARG cc_start: 0.7367 (ttt90) cc_final: 0.6958 (ttt-90) REVERT: I 139 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7495 (tptp) REVERT: I 299 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: I 354 ASN cc_start: 0.8290 (p0) cc_final: 0.7893 (p0) REVERT: B 22 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7849 (tptp) REVERT: B 122 MET cc_start: 0.8589 (mtt) cc_final: 0.8246 (mtt) REVERT: M 100 MET cc_start: 0.8699 (ttp) cc_final: 0.8473 (ttp) REVERT: M 139 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7210 (tptp) REVERT: M 296 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8305 (mm) REVERT: M 299 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: C 26 ARG cc_start: 0.7359 (ttt90) cc_final: 0.6956 (ttt-90) REVERT: C 139 LYS cc_start: 0.8016 (ttpp) cc_final: 0.7487 (tptp) REVERT: C 299 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: C 354 ASN cc_start: 0.8274 (p0) cc_final: 0.7873 (p0) REVERT: G 100 MET cc_start: 0.8710 (ttp) cc_final: 0.8479 (ttp) REVERT: G 139 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7206 (tptp) REVERT: G 296 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8302 (mm) REVERT: G 299 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8049 (m-80) outliers start: 46 outliers final: 16 residues processed: 483 average time/residue: 1.5710 time to fit residues: 851.3119 Evaluate side-chains 445 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 422 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 201 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN D 113 GLN F 108 GLN I 263 ASN A 37 ASN A 113 GLN B 37 ASN B 113 GLN L 82 ASN M 93 GLN M 263 ASN C 263 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23478 Z= 0.277 Angle : 0.710 7.318 31752 Z= 0.318 Chirality : 0.047 0.330 3986 Planarity : 0.004 0.053 3662 Dihedral : 14.214 178.369 5490 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.90 % Allowed : 11.12 % Favored : 85.98 % 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: 2.45 (0.16), residues: 2766 helix: 2.22 (0.12), residues: 1766 sheet: 1.92 (0.29), residues: 282 loop : 0.03 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 227 HIS 0.005 0.001 HIS I 176 PHE 0.033 0.002 PHE C 210 TYR 0.014 0.002 TYR F 70 ARG 0.004 0.000 ARG J 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 447 time to evaluate : 2.868 Fit side-chains revert: symmetry clash REVERT: H 60 GLU cc_start: 0.7457 (mp0) cc_final: 0.7245 (mp0) REVERT: H 69 ASP cc_start: 0.7881 (m-30) cc_final: 0.7647 (m-30) REVERT: E 66 LYS cc_start: 0.7826 (mppt) cc_final: 0.7435 (mmtm) REVERT: F 69 ASP cc_start: 0.7534 (m-30) cc_final: 0.7265 (m-30) REVERT: I 26 ARG cc_start: 0.7374 (ttt90) cc_final: 0.6917 (ttt-90) REVERT: I 139 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7503 (tptp) REVERT: I 299 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: L 104 ASN cc_start: 0.8204 (m-40) cc_final: 0.7991 (m110) REVERT: M 100 MET cc_start: 0.8701 (ttp) cc_final: 0.8479 (ttp) REVERT: M 139 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7254 (tptp) REVERT: M 299 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: C 26 ARG cc_start: 0.7375 (ttt90) cc_final: 0.6920 (ttt-90) REVERT: C 139 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7505 (tptp) REVERT: C 299 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: G 100 MET cc_start: 0.8705 (ttp) cc_final: 0.8503 (ttp) REVERT: G 139 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7249 (tptp) REVERT: G 299 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8085 (m-80) outliers start: 66 outliers final: 36 residues processed: 486 average time/residue: 1.5491 time to fit residues: 846.8420 Evaluate side-chains 466 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 426 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 119 optimal weight: 0.0980 chunk 168 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN D 37 ASN E 82 ASN F 108 GLN I 263 ASN I 342 GLN A 37 ASN B 37 ASN J 108 GLN L 82 ASN M 198 ASN M 263 ASN C 263 ASN C 342 GLN G 198 ASN G 263 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23478 Z= 0.221 Angle : 0.652 7.048 31752 Z= 0.293 Chirality : 0.044 0.293 3986 Planarity : 0.003 0.040 3662 Dihedral : 12.998 178.463 5484 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.59 % Allowed : 12.52 % Favored : 84.89 % 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: 2766 helix: 2.27 (0.12), residues: 1768 sheet: 1.90 (0.29), residues: 282 loop : 0.04 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 337 HIS 0.005 0.001 HIS I 176 PHE 0.032 0.002 PHE I 210 TYR 0.010 0.001 TYR F 70 ARG 0.003 0.000 ARG J 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 434 time to evaluate : 2.661 Fit side-chains revert: symmetry clash REVERT: F 30 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7452 (mm110) REVERT: F 69 ASP cc_start: 0.7522 (m-30) cc_final: 0.7271 (m-30) REVERT: I 26 ARG cc_start: 0.7347 (ttt90) cc_final: 0.6880 (ttt-90) REVERT: I 139 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7497 (tptp) REVERT: I 299 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: B 22 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7909 (tptp) REVERT: J 30 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7300 (mp-120) REVERT: L 30 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7426 (mm110) REVERT: M 139 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7251 (tptp) REVERT: M 299 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: C 26 ARG cc_start: 0.7348 (ttt90) cc_final: 0.6882 (ttt-90) REVERT: C 139 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7491 (tptp) REVERT: C 299 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: G 139 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7247 (tptp) REVERT: G 299 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8062 (m-80) outliers start: 59 outliers final: 33 residues processed: 465 average time/residue: 1.5574 time to fit residues: 814.0325 Evaluate side-chains 468 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 427 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN E 82 ASN I 263 ASN A 37 ASN A 113 GLN B 37 ASN B 113 GLN J 82 ASN J 108 GLN L 82 ASN L 108 GLN M 198 ASN M 263 ASN C 263 ASN G 198 ASN G 263 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23478 Z= 0.371 Angle : 0.724 7.511 31752 Z= 0.333 Chirality : 0.047 0.330 3986 Planarity : 0.004 0.042 3662 Dihedral : 12.592 173.556 5484 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.30 % Allowed : 12.65 % Favored : 84.05 % 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: 2.17 (0.16), residues: 2766 helix: 1.99 (0.12), residues: 1758 sheet: 1.65 (0.29), residues: 286 loop : 0.06 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 337 HIS 0.004 0.001 HIS C 176 PHE 0.033 0.002 PHE C 210 TYR 0.016 0.002 TYR F 70 ARG 0.004 0.001 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 431 time to evaluate : 2.563 Fit side-chains REVERT: E 38 GLU cc_start: 0.7584 (tt0) cc_final: 0.7327 (tt0) REVERT: E 66 LYS cc_start: 0.7893 (mppt) cc_final: 0.7472 (mmtm) REVERT: F 30 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7520 (mm110) REVERT: F 69 ASP cc_start: 0.7617 (m-30) cc_final: 0.7384 (m-30) REVERT: I 26 ARG cc_start: 0.7207 (ttt90) cc_final: 0.6675 (ttt90) REVERT: I 139 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7542 (tptp) REVERT: I 299 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: J 30 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7335 (mp-120) REVERT: M 139 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7270 (tptp) REVERT: M 299 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: C 26 ARG cc_start: 0.7209 (ttt90) cc_final: 0.6676 (ttt90) REVERT: C 139 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7523 (tptp) REVERT: C 299 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: G 139 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7267 (tptp) REVERT: G 299 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8045 (m-80) outliers start: 75 outliers final: 34 residues processed: 475 average time/residue: 1.4970 time to fit residues: 799.7271 Evaluate side-chains 459 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 419 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN D 37 ASN E 82 ASN I 263 ASN A 37 ASN A 113 GLN B 37 ASN B 113 GLN J 82 ASN J 108 GLN L 82 ASN M 263 ASN C 263 ASN G 263 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23478 Z= 0.159 Angle : 0.598 6.617 31752 Z= 0.272 Chirality : 0.042 0.311 3986 Planarity : 0.003 0.040 3662 Dihedral : 11.383 172.570 5484 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.42 % Allowed : 13.80 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.16), residues: 2766 helix: 2.37 (0.12), residues: 1756 sheet: 1.82 (0.28), residues: 282 loop : -0.08 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 337 HIS 0.004 0.001 HIS I 176 PHE 0.031 0.001 PHE I 210 TYR 0.011 0.001 TYR M 435 ARG 0.004 0.000 ARG F 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 441 time to evaluate : 2.609 Fit side-chains REVERT: E 38 GLU cc_start: 0.7476 (tt0) cc_final: 0.7224 (tt0) REVERT: F 66 LYS cc_start: 0.8609 (tppt) cc_final: 0.8359 (mtpt) REVERT: I 26 ARG cc_start: 0.7140 (ttt90) cc_final: 0.6681 (ttt90) REVERT: I 139 LYS cc_start: 0.8049 (ttpp) cc_final: 0.7508 (tptp) REVERT: I 299 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: I 354 ASN cc_start: 0.8321 (p0) cc_final: 0.7905 (p0) REVERT: A 22 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7838 (tptp) REVERT: B 22 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7881 (tptp) REVERT: J 30 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7417 (mp-120) REVERT: M 139 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7251 (tptp) REVERT: M 199 ASP cc_start: 0.7775 (m-30) cc_final: 0.7564 (m-30) REVERT: M 299 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: C 26 ARG cc_start: 0.7135 (ttt90) cc_final: 0.6674 (ttt90) REVERT: C 139 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7506 (tptp) REVERT: C 299 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: C 354 ASN cc_start: 0.8294 (p0) cc_final: 0.7870 (p0) REVERT: G 139 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7247 (tptp) REVERT: G 199 ASP cc_start: 0.7783 (m-30) cc_final: 0.7568 (m-30) REVERT: G 299 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7950 (m-80) outliers start: 55 outliers final: 31 residues processed: 469 average time/residue: 1.5806 time to fit residues: 832.8114 Evaluate side-chains 465 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 427 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN D 37 ASN E 82 ASN F 108 GLN I 263 ASN A 37 ASN A 113 GLN B 37 ASN B 113 GLN J 82 ASN J 108 GLN L 82 ASN C 263 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23478 Z= 0.248 Angle : 0.630 6.922 31752 Z= 0.290 Chirality : 0.043 0.304 3986 Planarity : 0.003 0.042 3662 Dihedral : 11.260 172.996 5482 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.86 % Allowed : 14.19 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.16), residues: 2766 helix: 2.29 (0.12), residues: 1760 sheet: 1.80 (0.29), residues: 282 loop : -0.01 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 337 HIS 0.005 0.001 HIS I 176 PHE 0.031 0.002 PHE I 210 TYR 0.012 0.002 TYR F 70 ARG 0.004 0.000 ARG F 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 426 time to evaluate : 2.421 Fit side-chains REVERT: H 135 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7904 (ptm) REVERT: E 38 GLU cc_start: 0.7503 (tt0) cc_final: 0.7255 (tt0) REVERT: F 30 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7411 (mm110) REVERT: F 66 LYS cc_start: 0.8633 (tppt) cc_final: 0.8342 (mtpt) REVERT: I 26 ARG cc_start: 0.7162 (ttt90) cc_final: 0.6694 (ttt90) REVERT: I 139 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7532 (tptp) REVERT: I 299 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: I 354 ASN cc_start: 0.8411 (p0) cc_final: 0.7999 (p0) REVERT: J 30 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7397 (mp-120) REVERT: L 38 GLU cc_start: 0.7614 (tt0) cc_final: 0.7396 (tt0) REVERT: M 139 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7261 (tptp) REVERT: M 199 ASP cc_start: 0.7715 (m-30) cc_final: 0.7513 (m-30) REVERT: M 299 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: C 26 ARG cc_start: 0.7159 (ttt90) cc_final: 0.6674 (ttt90) REVERT: C 139 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7495 (tptp) REVERT: C 299 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: G 139 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7258 (tptp) REVERT: G 199 ASP cc_start: 0.7728 (m-30) cc_final: 0.7524 (m-30) REVERT: G 299 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8004 (m-80) outliers start: 65 outliers final: 38 residues processed: 464 average time/residue: 1.5223 time to fit residues: 794.6905 Evaluate side-chains 468 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 423 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 194 MET Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 194 MET Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 0.0050 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 209 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN D 37 ASN F 108 GLN I 263 ASN A 37 ASN A 113 GLN B 37 ASN B 113 GLN J 82 ASN L 82 ASN C 263 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23478 Z= 0.139 Angle : 0.569 6.492 31752 Z= 0.259 Chirality : 0.040 0.264 3986 Planarity : 0.003 0.040 3662 Dihedral : 10.366 174.615 5482 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.42 % Allowed : 14.63 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.16), residues: 2766 helix: 2.57 (0.12), residues: 1748 sheet: 1.97 (0.29), residues: 282 loop : -0.16 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 337 HIS 0.004 0.001 HIS I 176 PHE 0.030 0.001 PHE I 210 TYR 0.016 0.001 TYR M 435 ARG 0.006 0.000 ARG F 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 442 time to evaluate : 2.327 Fit side-chains REVERT: H 69 ASP cc_start: 0.7892 (m-30) cc_final: 0.7691 (m-30) REVERT: E 68 ASP cc_start: 0.7811 (p0) cc_final: 0.7398 (p0) REVERT: F 66 LYS cc_start: 0.8615 (tppt) cc_final: 0.8365 (mtpt) REVERT: I 26 ARG cc_start: 0.7106 (ttt90) cc_final: 0.6658 (ttt90) REVERT: I 139 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7499 (tptp) REVERT: I 299 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: I 354 ASN cc_start: 0.8177 (p0) cc_final: 0.7790 (p0) REVERT: B 22 LYS cc_start: 0.8417 (ttpt) cc_final: 0.7893 (tptp) REVERT: J 30 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7434 (mp-120) REVERT: J 93 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.5834 (mp0) REVERT: L 30 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7186 (mp-120) REVERT: L 38 GLU cc_start: 0.7495 (tt0) cc_final: 0.7283 (tt0) REVERT: M 139 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7224 (tptp) REVERT: M 199 ASP cc_start: 0.7693 (m-30) cc_final: 0.7486 (m-30) REVERT: M 299 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: C 26 ARG cc_start: 0.7099 (ttt90) cc_final: 0.6642 (ttt90) REVERT: C 139 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7454 (tptp) REVERT: C 299 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: C 354 ASN cc_start: 0.8168 (p0) cc_final: 0.7777 (p0) REVERT: G 139 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7217 (tptp) REVERT: G 199 ASP cc_start: 0.7706 (m-30) cc_final: 0.7496 (m-30) REVERT: G 299 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7920 (m-80) outliers start: 55 outliers final: 29 residues processed: 471 average time/residue: 1.4961 time to fit residues: 795.4403 Evaluate side-chains 465 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 429 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 232 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN D 37 ASN F 108 GLN I 263 ASN A 37 ASN B 37 ASN B 113 GLN J 82 ASN C 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23478 Z= 0.200 Angle : 0.599 6.710 31752 Z= 0.277 Chirality : 0.041 0.234 3986 Planarity : 0.003 0.041 3662 Dihedral : 10.294 176.097 5482 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.89 % Allowed : 15.51 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.16), residues: 2766 helix: 2.50 (0.12), residues: 1750 sheet: 1.91 (0.29), residues: 282 loop : -0.08 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 337 HIS 0.005 0.001 HIS C 176 PHE 0.030 0.001 PHE I 210 TYR 0.012 0.001 TYR I 435 ARG 0.008 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 433 time to evaluate : 2.423 Fit side-chains REVERT: E 38 GLU cc_start: 0.7456 (tt0) cc_final: 0.7217 (tt0) REVERT: F 38 GLU cc_start: 0.7555 (tt0) cc_final: 0.7298 (tt0) REVERT: F 66 LYS cc_start: 0.8640 (tppt) cc_final: 0.8359 (mtpt) REVERT: I 26 ARG cc_start: 0.7132 (ttt90) cc_final: 0.6645 (ttt90) REVERT: I 139 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7523 (tptp) REVERT: I 299 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: I 354 ASN cc_start: 0.8282 (p0) cc_final: 0.7882 (p0) REVERT: B 130 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7169 (mmm160) REVERT: J 30 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7435 (mp-120) REVERT: L 38 GLU cc_start: 0.7609 (tt0) cc_final: 0.7386 (tt0) REVERT: M 139 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7228 (tptp) REVERT: M 299 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: C 26 ARG cc_start: 0.7122 (ttt90) cc_final: 0.6661 (ttt90) REVERT: C 139 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7514 (tptp) REVERT: C 299 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: C 354 ASN cc_start: 0.8283 (p0) cc_final: 0.7886 (p0) REVERT: G 139 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7245 (tptp) REVERT: G 299 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8041 (m-80) outliers start: 43 outliers final: 29 residues processed: 460 average time/residue: 1.5030 time to fit residues: 779.5623 Evaluate side-chains 461 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 427 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN D 37 ASN D 113 GLN F 108 GLN I 263 ASN A 37 ASN B 37 ASN J 82 ASN L 82 ASN C 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23478 Z= 0.207 Angle : 0.600 6.778 31752 Z= 0.278 Chirality : 0.042 0.226 3986 Planarity : 0.003 0.041 3662 Dihedral : 10.225 175.733 5482 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.76 % Allowed : 15.64 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.16), residues: 2766 helix: 2.41 (0.12), residues: 1760 sheet: 1.91 (0.29), residues: 282 loop : -0.06 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 337 HIS 0.005 0.001 HIS C 176 PHE 0.030 0.001 PHE I 210 TYR 0.017 0.001 TYR I 435 ARG 0.007 0.000 ARG E 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 434 time to evaluate : 3.237 Fit side-chains REVERT: E 38 GLU cc_start: 0.7468 (tt0) cc_final: 0.7235 (tt0) REVERT: F 38 GLU cc_start: 0.7536 (tt0) cc_final: 0.7270 (tt0) REVERT: F 66 LYS cc_start: 0.8649 (tppt) cc_final: 0.8378 (mtpt) REVERT: I 26 ARG cc_start: 0.7107 (ttt90) cc_final: 0.6666 (ttt90) REVERT: I 139 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7498 (tptp) REVERT: I 299 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: I 354 ASN cc_start: 0.8348 (p0) cc_final: 0.7945 (p0) REVERT: B 130 ARG cc_start: 0.7448 (mtp180) cc_final: 0.7212 (mmm160) REVERT: J 30 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7434 (mp-120) REVERT: L 38 GLU cc_start: 0.7598 (tt0) cc_final: 0.7363 (tt0) REVERT: M 139 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7251 (tptp) REVERT: M 299 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: C 26 ARG cc_start: 0.7108 (ttt90) cc_final: 0.6670 (ttt90) REVERT: C 139 LYS cc_start: 0.8036 (ttpp) cc_final: 0.7511 (tptp) REVERT: C 299 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: C 354 ASN cc_start: 0.8345 (p0) cc_final: 0.7928 (p0) REVERT: G 139 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7246 (tptp) REVERT: G 299 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8057 (m-80) outliers start: 40 outliers final: 30 residues processed: 460 average time/residue: 1.5618 time to fit residues: 814.4001 Evaluate side-chains 457 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 422 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 ASN D 37 ASN F 108 GLN I 263 ASN A 37 ASN B 37 ASN J 82 ASN C 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101868 restraints weight = 34032.238| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.90 r_work: 0.2951 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23478 Z= 0.206 Angle : 0.603 6.773 31752 Z= 0.280 Chirality : 0.041 0.227 3986 Planarity : 0.003 0.041 3662 Dihedral : 10.125 175.555 5482 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.89 % Allowed : 16.04 % Favored : 82.07 % 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: 2766 helix: 2.41 (0.12), residues: 1754 sheet: 1.89 (0.29), residues: 282 loop : -0.08 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 337 HIS 0.005 0.001 HIS C 176 PHE 0.030 0.001 PHE C 210 TYR 0.018 0.001 TYR I 435 ARG 0.007 0.000 ARG E 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11450.67 seconds wall clock time: 203 minutes 47.90 seconds (12227.90 seconds total)