Starting phenix.real_space_refine on Tue Jul 23 17:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/07_2024/7zp9_14851_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/07_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_14851/07_2024/7zp9_14851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/07_2024/7zp9_14851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/07_2024/7zp9_14851_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp9_14851/07_2024/7zp9_14851_neut.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 16.69, per 1000 atoms: 0.72 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: 8.72 Conformation dependent library (CDL) restraints added in 5.0 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... Secondary structure from input PDB file: 122 helices and 12 sheets defined 68.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'H' and resid 14 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 37 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 58 through 66 Processing helix chain 'H' and resid 80 through 94 Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 122 through 137 Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.762A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 80 through 95 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'E' and resid 14 through 28 Processing helix chain 'E' and resid 37 through 46 removed outlier: 4.232A pdb=" N GLY E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 14 through 28 Processing helix chain 'F' and resid 37 through 46 removed outlier: 4.024A pdb=" N GLY F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 Processing helix chain 'F' and resid 67 through 70 Processing helix chain 'F' and resid 80 through 95 Processing helix chain 'F' and resid 105 through 116 Processing helix chain 'F' and resid 122 through 137 Processing helix chain 'I' and resid 23 through 44 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 removed outlier: 3.530A pdb=" N THR I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 67 Processing helix chain 'I' and resid 75 through 80 removed outlier: 3.612A pdb=" N PHE I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 122 Processing helix chain 'I' and resid 133 through 165 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 167 through 182 Processing helix chain 'I' and resid 199 through 214 Processing helix chain 'I' and resid 216 through 227 Processing helix chain 'I' and resid 230 through 234 Processing helix chain 'I' and resid 235 through 261 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 271 through 286 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 300 through 314 Processing helix chain 'I' and resid 325 through 341 Processing helix chain 'I' and resid 354 through 383 Processing helix chain 'I' and resid 386 through 399 Processing helix chain 'I' and resid 407 through 411 Processing helix chain 'I' and resid 412 through 439 Proline residue: I 430 - end of helix Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 37 through 48 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 58 through 66 Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'B' and resid 14 through 27 Processing helix chain 'B' and resid 37 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 58 through 66 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'J' and resid 14 through 27 removed outlier: 3.535A pdb=" N SER J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 46 removed outlier: 4.242A pdb=" N GLY J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 65 Processing helix chain 'J' and resid 80 through 94 Processing helix chain 'J' and resid 105 through 116 Processing helix chain 'J' and resid 122 through 137 Processing helix chain 'L' and resid 14 through 28 removed outlier: 3.619A pdb=" N SER L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 46 removed outlier: 4.247A pdb=" N GLY L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 66 Processing helix chain 'L' and resid 67 through 70 Processing helix chain 'L' and resid 80 through 94 removed outlier: 3.549A pdb=" N SER L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 116 Processing helix chain 'L' and resid 122 through 137 Processing helix chain 'M' and resid 23 through 45 Proline residue: M 38 - end of helix removed outlier: 3.771A pdb=" N THR M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 45 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 67 Processing helix chain 'M' and resid 75 through 80 removed outlier: 3.686A pdb=" N PHE M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 122 removed outlier: 3.582A pdb=" N GLN M 99 " --> pdb=" O GLY M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 165 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 165 through 182 removed outlier: 3.593A pdb=" N PHE M 171 " --> pdb=" O GLN M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 214 Processing helix chain 'M' and resid 216 through 227 Processing helix chain 'M' and resid 230 through 234 Processing helix chain 'M' and resid 235 through 261 Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 286 Processing helix chain 'M' and resid 295 through 299 Processing helix chain 'M' and resid 300 through 314 Processing helix chain 'M' and resid 325 through 342 Processing helix chain 'M' and resid 354 through 383 Processing helix chain 'M' and resid 386 through 399 Processing helix chain 'M' and resid 412 through 439 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 23 through 44 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 removed outlier: 3.530A pdb=" N THR C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.612A pdb=" N PHE C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 122 Processing helix chain 'C' and resid 133 through 165 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 167 through 182 Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 235 through 261 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 300 through 314 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 354 through 383 Processing helix chain 'C' and resid 386 through 399 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 439 Proline residue: C 430 - end of helix Processing helix chain 'G' and resid 23 through 45 Proline residue: G 38 - end of helix removed outlier: 3.771A pdb=" N THR G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 67 Processing helix chain 'G' and resid 75 through 80 removed outlier: 3.686A pdb=" N PHE G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 122 removed outlier: 3.581A pdb=" N GLN G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 165 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 165 through 182 removed outlier: 3.593A pdb=" N PHE G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 214 Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 230 through 234 Processing helix chain 'G' and resid 235 through 261 Proline residue: G 246 - end of helix Processing helix chain 'G' and resid 271 through 286 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 300 through 314 Processing helix chain 'G' and resid 325 through 342 Processing helix chain 'G' and resid 354 through 383 Processing helix chain 'G' and resid 386 through 399 Processing helix chain 'G' and resid 412 through 439 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=AA1, first strand: chain 'H' and resid 50 through 53 removed outlier: 6.167A pdb=" N VAL H 31 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE H 52 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA H 33 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET H 72 " --> pdb=" O GLN H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 50 through 53 removed outlier: 6.171A pdb=" N VAL D 31 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE D 52 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA D 33 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 8 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL D 34 " --> pdb=" O PHE D 8 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL D 10 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN D 7 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N MET D 74 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA D 9 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 99 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 121 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 101 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 119 through 121 removed outlier: 3.829A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL E 31 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE E 52 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA E 33 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA E 54 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP E 35 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 119 through 121 removed outlier: 3.771A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL F 31 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE F 52 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 33 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA F 54 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP F 35 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 346 through 347 removed outlier: 4.464A pdb=" N VAL I 346 " --> pdb=" O VAL I 353 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR I 352 " --> pdb=" O ASP M 450 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.257A pdb=" N VAL A 31 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 52 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA A 33 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN A 7 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N MET A 74 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 9 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 99 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 121 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 101 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 53 removed outlier: 6.120A pdb=" N VAL B 31 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE B 52 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 33 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE B 8 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 34 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 10 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN B 7 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N MET B 74 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA B 9 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 99 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 121 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 101 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AA8, 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: 6.329A pdb=" N VAL J 31 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE J 52 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA J 33 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA J 54 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP J 35 " --> pdb=" O ALA J 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 119 through 121 removed outlier: 6.577A pdb=" N VAL L 99 " --> pdb=" O HIS L 119 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE L 121 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL L 101 " --> pdb=" O ILE L 121 " (cutoff:3.500A) 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: 6.448A pdb=" N VAL L 31 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE L 52 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA L 33 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA L 54 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP L 35 " --> pdb=" O ALA L 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 346 through 347 removed outlier: 4.421A pdb=" N VAL M 346 " --> pdb=" O VAL M 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 346 through 347 removed outlier: 4.464A pdb=" N VAL C 346 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR C 352 " --> pdb=" O ASP G 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 346 through 347 removed outlier: 4.421A pdb=" N VAL G 346 " --> pdb=" O VAL G 353 " (cutoff:3.500A) 1451 hydrogen bonds defined for protein. 4266 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: 7.16 Time building geometry restraints manager: 9.55 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: 6254 2.82 - 3.59: 38649 3.59 - 4.37: 70897 4.37 - 5.14: 123080 Nonbonded interactions: 238900 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 238895 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 65.860 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.370 ------------------------------------------------------------------------------- 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= 0.526 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 : 2.487 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: 1.6146 time to fit residues: 959.6776 Evaluate side-chains 434 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 424 time to evaluate : 2.570 ------------------------------------------------------------------------------- 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: 1.9990 chunk 116 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 161 optimal weight: 0.0040 chunk 250 optimal weight: 4.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 GLN D 50 GLN D 113 GLN F 108 GLN I 119 GLN I 263 ASN I 342 GLN A 50 GLN A 113 GLN B 30 GLN B 37 ASN B 50 GLN B 113 GLN J 108 GLN L 25 GLN M 93 GLN M 263 ASN M 301 GLN M 342 GLN C 119 GLN C 263 ASN C 342 GLN G 263 ASN G 301 GLN G 342 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1644 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= 0.185 Angle : 0.754 10.436 31752 Z= 0.328 Chirality : 0.048 0.377 3986 Planarity : 0.004 0.037 3662 Dihedral : 18.321 178.760 5494 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.01 % Rotamer: Outliers : 1.98 % Allowed : 9.09 % Favored : 88.93 % 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: 2.48 (0.16), residues: 2766 helix: 2.29 (0.12), residues: 1774 sheet: 1.73 (0.27), residues: 270 loop : -0.03 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 100 HIS 0.004 0.001 HIS I 176 PHE 0.039 0.002 PHE I 210 TYR 0.017 0.001 TYR E 70 ARG 0.004 0.000 ARG L 15 *********************** 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 506 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 461 time to evaluate : 2.161 Fit side-chains revert: symmetry clash REVERT: H 60 GLU cc_start: 0.7332 (mp0) cc_final: 0.7098 (mp0) REVERT: H 130 ARG cc_start: 0.7520 (mtp180) cc_final: 0.7278 (mmm160) REVERT: E 38 GLU cc_start: 0.7425 (tt0) cc_final: 0.7198 (tt0) REVERT: E 66 LYS cc_start: 0.7554 (mppt) cc_final: 0.7260 (mmtm) REVERT: F 69 ASP cc_start: 0.7638 (m-30) cc_final: 0.7303 (m-30) REVERT: I 26 ARG cc_start: 0.7332 (ttt90) cc_final: 0.6924 (ttt-90) REVERT: I 139 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7483 (tptp) REVERT: I 299 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: A 22 LYS cc_start: 0.8423 (ttmt) cc_final: 0.7854 (tptp) REVERT: B 22 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7824 (tptp) REVERT: J 30 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7476 (mm110) REVERT: L 38 GLU cc_start: 0.7336 (tt0) cc_final: 0.7133 (tt0) REVERT: M 100 MET cc_start: 0.8700 (ttp) cc_final: 0.8481 (ttp) REVERT: M 139 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7222 (tptp) REVERT: M 299 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: C 26 ARG cc_start: 0.7323 (ttt90) cc_final: 0.6923 (ttt-90) REVERT: C 139 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7473 (tptp) REVERT: C 299 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: G 100 MET cc_start: 0.8705 (ttp) cc_final: 0.8487 (ttp) REVERT: G 139 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7222 (tptp) REVERT: G 299 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8102 (m-80) outliers start: 45 outliers final: 14 residues processed: 486 average time/residue: 1.4965 time to fit residues: 818.0759 Evaluate side-chains 439 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 419 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 E residue 29 SER 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 J residue 30 GLN Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 93 GLN 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 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 271 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN F 108 GLN I 263 ASN A 37 ASN A 113 GLN B 113 GLN J 108 GLN L 82 ASN M 198 ASN M 263 ASN C 263 ASN G 93 GLN G 198 ASN G 263 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23478 Z= 0.176 Angle : 0.670 7.076 31752 Z= 0.296 Chirality : 0.044 0.299 3986 Planarity : 0.004 0.065 3662 Dihedral : 13.534 177.840 5486 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.88 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 11.47 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.16), residues: 2766 helix: 2.49 (0.12), residues: 1778 sheet: 1.70 (0.28), residues: 270 loop : 0.08 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 337 HIS 0.005 0.001 HIS I 176 PHE 0.031 0.001 PHE C 210 TYR 0.015 0.001 TYR F 70 ARG 0.004 0.000 ARG L 106 *********************** 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 494 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 440 time to evaluate : 2.432 Fit side-chains REVERT: H 60 GLU cc_start: 0.7454 (mp0) cc_final: 0.7180 (mp0) REVERT: H 69 ASP cc_start: 0.7872 (m-30) cc_final: 0.7671 (m-30) REVERT: E 38 GLU cc_start: 0.7425 (tt0) cc_final: 0.7218 (tt0) REVERT: E 66 LYS cc_start: 0.7596 (mppt) cc_final: 0.7264 (mmtm) REVERT: E 122 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7933 (mtm) REVERT: F 69 ASP cc_start: 0.7545 (m-30) cc_final: 0.7335 (m-30) REVERT: I 26 ARG cc_start: 0.7317 (ttt90) cc_final: 0.6857 (ttt-90) REVERT: I 139 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7467 (tptp) REVERT: I 299 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: A 22 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7873 (tptp) REVERT: B 22 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7852 (tptp) REVERT: B 130 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6923 (mmm160) REVERT: J 130 ARG cc_start: 0.6998 (mtp85) cc_final: 0.6545 (mtp180) REVERT: M 100 MET cc_start: 0.8645 (ttp) cc_final: 0.8430 (ttp) REVERT: M 139 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7236 (tptp) REVERT: M 170 MET cc_start: 0.7834 (mmm) cc_final: 0.7605 (mmp) REVERT: M 299 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: C 26 ARG cc_start: 0.7316 (ttt90) cc_final: 0.6862 (ttt-90) REVERT: C 139 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7469 (tptp) REVERT: C 299 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: G 139 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7234 (tptp) REVERT: G 170 MET cc_start: 0.7824 (mmm) cc_final: 0.7593 (mmp) REVERT: G 299 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8124 (m-80) outliers start: 54 outliers final: 23 residues processed: 471 average time/residue: 1.5624 time to fit residues: 826.0634 Evaluate side-chains 447 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 418 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 ASP 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 39 ASP 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 L residue 29 SER Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 194 MET Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 194 MET 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: 5.9990 chunk 188 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 266 optimal weight: 0.0470 chunk 131 optimal weight: 0.9990 chunk 238 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN F 108 GLN I 263 ASN A 37 ASN J 108 GLN L 82 ASN M 198 ASN M 263 ASN C 263 ASN C 342 GLN G 93 GLN G 198 ASN G 263 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23478 Z= 0.254 Angle : 0.672 7.144 31752 Z= 0.307 Chirality : 0.045 0.343 3986 Planarity : 0.003 0.037 3662 Dihedral : 12.382 178.393 5484 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.28 % Favored : 97.68 % Rotamer: Outliers : 2.64 % Allowed : 12.74 % Favored : 84.62 % 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: 2.66 (0.16), residues: 2766 helix: 2.48 (0.12), residues: 1774 sheet: 1.49 (0.28), residues: 270 loop : 0.07 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 337 HIS 0.004 0.001 HIS I 176 PHE 0.032 0.002 PHE I 210 TYR 0.016 0.002 TYR F 70 ARG 0.003 0.000 ARG J 130 *********************** 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 494 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 434 time to evaluate : 2.661 Fit side-chains REVERT: H 60 GLU cc_start: 0.7440 (mp0) cc_final: 0.7195 (mp0) REVERT: H 69 ASP cc_start: 0.7885 (m-30) cc_final: 0.7680 (m-30) REVERT: E 38 GLU cc_start: 0.7396 (tt0) cc_final: 0.7188 (tt0) REVERT: E 66 LYS cc_start: 0.7686 (mppt) cc_final: 0.7314 (mmtm) REVERT: F 30 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7442 (mm110) REVERT: I 26 ARG cc_start: 0.7257 (ttt90) cc_final: 0.6836 (ttt-90) REVERT: I 139 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7482 (tptp) REVERT: A 22 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7908 (tptp) REVERT: B 22 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7874 (tptp) REVERT: J 30 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7426 (mm110) REVERT: J 130 ARG cc_start: 0.7070 (mtp85) cc_final: 0.6779 (ttt-90) REVERT: L 30 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7482 (mm110) REVERT: M 100 MET cc_start: 0.8640 (ttp) cc_final: 0.8364 (ttp) REVERT: M 139 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7263 (tptp) REVERT: M 170 MET cc_start: 0.7777 (mmm) cc_final: 0.7555 (mmp) REVERT: M 299 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: C 26 ARG cc_start: 0.7259 (ttt90) cc_final: 0.6843 (ttt-90) REVERT: C 139 LYS cc_start: 0.8042 (ttpp) cc_final: 0.7492 (tptp) REVERT: G 139 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7260 (tptp) REVERT: G 170 MET cc_start: 0.7767 (mmm) cc_final: 0.7550 (mmp) REVERT: G 299 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8077 (m-80) outliers start: 60 outliers final: 28 residues processed: 471 average time/residue: 1.5106 time to fit residues: 801.7085 Evaluate side-chains 452 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 418 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 98 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 96 VAL 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 29 SER 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 299 PHE 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 C residue 344 LYS 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 299 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN I 263 ASN I 342 GLN A 37 ASN J 82 ASN J 108 GLN L 82 ASN M 198 ASN M 263 ASN C 263 ASN G 198 ASN G 263 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23478 Z= 0.232 Angle : 0.644 6.943 31752 Z= 0.297 Chirality : 0.044 0.329 3986 Planarity : 0.003 0.037 3662 Dihedral : 11.758 179.731 5482 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % Rotamer: Outliers : 2.90 % Allowed : 12.96 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.16), residues: 2766 helix: 2.53 (0.12), residues: 1772 sheet: 1.39 (0.28), residues: 270 loop : 0.03 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 337 HIS 0.004 0.001 HIS C 176 PHE 0.032 0.002 PHE I 210 TYR 0.012 0.001 TYR F 70 ARG 0.004 0.000 ARG F 106 *********************** 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 488 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 422 time to evaluate : 2.522 Fit side-chains REVERT: H 60 GLU cc_start: 0.7411 (mp0) cc_final: 0.7184 (mp0) REVERT: E 38 GLU cc_start: 0.7391 (tt0) cc_final: 0.7177 (tt0) REVERT: E 66 LYS cc_start: 0.7644 (mppt) cc_final: 0.7280 (mmtm) REVERT: F 30 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7373 (mm110) REVERT: F 38 GLU cc_start: 0.7497 (tt0) cc_final: 0.7256 (tt0) REVERT: I 26 ARG cc_start: 0.7195 (ttt90) cc_final: 0.6670 (ttt90) REVERT: I 139 LYS cc_start: 0.8050 (ttpp) cc_final: 0.7513 (tptp) REVERT: I 193 MET cc_start: 0.8059 (mmt) cc_final: 0.6609 (mmt) REVERT: A 22 LYS cc_start: 0.8428 (ttmt) cc_final: 0.7908 (tptp) REVERT: A 113 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7754 (mt0) REVERT: B 22 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7856 (tptp) REVERT: B 113 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7763 (mt0) REVERT: J 130 ARG cc_start: 0.7035 (mtp85) cc_final: 0.6723 (ttt-90) REVERT: L 30 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7452 (mm110) REVERT: M 139 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7272 (tptp) REVERT: M 247 LEU cc_start: 0.8422 (tp) cc_final: 0.8154 (mp) REVERT: M 299 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: C 26 ARG cc_start: 0.7200 (ttt90) cc_final: 0.6674 (ttt90) REVERT: C 139 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7504 (tptp) REVERT: C 193 MET cc_start: 0.8059 (mmt) cc_final: 0.6605 (mmt) REVERT: G 139 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7271 (tptp) REVERT: G 247 LEU cc_start: 0.8432 (tp) cc_final: 0.8161 (mp) REVERT: G 299 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7991 (m-80) outliers start: 66 outliers final: 37 residues processed: 465 average time/residue: 1.4890 time to fit residues: 779.8509 Evaluate side-chains 459 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 417 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 F residue 29 SER Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 98 SER 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 48 VAL Chi-restraints excluded: chain A residue 96 VAL 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 34 VAL Chi-restraints excluded: chain L residue 29 SER 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 89 MET Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 360 LYS 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 C residue 344 LYS 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 Chi-restraints excluded: chain G residue 360 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 GLN I 263 ASN A 37 ASN J 82 ASN J 108 GLN L 82 ASN M 198 ASN C 263 ASN G 198 ASN G 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2211 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= 0.193 Angle : 0.613 6.701 31752 Z= 0.283 Chirality : 0.042 0.306 3986 Planarity : 0.003 0.037 3662 Dihedral : 11.118 179.061 5482 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 13.80 % Favored : 83.83 % 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: 2.77 (0.16), residues: 2766 helix: 2.60 (0.12), residues: 1778 sheet: 1.36 (0.28), residues: 270 loop : 0.08 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 337 HIS 0.005 0.001 HIS C 176 PHE 0.032 0.001 PHE I 210 TYR 0.013 0.001 TYR M 108 ARG 0.005 0.000 ARG J 130 *********************** 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 487 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 433 time to evaluate : 2.309 Fit side-chains REVERT: H 60 GLU cc_start: 0.7403 (mp0) cc_final: 0.7184 (mp0) REVERT: D 113 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7772 (mt0) REVERT: E 38 GLU cc_start: 0.7330 (tt0) cc_final: 0.7098 (tt0) REVERT: F 130 ARG cc_start: 0.7138 (ttt-90) cc_final: 0.6615 (mtp85) REVERT: I 26 ARG cc_start: 0.7179 (ttt90) cc_final: 0.6687 (ttt90) REVERT: I 139 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7509 (tptp) REVERT: I 193 MET cc_start: 0.8001 (mmt) cc_final: 0.6513 (mmt) REVERT: A 22 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7912 (tptp) REVERT: A 113 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7774 (mt0) REVERT: B 22 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7845 (tptp) REVERT: B 113 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7782 (mt0) REVERT: J 93 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5877 (mp0) REVERT: J 130 ARG cc_start: 0.7026 (mtp85) cc_final: 0.6732 (ttt90) REVERT: L 130 ARG cc_start: 0.7118 (ttt-90) cc_final: 0.6747 (mtp85) REVERT: M 139 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7247 (tptp) REVERT: C 26 ARG cc_start: 0.7144 (ttt90) cc_final: 0.6669 (ttt90) REVERT: C 139 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7481 (tptp) REVERT: C 193 MET cc_start: 0.8011 (mmt) cc_final: 0.6516 (mmt) REVERT: G 93 GLN cc_start: 0.8388 (tp40) cc_final: 0.8139 (tp40) REVERT: G 139 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7247 (tptp) outliers start: 54 outliers final: 38 residues processed: 465 average time/residue: 1.5124 time to fit residues: 793.3759 Evaluate side-chains 456 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 416 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER 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 39 ASP Chi-restraints excluded: chain A residue 48 VAL 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 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER 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 299 PHE Chi-restraints excluded: chain M residue 360 LYS 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 C residue 344 LYS 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 89 MET Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 360 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 266 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 F 108 GLN I 263 ASN A 37 ASN J 82 ASN J 108 GLN L 82 ASN C 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23478 Z= 0.312 Angle : 0.681 7.434 31752 Z= 0.319 Chirality : 0.045 0.294 3986 Planarity : 0.004 0.037 3662 Dihedral : 11.286 174.620 5482 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 2.68 % Allowed : 13.93 % Favored : 83.39 % 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: 2.55 (0.16), residues: 2766 helix: 2.41 (0.12), residues: 1774 sheet: 1.09 (0.28), residues: 286 loop : 0.11 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 337 HIS 0.004 0.001 HIS I 176 PHE 0.031 0.002 PHE I 210 TYR 0.014 0.002 TYR G 108 ARG 0.004 0.000 ARG B 130 *********************** 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 480 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 419 time to evaluate : 2.461 Fit side-chains REVERT: H 60 GLU cc_start: 0.7410 (mp0) cc_final: 0.7165 (mp0) REVERT: D 113 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7810 (mt0) REVERT: E 38 GLU cc_start: 0.7411 (tt0) cc_final: 0.7185 (tt0) REVERT: E 66 LYS cc_start: 0.7674 (mppt) cc_final: 0.7301 (mmtm) REVERT: I 26 ARG cc_start: 0.7202 (ttt90) cc_final: 0.6755 (ttt90) REVERT: I 139 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7522 (tptp) REVERT: I 299 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: A 22 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7932 (tptp) REVERT: A 113 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7788 (mt0) REVERT: B 113 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7785 (mt0) REVERT: J 93 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.5774 (mp0) REVERT: J 130 ARG cc_start: 0.7121 (mtp85) cc_final: 0.6843 (ttt90) REVERT: M 139 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7278 (tptp) REVERT: M 299 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: C 26 ARG cc_start: 0.7200 (ttt90) cc_final: 0.6755 (ttt90) REVERT: C 139 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7509 (tptp) REVERT: C 299 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: G 139 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7279 (tptp) REVERT: G 299 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7912 (m-80) outliers start: 61 outliers final: 39 residues processed: 461 average time/residue: 1.4694 time to fit residues: 764.1888 Evaluate side-chains 454 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 410 time to evaluate : 2.354 ------------------------------------------------------------------------------- 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 104 ASN 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 F residue 29 SER Chi-restraints excluded: chain F residue 98 SER 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 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 96 VAL 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 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER 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 247 LEU Chi-restraints excluded: chain M residue 299 PHE 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 C residue 344 LYS 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 247 LEU 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: 0.9980 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN F 82 ASN F 108 GLN I 263 ASN A 37 ASN J 108 GLN L 82 ASN C 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23478 Z= 0.165 Angle : 0.590 6.628 31752 Z= 0.275 Chirality : 0.041 0.242 3986 Planarity : 0.003 0.037 3662 Dihedral : 10.380 174.442 5482 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.02 % Allowed : 14.98 % Favored : 83.00 % 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: 2.79 (0.16), residues: 2766 helix: 2.62 (0.12), residues: 1776 sheet: 1.19 (0.29), residues: 282 loop : 0.11 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 337 HIS 0.004 0.001 HIS I 176 PHE 0.031 0.001 PHE C 210 TYR 0.011 0.001 TYR G 108 ARG 0.005 0.000 ARG E 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 474 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 428 time to evaluate : 2.482 Fit side-chains REVERT: H 60 GLU cc_start: 0.7364 (mp0) cc_final: 0.7134 (mp0) REVERT: D 113 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7794 (mt0) REVERT: I 26 ARG cc_start: 0.7084 (ttt90) cc_final: 0.6673 (ttt90) REVERT: I 139 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7467 (tptp) REVERT: A 22 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7905 (tptp) REVERT: A 113 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7789 (mt0) REVERT: B 22 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7839 (tptp) REVERT: B 113 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7781 (mt0) REVERT: J 93 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5906 (mp0) REVERT: J 130 ARG cc_start: 0.7027 (mtp85) cc_final: 0.6792 (ttt90) REVERT: M 139 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7243 (tptp) REVERT: C 26 ARG cc_start: 0.7082 (ttt90) cc_final: 0.6672 (ttt90) REVERT: C 139 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7484 (tptp) REVERT: G 139 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7243 (tptp) outliers start: 46 outliers final: 36 residues processed: 460 average time/residue: 1.4751 time to fit residues: 767.0687 Evaluate side-chains 455 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 417 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 104 ASN 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 F residue 29 SER Chi-restraints excluded: chain F residue 98 SER 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 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL 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 93 GLU Chi-restraints excluded: chain L residue 29 SER 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 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 299 PHE Chi-restraints excluded: chain C residue 344 LYS 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: 5.9990 chunk 254 optimal weight: 0.8980 chunk 232 optimal weight: 0.4980 chunk 247 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 234 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN I 263 ASN A 37 ASN J 108 GLN L 82 ASN C 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23478 Z= 0.193 Angle : 0.604 6.734 31752 Z= 0.283 Chirality : 0.041 0.225 3986 Planarity : 0.003 0.037 3662 Dihedral : 10.186 176.618 5482 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.33 % Allowed : 14.89 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.16), residues: 2766 helix: 2.63 (0.12), residues: 1778 sheet: 1.17 (0.29), residues: 282 loop : 0.15 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 337 HIS 0.004 0.001 HIS C 176 PHE 0.031 0.001 PHE C 210 TYR 0.009 0.001 TYR F 70 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 471 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 418 time to evaluate : 2.407 Fit side-chains REVERT: F 66 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8052 (ttmm) REVERT: I 26 ARG cc_start: 0.7169 (ttt90) cc_final: 0.6710 (ttt90) REVERT: I 139 LYS cc_start: 0.8064 (ttpp) cc_final: 0.7498 (tptp) REVERT: A 22 LYS cc_start: 0.8446 (ttmt) cc_final: 0.7913 (tptp) REVERT: A 113 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7795 (mt0) REVERT: B 22 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7847 (tptp) REVERT: B 113 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7785 (mt0) REVERT: J 93 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.5894 (mp0) REVERT: J 130 ARG cc_start: 0.7082 (mtp85) cc_final: 0.6818 (ttt90) REVERT: L 130 ARG cc_start: 0.7073 (ttt-90) cc_final: 0.6602 (mtp85) REVERT: M 139 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7243 (tptp) REVERT: M 299 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: C 26 ARG cc_start: 0.7162 (ttt90) cc_final: 0.6707 (ttt90) REVERT: C 139 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7463 (tptp) REVERT: C 307 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7995 (tpp) REVERT: G 139 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7265 (tptp) REVERT: G 299 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7956 (m-80) outliers start: 53 outliers final: 36 residues processed: 453 average time/residue: 1.4586 time to fit residues: 746.4881 Evaluate side-chains 456 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 414 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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 104 ASN 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 F residue 29 SER Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 98 SER 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 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL 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 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER 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 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 299 PHE Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 344 LYS 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: 5.9990 chunk 159 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 274 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN F 108 GLN I 263 ASN A 37 ASN J 108 GLN L 82 ASN L 108 GLN C 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23478 Z= 0.169 Angle : 0.592 6.630 31752 Z= 0.277 Chirality : 0.041 0.231 3986 Planarity : 0.003 0.037 3662 Dihedral : 9.876 177.629 5482 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.89 % Allowed : 15.29 % Favored : 82.82 % 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: 2.81 (0.16), residues: 2766 helix: 2.69 (0.12), residues: 1766 sheet: 1.28 (0.29), residues: 270 loop : 0.00 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 337 HIS 0.004 0.001 HIS I 176 PHE 0.031 0.001 PHE C 210 TYR 0.012 0.001 TYR G 108 ARG 0.008 0.000 ARG J 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 471 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 428 time to evaluate : 2.582 Fit side-chains REVERT: F 66 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8007 (ttmm) REVERT: I 26 ARG cc_start: 0.7137 (ttt90) cc_final: 0.6732 (ttt90) REVERT: I 139 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7484 (tptp) REVERT: A 22 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7910 (tptp) REVERT: A 113 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7769 (mt0) REVERT: B 22 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7848 (tptp) REVERT: J 93 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.5912 (mp0) REVERT: J 130 ARG cc_start: 0.6974 (mtp85) cc_final: 0.6722 (ttt90) REVERT: M 139 LYS cc_start: 0.7860 (ttpt) cc_final: 0.7266 (tptp) REVERT: M 299 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: C 26 ARG cc_start: 0.7136 (ttt90) cc_final: 0.6739 (ttt90) REVERT: C 139 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7476 (tptp) REVERT: C 307 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7993 (tpp) REVERT: G 139 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7266 (tptp) REVERT: G 299 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7950 (m-80) outliers start: 43 outliers final: 31 residues processed: 456 average time/residue: 1.5128 time to fit residues: 778.6492 Evaluate side-chains 447 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 410 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 F residue 29 SER Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 98 SER 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 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL 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 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 93 GLU 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 299 PHE Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 344 LYS 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: 5.9990 chunk 67 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN E 108 GLN F 108 GLN I 263 ASN A 37 ASN J 108 GLN L 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 = 0.3536 r_free = 0.3536 target = 0.131045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104944 restraints weight = 33849.469| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.89 r_work: 0.2996 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2468 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= 0.173 Angle : 0.593 7.124 31752 Z= 0.279 Chirality : 0.041 0.229 3986 Planarity : 0.003 0.036 3662 Dihedral : 9.739 178.722 5482 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.89 % Allowed : 15.60 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.16), residues: 2766 helix: 2.71 (0.12), residues: 1766 sheet: 1.30 (0.29), residues: 270 loop : 0.01 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 337 HIS 0.005 0.001 HIS C 176 PHE 0.031 0.001 PHE C 210 TYR 0.012 0.001 TYR C 417 ARG 0.008 0.000 ARG J 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11350.65 seconds wall clock time: 198 minutes 34.30 seconds (11914.30 seconds total)