Starting phenix.real_space_refine on Tue Jul 23 04:55:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/07_2024/7zpr_14862_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/07_2024/7zpr_14862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/07_2024/7zpr_14862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/07_2024/7zpr_14862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/07_2024/7zpr_14862_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpr_14862/07_2024/7zpr_14862_neut.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 Mg 8 5.21 5 S 140 5.16 5 C 13782 2.51 5 N 3576 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 23": "OE1" <-> "OE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "I GLU 24": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "M GLU 24": "OE1" <-> "OE2" Residue "M GLU 149": "OE1" <-> "OE2" Residue "M GLU 260": "OE1" <-> "OE2" Residue "M GLU 393": "OE1" <-> "OE2" Residue "M GLU 413": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 393": "OE1" <-> "OE2" Residue "G GLU 413": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21350 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "I" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "J" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "L" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "M" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "C" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "G" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.68, per 1000 atoms: 0.64 Number of scatterers: 21350 At special positions: 0 Unit cell: (95.9651, 110.921, 173.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 140 16.00 P 16 15.00 Mg 8 11.99 O 3824 8.00 N 3576 7.00 C 13782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.79 Conformation dependent library (CDL) restraints added in 5.3 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 12 sheets defined 69.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 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: 4.231A 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: 3.549A pdb=" N VAL I 35 " --> pdb=" O SER I 31 " (cutoff:3.500A) Proline residue: I 38 - end of helix removed outlier: 3.531A 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: 3.710A pdb=" N ARG I 159 " --> pdb=" O PHE I 155 " (cutoff:3.500A) Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 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: 3.842A pdb=" N GLU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 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: 3.618A 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: 3.548A 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: 3.770A 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: 3.687A 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: 3.846A pdb=" N ARG M 159 " --> pdb=" O PHE M 155 " (cutoff:3.500A) Proline residue: M 162 - end of helix Processing helix chain 'M' and resid 165 through 182 removed outlier: 3.594A 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: 3.536A pdb=" N TYR M 417 " --> pdb=" O GLU M 413 " (cutoff:3.500A) Proline residue: M 430 - end of helix Processing helix chain 'C' and resid 23 through 44 removed outlier: 3.525A pdb=" N PHE C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Proline residue: C 38 - end of helix 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: 3.611A 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: 3.770A 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: 3.685A 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: 3.846A pdb=" N ARG G 159 " --> pdb=" O PHE G 155 " (cutoff:3.500A) Proline residue: G 162 - end of helix Processing helix chain 'G' and resid 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: 6.168A pdb=" N VAL H 31 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE H 52 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.191A 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: 6.172A 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: 6.309A pdb=" N ALA D 33 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE D 8 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 7.924A 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: 6.961A pdb=" N GLN D 7 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 8.268A 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 50 through 53 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: 3.828A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 50 through 53 removed outlier: 6.419A pdb=" N VAL F 31 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 7.800A 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: 3.771A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 346 through 347 removed outlier: 4.466A 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: 6.172A 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: 6.310A 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: 7.842A pdb=" N ILE A 121 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.553A 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: 6.284A pdb=" N ALA B 33 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.863A 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: 6.387A pdb=" N VAL B 10 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.935A 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: 7.984A pdb=" N ILE B 121 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 101 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 50 through 53 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: 6.344A pdb=" N ALA J 33 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET J 72 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL J 73 " --> pdb=" O TRP J 100 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS J 102 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE J 75 " --> pdb=" O LYS J 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 50 through 53 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: 3.697A pdb=" N MET L 72 " --> pdb=" O GLN L 7 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL L 73 " --> pdb=" O SER L 98 " (cutoff:3.500A) 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: 6.552A pdb=" N VAL L 101 " --> pdb=" O ILE L 121 " (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: 4.420A pdb=" N VAL G 346 " --> pdb=" O VAL G 353 " (cutoff:3.500A) 1443 hydrogen bonds defined for protein. 4242 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: 7.82 Time building geometry restraints manager: 9.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4195 1.33 - 1.45: 4835 1.45 - 1.57: 12413 1.57 - 1.69: 24 1.69 - 1.82: 261 Bond restraints: 21728 Sorted by residual: bond pdb=" N PRO H 123 " pdb=" CD PRO H 123 " ideal model delta sigma weight residual 1.473 1.729 -0.256 1.40e-02 5.10e+03 3.35e+02 bond pdb=" C4 ADP J 301 " pdb=" C5 ADP J 301 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N PRO A 123 " pdb=" CD PRO A 123 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C5 ADP A1002 " pdb=" C6 ADP A1002 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 21723 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.51: 385 105.51 - 113.22: 12482 113.22 - 120.93: 11159 120.93 - 128.64: 5263 128.64 - 136.35: 169 Bond angle restraints: 29458 Sorted by residual: angle pdb=" C THR G 288 " pdb=" CA THR G 288 " pdb=" CB THR G 288 " ideal model delta sigma weight residual 110.42 119.31 -8.89 1.99e+00 2.53e-01 2.00e+01 angle pdb=" C THR M 288 " pdb=" CA THR M 288 " pdb=" CB THR M 288 " ideal model delta sigma weight residual 110.42 119.28 -8.86 1.99e+00 2.53e-01 1.98e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" C LEU G 296 " ideal model delta sigma weight residual 112.89 107.50 5.39 1.24e+00 6.50e-01 1.89e+01 angle pdb=" N LEU M 296 " pdb=" CA LEU M 296 " pdb=" C LEU M 296 " ideal model delta sigma weight residual 112.89 107.58 5.31 1.24e+00 6.50e-01 1.84e+01 angle pdb=" N LEU C 296 " pdb=" CA LEU C 296 " pdb=" C LEU C 296 " ideal model delta sigma weight residual 112.89 107.71 5.18 1.24e+00 6.50e-01 1.75e+01 ... (remaining 29453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 12514 33.64 - 67.28: 281 67.28 - 100.92: 16 100.92 - 134.56: 5 134.56 - 168.20: 6 Dihedral angle restraints: 12822 sinusoidal: 4956 harmonic: 7866 Sorted by residual: dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual 300.00 131.80 168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP A1002 " pdb=" O5' ADP A1002 " pdb=" PA ADP A1002 " pdb=" O2A ADP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 100.80 -160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP L 301 " pdb=" O5' ADP L 301 " pdb=" PA ADP L 301 " pdb=" O2A ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 100.02 -160.01 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 12819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3354 0.108 - 0.215: 188 0.215 - 0.322: 2 0.322 - 0.430: 0 0.430 - 0.537: 4 Chirality restraints: 3548 Sorted by residual: chirality pdb=" CA THR G 288 " pdb=" N THR G 288 " pdb=" C THR G 288 " pdb=" CB THR G 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" CA THR M 288 " pdb=" N THR M 288 " pdb=" C THR M 288 " pdb=" CB THR M 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" CA THR C 288 " pdb=" N THR C 288 " pdb=" C THR C 288 " pdb=" CB THR C 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.09e+00 ... (remaining 3545 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 92 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C MET M 92 " 0.041 2.00e-02 2.50e+03 pdb=" O MET M 92 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN M 93 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 92 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET G 92 " -0.041 2.00e-02 2.50e+03 pdb=" O MET G 92 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN G 93 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 122 " 0.032 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 123 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.026 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 141 2.56 - 3.21: 19848 3.21 - 3.85: 43220 3.85 - 4.50: 61039 4.50 - 5.14: 95532 Nonbonded interactions: 219780 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O3B ADP A1002 " model vdw 1.919 2.170 nonbonded pdb=" OD1 ASN H 82 " pdb=" ND2 ASN B 82 " model vdw 1.954 2.520 nonbonded pdb=" O2B ADP L 301 " pdb="MG MG L 302 " model vdw 1.977 2.170 nonbonded pdb=" O3B ADP B1001 " pdb="MG MG B1002 " model vdw 1.984 2.170 nonbonded pdb=" O3B ADP E 301 " pdb="MG MG E 302 " model vdw 1.988 2.170 ... (remaining 219775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 137) selection = (chain 'B' and resid 6 through 137) selection = (chain 'D' and resid 6 through 137) selection = (chain 'E' and resid 6 through 137) selection = (chain 'F' and resid 6 through 137) selection = (chain 'H' and resid 6 through 137) selection = (chain 'J' and resid 6 through 137) selection = (chain 'L' and resid 6 through 137) } ncs_group { reference = (chain 'C' and (resid 21 through 350 or resid 352 through 455 or resid 601)) selection = (chain 'G' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 455 or resid 501)) selection = (chain 'I' and (resid 21 through 350 or resid 352 through 455 or resid 601)) selection = (chain 'M' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 455 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 62.740 Find NCS groups from input model: 1.710 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.256 21728 Z= 0.364 Angle : 0.800 10.803 29458 Z= 0.497 Chirality : 0.053 0.537 3548 Planarity : 0.004 0.047 3608 Dihedral : 14.454 168.201 7742 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.27 % Favored : 97.51 % Rotamer: Outliers : 0.89 % Allowed : 1.16 % Favored : 97.95 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.15), residues: 2736 helix: 1.46 (0.12), residues: 1760 sheet: 1.61 (0.28), residues: 282 loop : -0.34 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 337 HIS 0.005 0.001 HIS G 345 PHE 0.026 0.001 PHE I 210 TYR 0.014 0.002 TYR F 70 ARG 0.005 0.000 ARG J 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 772 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7987 (tp30) cc_final: 0.7136 (tp30) REVERT: H 127 MET cc_start: 0.8929 (tpt) cc_final: 0.8175 (tpp) REVERT: D 23 GLU cc_start: 0.7866 (tp30) cc_final: 0.7666 (tp30) REVERT: D 110 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8190 (mtm180) REVERT: D 133 ARG cc_start: 0.7368 (mtt90) cc_final: 0.7025 (mtm-85) REVERT: E 29 SER cc_start: 0.7901 (m) cc_final: 0.7690 (p) REVERT: E 96 VAL cc_start: 0.8462 (t) cc_final: 0.8256 (t) REVERT: E 127 MET cc_start: 0.8340 (mmm) cc_final: 0.8095 (mmm) REVERT: I 92 MET cc_start: 0.7593 (ptt) cc_final: 0.7332 (ptt) REVERT: I 387 PHE cc_start: 0.7513 (t80) cc_final: 0.7042 (t80) REVERT: I 389 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7597 (ttmt) REVERT: I 420 ILE cc_start: 0.7474 (mt) cc_final: 0.7060 (mt) REVERT: I 447 TYR cc_start: 0.8776 (m-80) cc_final: 0.8502 (m-80) REVERT: A 23 GLU cc_start: 0.7777 (tp30) cc_final: 0.7219 (tp30) REVERT: A 133 ARG cc_start: 0.7424 (mtt90) cc_final: 0.7215 (mtm180) REVERT: B 23 GLU cc_start: 0.7382 (tp30) cc_final: 0.7021 (tp30) REVERT: B 127 MET cc_start: 0.9040 (tpt) cc_final: 0.8791 (tpp) REVERT: B 133 ARG cc_start: 0.7327 (mtt90) cc_final: 0.7040 (mtm-85) REVERT: J 122 MET cc_start: 0.7679 (mtp) cc_final: 0.6736 (mtm) REVERT: J 126 ASP cc_start: 0.7860 (m-30) cc_final: 0.7548 (m-30) REVERT: L 98 SER cc_start: 0.7307 (p) cc_final: 0.6760 (p) REVERT: L 122 MET cc_start: 0.7622 (mtp) cc_final: 0.6897 (mtm) REVERT: M 76 THR cc_start: 0.7360 (m) cc_final: 0.7095 (m) REVERT: M 93 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6901 (tp-100) REVERT: M 298 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: M 420 ILE cc_start: 0.7844 (mt) cc_final: 0.7505 (mt) REVERT: M 447 TYR cc_start: 0.8739 (m-80) cc_final: 0.8474 (m-80) REVERT: C 92 MET cc_start: 0.7635 (ptt) cc_final: 0.7375 (ptt) REVERT: C 93 GLN cc_start: 0.7529 (tp-100) cc_final: 0.7235 (tp-100) REVERT: C 108 TYR cc_start: 0.7607 (t80) cc_final: 0.7366 (t80) REVERT: C 136 ARG cc_start: 0.5225 (ttt180) cc_final: 0.4998 (tpt170) REVERT: C 387 PHE cc_start: 0.7615 (t80) cc_final: 0.7195 (t80) REVERT: C 389 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7639 (ttmt) REVERT: C 420 ILE cc_start: 0.7642 (mt) cc_final: 0.7243 (mt) REVERT: C 447 TYR cc_start: 0.8841 (m-80) cc_final: 0.8597 (m-80) REVERT: C 449 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6444 (mt-10) REVERT: G 93 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6857 (tp-100) REVERT: G 277 LEU cc_start: 0.8276 (tp) cc_final: 0.7858 (tt) REVERT: G 298 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: G 400 THR cc_start: 0.8878 (m) cc_final: 0.8576 (m) REVERT: G 420 ILE cc_start: 0.7862 (mt) cc_final: 0.7609 (mt) REVERT: G 447 TYR cc_start: 0.8782 (m-80) cc_final: 0.8549 (m-80) outliers start: 20 outliers final: 2 residues processed: 782 average time/residue: 0.3437 time to fit residues: 400.2163 Evaluate side-chains 481 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 475 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN I 78 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN I 301 GLN J 30 GLN J 108 GLN J 113 GLN M 262 HIS C 78 GLN C 282 GLN C 301 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21728 Z= 0.222 Angle : 0.650 7.244 29458 Z= 0.320 Chirality : 0.044 0.160 3548 Planarity : 0.004 0.035 3608 Dihedral : 9.569 178.293 3010 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.65 % Favored : 98.28 % Rotamer: Outliers : 2.27 % Allowed : 11.53 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.16), residues: 2736 helix: 2.17 (0.12), residues: 1792 sheet: 1.73 (0.28), residues: 282 loop : -0.07 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 257 HIS 0.008 0.001 HIS G 79 PHE 0.038 0.002 PHE C 210 TYR 0.010 0.001 TYR I 158 ARG 0.007 0.001 ARG I 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 510 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7810 (tp30) cc_final: 0.6974 (tp30) REVERT: H 134 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8162 (mtpt) REVERT: D 23 GLU cc_start: 0.7679 (tp30) cc_final: 0.7437 (tp30) REVERT: D 107 PHE cc_start: 0.8615 (m-80) cc_final: 0.8395 (m-80) REVERT: D 133 ARG cc_start: 0.7167 (mtt90) cc_final: 0.6841 (mtm-85) REVERT: E 23 GLU cc_start: 0.7654 (tp30) cc_final: 0.7450 (tp30) REVERT: E 72 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6361 (mmm) REVERT: E 127 MET cc_start: 0.8413 (mmm) cc_final: 0.8135 (mmm) REVERT: I 241 MET cc_start: 0.7853 (mmt) cc_final: 0.7561 (mmt) REVERT: I 387 PHE cc_start: 0.7518 (t80) cc_final: 0.6804 (t80) REVERT: I 389 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7577 (ttmt) REVERT: I 420 ILE cc_start: 0.7911 (mt) cc_final: 0.7489 (mt) REVERT: I 447 TYR cc_start: 0.8897 (m-80) cc_final: 0.8629 (m-80) REVERT: A 23 GLU cc_start: 0.7559 (tp30) cc_final: 0.7158 (tp30) REVERT: A 74 MET cc_start: 0.7642 (tpp) cc_final: 0.7427 (tpp) REVERT: A 133 ARG cc_start: 0.7315 (mtt90) cc_final: 0.6927 (mmm-85) REVERT: B 133 ARG cc_start: 0.7303 (mtt90) cc_final: 0.7035 (mtm-85) REVERT: J 25 GLN cc_start: 0.7310 (pt0) cc_final: 0.7057 (tt0) REVERT: L 23 GLU cc_start: 0.7614 (tp30) cc_final: 0.7411 (tp30) REVERT: L 98 SER cc_start: 0.7768 (p) cc_final: 0.7557 (p) REVERT: M 99 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: M 241 MET cc_start: 0.7837 (mmt) cc_final: 0.7594 (mmt) REVERT: M 298 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7217 (mt0) REVERT: M 387 PHE cc_start: 0.7863 (t80) cc_final: 0.6847 (t80) REVERT: M 401 VAL cc_start: 0.8558 (t) cc_final: 0.8322 (t) REVERT: M 420 ILE cc_start: 0.8230 (mt) cc_final: 0.7877 (mt) REVERT: M 447 TYR cc_start: 0.8858 (m-80) cc_final: 0.8622 (m-80) REVERT: C 241 MET cc_start: 0.7878 (mmt) cc_final: 0.7649 (mmt) REVERT: C 387 PHE cc_start: 0.7565 (t80) cc_final: 0.6845 (t80) REVERT: C 389 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7542 (ttmt) REVERT: C 420 ILE cc_start: 0.8007 (mt) cc_final: 0.7576 (mt) REVERT: C 447 TYR cc_start: 0.8917 (m-80) cc_final: 0.8696 (m-80) REVERT: G 99 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: G 193 MET cc_start: 0.8040 (mmt) cc_final: 0.7836 (mmt) REVERT: G 241 MET cc_start: 0.7842 (mmt) cc_final: 0.7599 (mmt) REVERT: G 387 PHE cc_start: 0.7780 (t80) cc_final: 0.6848 (t80) REVERT: G 401 VAL cc_start: 0.8612 (t) cc_final: 0.8384 (t) REVERT: G 420 ILE cc_start: 0.8315 (mt) cc_final: 0.8037 (mt) REVERT: G 447 TYR cc_start: 0.8883 (m-80) cc_final: 0.8640 (m-80) outliers start: 51 outliers final: 31 residues processed: 543 average time/residue: 0.3057 time to fit residues: 258.3344 Evaluate side-chains 472 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 437 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 0.0170 chunk 76 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 198 optimal weight: 7.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN A 50 GLN M 93 GLN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN G 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21728 Z= 0.173 Angle : 0.602 8.972 29458 Z= 0.291 Chirality : 0.042 0.157 3548 Planarity : 0.003 0.036 3608 Dihedral : 8.563 173.522 3001 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.68 % Favored : 98.24 % Rotamer: Outliers : 2.49 % Allowed : 13.40 % Favored : 84.11 % 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: 2.62 (0.16), residues: 2736 helix: 2.44 (0.12), residues: 1766 sheet: 1.81 (0.28), residues: 282 loop : -0.20 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 257 HIS 0.004 0.001 HIS G 79 PHE 0.028 0.001 PHE I 210 TYR 0.009 0.001 TYR C 158 ARG 0.003 0.000 ARG G 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 472 time to evaluate : 2.041 Fit side-chains REVERT: H 23 GLU cc_start: 0.7806 (tp30) cc_final: 0.7072 (tp30) REVERT: H 134 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8276 (mtpt) REVERT: D 23 GLU cc_start: 0.7672 (tp30) cc_final: 0.7131 (tp30) REVERT: D 133 ARG cc_start: 0.7199 (mtt90) cc_final: 0.6937 (mtm-85) REVERT: E 23 GLU cc_start: 0.7619 (tp30) cc_final: 0.7370 (tp30) REVERT: E 126 ASP cc_start: 0.7676 (m-30) cc_final: 0.7052 (m-30) REVERT: F 114 LYS cc_start: 0.8675 (mttm) cc_final: 0.8351 (mttt) REVERT: I 89 MET cc_start: 0.7788 (ptp) cc_final: 0.7576 (ptp) REVERT: I 241 MET cc_start: 0.8002 (mmt) cc_final: 0.7712 (mmt) REVERT: I 389 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7602 (ttmt) REVERT: I 420 ILE cc_start: 0.7962 (mt) cc_final: 0.7577 (mt) REVERT: I 447 TYR cc_start: 0.8911 (m-80) cc_final: 0.8683 (m-80) REVERT: A 23 GLU cc_start: 0.7500 (tp30) cc_final: 0.7225 (tp30) REVERT: A 133 ARG cc_start: 0.7312 (mtt90) cc_final: 0.6944 (mmm-85) REVERT: B 23 GLU cc_start: 0.7610 (tp30) cc_final: 0.7405 (tp30) REVERT: B 133 ARG cc_start: 0.7224 (mtt90) cc_final: 0.7008 (mmm-85) REVERT: J 22 LYS cc_start: 0.8334 (mttt) cc_final: 0.8129 (mttt) REVERT: J 25 GLN cc_start: 0.7400 (pt0) cc_final: 0.7125 (tt0) REVERT: L 23 GLU cc_start: 0.7631 (tp30) cc_final: 0.7402 (tp30) REVERT: L 72 MET cc_start: 0.6630 (mmm) cc_final: 0.6214 (mmt) REVERT: L 98 SER cc_start: 0.7804 (p) cc_final: 0.6672 (p) REVERT: M 241 MET cc_start: 0.7880 (mmt) cc_final: 0.7576 (mmt) REVERT: M 400 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8777 (m) REVERT: M 410 GLU cc_start: 0.6777 (pp20) cc_final: 0.6351 (pt0) REVERT: M 420 ILE cc_start: 0.8228 (mt) cc_final: 0.8022 (mt) REVERT: M 447 TYR cc_start: 0.8931 (m-80) cc_final: 0.8689 (m-80) REVERT: C 241 MET cc_start: 0.7946 (mmt) cc_final: 0.7670 (mmt) REVERT: C 299 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: C 389 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7603 (ttmt) REVERT: C 420 ILE cc_start: 0.8045 (mt) cc_final: 0.7668 (mt) REVERT: C 447 TYR cc_start: 0.8945 (m-80) cc_final: 0.8730 (m-80) REVERT: G 241 MET cc_start: 0.7919 (mmt) cc_final: 0.7655 (mmt) REVERT: G 292 ASN cc_start: 0.6819 (p0) cc_final: 0.6244 (p0) REVERT: G 400 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8701 (m) REVERT: G 410 GLU cc_start: 0.6891 (pp20) cc_final: 0.6473 (pt0) outliers start: 56 outliers final: 33 residues processed: 506 average time/residue: 0.3000 time to fit residues: 241.8868 Evaluate side-chains 475 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 439 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 58 HIS Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 400 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 262 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21728 Z= 0.243 Angle : 0.621 8.114 29458 Z= 0.301 Chirality : 0.044 0.226 3548 Planarity : 0.003 0.034 3608 Dihedral : 7.903 174.462 2998 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.63 % Allowed : 14.29 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.16), residues: 2736 helix: 2.42 (0.12), residues: 1784 sheet: 1.61 (0.29), residues: 282 loop : -0.20 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 257 HIS 0.005 0.001 HIS B 58 PHE 0.032 0.002 PHE I 210 TYR 0.019 0.002 TYR C 158 ARG 0.003 0.000 ARG M 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 489 time to evaluate : 2.393 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7890 (tp30) cc_final: 0.7233 (tp30) REVERT: H 134 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8231 (mtpt) REVERT: D 23 GLU cc_start: 0.7757 (tp30) cc_final: 0.7508 (tp30) REVERT: D 40 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7621 (mtt180) REVERT: D 133 ARG cc_start: 0.7221 (mtt90) cc_final: 0.6930 (mtm-85) REVERT: E 126 ASP cc_start: 0.7980 (m-30) cc_final: 0.7691 (m-30) REVERT: I 89 MET cc_start: 0.7860 (ptp) cc_final: 0.7626 (ptp) REVERT: I 228 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6893 (ptp-110) REVERT: I 241 MET cc_start: 0.8175 (mmt) cc_final: 0.7873 (mmt) REVERT: I 292 ASN cc_start: 0.6997 (p0) cc_final: 0.6519 (p0) REVERT: I 389 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7519 (ttmt) REVERT: I 420 ILE cc_start: 0.8484 (mt) cc_final: 0.8207 (mt) REVERT: A 23 GLU cc_start: 0.7674 (tp30) cc_final: 0.7285 (tp30) REVERT: A 42 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8144 (mtpt) REVERT: A 101 VAL cc_start: 0.9432 (t) cc_final: 0.9207 (p) REVERT: A 133 ARG cc_start: 0.7470 (mtt90) cc_final: 0.7166 (mtm-85) REVERT: B 107 PHE cc_start: 0.8500 (m-80) cc_final: 0.8298 (m-10) REVERT: B 133 ARG cc_start: 0.7261 (mtt90) cc_final: 0.6973 (mtm-85) REVERT: J 23 GLU cc_start: 0.7864 (tp30) cc_final: 0.7594 (tp30) REVERT: J 25 GLN cc_start: 0.7530 (pt0) cc_final: 0.7217 (tt0) REVERT: L 23 GLU cc_start: 0.7656 (tp30) cc_final: 0.7416 (tp30) REVERT: L 36 ILE cc_start: 0.8687 (tp) cc_final: 0.8273 (tp) REVERT: L 72 MET cc_start: 0.6719 (mmm) cc_final: 0.6223 (mmt) REVERT: L 98 SER cc_start: 0.8090 (p) cc_final: 0.6961 (p) REVERT: M 241 MET cc_start: 0.8108 (mmt) cc_final: 0.7744 (mmt) REVERT: M 292 ASN cc_start: 0.6986 (p0) cc_final: 0.6485 (p0) REVERT: C 292 ASN cc_start: 0.6889 (p0) cc_final: 0.6430 (p0) REVERT: C 299 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: C 389 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7527 (ttmt) REVERT: C 420 ILE cc_start: 0.8617 (mt) cc_final: 0.8367 (mt) REVERT: G 292 ASN cc_start: 0.6904 (p0) cc_final: 0.6663 (p0) outliers start: 59 outliers final: 46 residues processed: 532 average time/residue: 0.3006 time to fit residues: 253.1207 Evaluate side-chains 503 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 455 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 58 HIS Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 224 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 ASN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 HIS ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 345 HIS ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 HIS ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21728 Z= 0.285 Angle : 0.645 9.380 29458 Z= 0.315 Chirality : 0.045 0.221 3548 Planarity : 0.003 0.034 3608 Dihedral : 7.542 173.784 2998 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.43 % Allowed : 16.12 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.16), residues: 2736 helix: 2.36 (0.12), residues: 1782 sheet: 1.39 (0.29), residues: 282 loop : -0.26 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 100 HIS 0.005 0.001 HIS D 58 PHE 0.033 0.002 PHE M 217 TYR 0.027 0.002 TYR C 158 ARG 0.011 0.001 ARG G 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 500 time to evaluate : 2.420 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7940 (tp30) cc_final: 0.7376 (tp30) REVERT: H 134 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8304 (mtpt) REVERT: D 40 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7914 (mtt180) REVERT: D 133 ARG cc_start: 0.7264 (mtt90) cc_final: 0.6878 (mtm-85) REVERT: E 113 GLN cc_start: 0.7390 (tm-30) cc_final: 0.7132 (tm-30) REVERT: E 126 ASP cc_start: 0.8076 (m-30) cc_final: 0.7301 (m-30) REVERT: F 58 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.7061 (t70) REVERT: F 126 ASP cc_start: 0.8056 (m-30) cc_final: 0.7326 (m-30) REVERT: I 292 ASN cc_start: 0.6995 (p0) cc_final: 0.6613 (p0) REVERT: I 299 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: I 389 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7642 (ttmt) REVERT: A 23 GLU cc_start: 0.7644 (tp30) cc_final: 0.7238 (tp30) REVERT: A 133 ARG cc_start: 0.7462 (mtt90) cc_final: 0.7175 (mtm-85) REVERT: B 133 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6965 (mtm-85) REVERT: J 15 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7811 (mtm180) REVERT: J 126 ASP cc_start: 0.7965 (m-30) cc_final: 0.7446 (m-30) REVERT: L 23 GLU cc_start: 0.7751 (tp30) cc_final: 0.7522 (tp30) REVERT: L 72 MET cc_start: 0.6762 (mmm) cc_final: 0.6416 (mmt) REVERT: L 98 SER cc_start: 0.7989 (p) cc_final: 0.7555 (t) REVERT: M 199 ASP cc_start: 0.6904 (t0) cc_final: 0.6700 (t0) REVERT: M 241 MET cc_start: 0.7945 (mmt) cc_final: 0.7672 (mmt) REVERT: M 292 ASN cc_start: 0.6808 (p0) cc_final: 0.6537 (p0) REVERT: M 343 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8376 (mtpt) REVERT: M 423 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7127 (mtm) REVERT: C 292 ASN cc_start: 0.7050 (p0) cc_final: 0.6698 (p0) REVERT: C 299 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: C 304 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8682 (mp) REVERT: C 389 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7640 (ttmt) REVERT: G 343 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8388 (mtpt) REVERT: G 423 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7100 (mtm) outliers start: 77 outliers final: 57 residues processed: 549 average time/residue: 0.3121 time to fit residues: 268.2901 Evaluate side-chains 524 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 461 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 423 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN L 50 GLN ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21728 Z= 0.202 Angle : 0.603 8.315 29458 Z= 0.292 Chirality : 0.043 0.183 3548 Planarity : 0.003 0.034 3608 Dihedral : 7.291 173.630 2998 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.85 % Allowed : 18.88 % Favored : 78.27 % 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: 2736 helix: 2.46 (0.12), residues: 1780 sheet: 1.60 (0.30), residues: 274 loop : -0.40 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 166 HIS 0.004 0.001 HIS C 262 PHE 0.034 0.001 PHE G 217 TYR 0.028 0.001 TYR C 158 ARG 0.009 0.000 ARG M 427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 478 time to evaluate : 2.328 Fit side-chains REVERT: H 23 GLU cc_start: 0.7917 (tp30) cc_final: 0.7426 (tp30) REVERT: H 134 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8303 (mtpt) REVERT: D 40 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7898 (mtt180) REVERT: D 110 ARG cc_start: 0.8506 (mtm110) cc_final: 0.7922 (mtm110) REVERT: D 133 ARG cc_start: 0.7215 (mtt90) cc_final: 0.6843 (mtm-85) REVERT: E 113 GLN cc_start: 0.7349 (tm-30) cc_final: 0.7101 (tm-30) REVERT: E 126 ASP cc_start: 0.7994 (m-30) cc_final: 0.7700 (m-30) REVERT: F 82 ASN cc_start: 0.8409 (t0) cc_final: 0.8154 (t0) REVERT: F 126 ASP cc_start: 0.7964 (m-30) cc_final: 0.7668 (m-30) REVERT: I 241 MET cc_start: 0.8313 (tpp) cc_final: 0.8010 (mmt) REVERT: I 292 ASN cc_start: 0.6862 (p0) cc_final: 0.6565 (p0) REVERT: I 389 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7668 (ttmt) REVERT: A 23 GLU cc_start: 0.7594 (tp30) cc_final: 0.7220 (tp30) REVERT: A 101 VAL cc_start: 0.9409 (t) cc_final: 0.9193 (p) REVERT: A 133 ARG cc_start: 0.7423 (mtt90) cc_final: 0.7119 (mtm-85) REVERT: B 133 ARG cc_start: 0.7272 (mtt90) cc_final: 0.6935 (mtm-85) REVERT: J 113 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7220 (tm-30) REVERT: J 126 ASP cc_start: 0.7855 (m-30) cc_final: 0.7635 (m-30) REVERT: L 50 GLN cc_start: 0.7997 (tt0) cc_final: 0.7658 (tt0) REVERT: L 72 MET cc_start: 0.6716 (mmm) cc_final: 0.6357 (mmt) REVERT: L 98 SER cc_start: 0.8080 (p) cc_final: 0.7504 (t) REVERT: M 241 MET cc_start: 0.8086 (mmt) cc_final: 0.7769 (mmt) REVERT: M 292 ASN cc_start: 0.6814 (p0) cc_final: 0.6599 (p0) REVERT: M 343 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8339 (mtpt) REVERT: C 241 MET cc_start: 0.8374 (tpp) cc_final: 0.7969 (mmt) REVERT: C 292 ASN cc_start: 0.7062 (p0) cc_final: 0.6544 (p0) REVERT: C 299 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: C 304 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8534 (mp) REVERT: C 389 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7639 (ttmt) REVERT: G 35 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7452 (p) REVERT: G 292 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6893 (p0) REVERT: G 343 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8393 (mtpt) REVERT: G 423 MET cc_start: 0.7622 (mtm) cc_final: 0.7309 (mtm) outliers start: 64 outliers final: 49 residues processed: 526 average time/residue: 0.3369 time to fit residues: 280.8691 Evaluate side-chains 502 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 449 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 292 ASN Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 396 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 0.0980 chunk 146 optimal weight: 9.9990 chunk 262 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21728 Z= 0.248 Angle : 0.622 8.386 29458 Z= 0.303 Chirality : 0.044 0.172 3548 Planarity : 0.003 0.033 3608 Dihedral : 7.156 170.569 2998 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.98 % Allowed : 19.59 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.16), residues: 2736 helix: 2.42 (0.12), residues: 1762 sheet: 1.56 (0.30), residues: 274 loop : -0.41 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 227 HIS 0.004 0.001 HIS G 176 PHE 0.029 0.002 PHE I 210 TYR 0.009 0.001 TYR G 447 ARG 0.009 0.000 ARG M 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 450 time to evaluate : 2.498 Fit side-chains REVERT: H 23 GLU cc_start: 0.7914 (tp30) cc_final: 0.7517 (tp30) REVERT: H 134 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8282 (mtpt) REVERT: D 40 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7936 (mtt180) REVERT: D 133 ARG cc_start: 0.7217 (mtt90) cc_final: 0.6840 (mtm-85) REVERT: E 50 GLN cc_start: 0.8055 (tt0) cc_final: 0.7848 (tt0) REVERT: E 126 ASP cc_start: 0.8032 (m-30) cc_final: 0.7689 (m-30) REVERT: F 82 ASN cc_start: 0.8455 (t0) cc_final: 0.8227 (t0) REVERT: F 126 ASP cc_start: 0.7932 (m-30) cc_final: 0.7608 (m-30) REVERT: I 194 MET cc_start: 0.6940 (mmm) cc_final: 0.6689 (mmt) REVERT: I 241 MET cc_start: 0.8344 (tpp) cc_final: 0.7991 (mmt) REVERT: I 292 ASN cc_start: 0.6848 (p0) cc_final: 0.6614 (p0) REVERT: I 389 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7625 (ttmt) REVERT: I 404 THR cc_start: 0.7860 (m) cc_final: 0.7649 (m) REVERT: A 101 VAL cc_start: 0.9397 (t) cc_final: 0.9196 (p) REVERT: A 110 ARG cc_start: 0.8818 (mtm-85) cc_final: 0.8482 (mtm180) REVERT: A 133 ARG cc_start: 0.7463 (mtt90) cc_final: 0.7242 (mtm-85) REVERT: B 133 ARG cc_start: 0.7270 (mtt90) cc_final: 0.6950 (mtm-85) REVERT: J 126 ASP cc_start: 0.7881 (m-30) cc_final: 0.7510 (m-30) REVERT: L 50 GLN cc_start: 0.7946 (tt0) cc_final: 0.7563 (tt0) REVERT: L 72 MET cc_start: 0.6841 (mmm) cc_final: 0.6510 (mmt) REVERT: L 98 SER cc_start: 0.8105 (p) cc_final: 0.7563 (t) REVERT: M 35 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7483 (p) REVERT: M 241 MET cc_start: 0.8096 (mmt) cc_final: 0.7791 (mmt) REVERT: M 292 ASN cc_start: 0.6840 (p0) cc_final: 0.6635 (p0) REVERT: M 343 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8414 (mtpt) REVERT: M 423 MET cc_start: 0.7670 (mtm) cc_final: 0.7327 (mtm) REVERT: C 241 MET cc_start: 0.8369 (tpp) cc_final: 0.8043 (mmt) REVERT: C 292 ASN cc_start: 0.7170 (p0) cc_final: 0.6697 (p0) REVERT: C 304 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8539 (mp) REVERT: C 389 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7662 (ttmt) REVERT: C 404 THR cc_start: 0.7932 (m) cc_final: 0.7717 (m) REVERT: G 35 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7569 (p) REVERT: G 423 MET cc_start: 0.7454 (mtm) cc_final: 0.7105 (mtm) outliers start: 67 outliers final: 57 residues processed: 501 average time/residue: 0.3062 time to fit residues: 240.4446 Evaluate side-chains 493 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 433 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 396 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 9.9990 chunk 104 optimal weight: 0.4980 chunk 156 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 166 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 129 optimal weight: 0.0270 chunk 24 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21728 Z= 0.199 Angle : 0.600 8.802 29458 Z= 0.292 Chirality : 0.043 0.170 3548 Planarity : 0.003 0.034 3608 Dihedral : 6.954 168.358 2998 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.98 % Allowed : 20.12 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.16), residues: 2736 helix: 2.47 (0.12), residues: 1756 sheet: 1.64 (0.30), residues: 274 loop : -0.49 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 227 HIS 0.005 0.001 HIS M 176 PHE 0.028 0.001 PHE I 210 TYR 0.027 0.001 TYR C 158 ARG 0.007 0.000 ARG G 427 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 451 time to evaluate : 2.360 Fit side-chains REVERT: H 23 GLU cc_start: 0.7869 (tp30) cc_final: 0.7370 (tp30) REVERT: H 110 ARG cc_start: 0.8596 (mtm110) cc_final: 0.8104 (mtm110) REVERT: H 134 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8289 (mtpt) REVERT: D 110 ARG cc_start: 0.8527 (mtm110) cc_final: 0.7909 (mtm110) REVERT: D 133 ARG cc_start: 0.7185 (mtt90) cc_final: 0.6828 (mtm-85) REVERT: E 126 ASP cc_start: 0.7986 (m-30) cc_final: 0.7635 (m-30) REVERT: F 126 ASP cc_start: 0.7935 (m-30) cc_final: 0.7635 (m-30) REVERT: I 241 MET cc_start: 0.8268 (tpp) cc_final: 0.7991 (mmt) REVERT: I 304 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8449 (mp) REVERT: I 389 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7484 (ptpt) REVERT: A 23 GLU cc_start: 0.7570 (tp30) cc_final: 0.7266 (tp30) REVERT: A 101 VAL cc_start: 0.9404 (t) cc_final: 0.9176 (p) REVERT: A 110 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8431 (mtm180) REVERT: A 133 ARG cc_start: 0.7435 (mtt90) cc_final: 0.7064 (mtm-85) REVERT: B 93 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7889 (mt-10) REVERT: B 133 ARG cc_start: 0.7252 (mtt90) cc_final: 0.6929 (mtm-85) REVERT: J 126 ASP cc_start: 0.7865 (m-30) cc_final: 0.7477 (m-30) REVERT: J 133 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7500 (mmm160) REVERT: L 50 GLN cc_start: 0.7795 (tt0) cc_final: 0.7438 (tt0) REVERT: L 72 MET cc_start: 0.6771 (mmm) cc_final: 0.6404 (mmt) REVERT: L 98 SER cc_start: 0.8140 (p) cc_final: 0.7478 (t) REVERT: M 241 MET cc_start: 0.8157 (mmt) cc_final: 0.7840 (mmt) REVERT: C 292 ASN cc_start: 0.7114 (p0) cc_final: 0.6732 (p0) REVERT: C 388 ASP cc_start: 0.7244 (p0) cc_final: 0.6878 (p0) REVERT: C 389 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7547 (ttmt) REVERT: C 404 THR cc_start: 0.7901 (m) cc_final: 0.7694 (m) outliers start: 67 outliers final: 56 residues processed: 503 average time/residue: 0.3109 time to fit residues: 243.2475 Evaluate side-chains 495 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 438 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 292 ASN Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 396 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 229 optimal weight: 0.3980 chunk 244 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 220 optimal weight: 0.7980 chunk 231 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN M 282 GLN M 292 ASN C 282 GLN ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21728 Z= 0.252 Angle : 0.638 9.441 29458 Z= 0.311 Chirality : 0.044 0.196 3548 Planarity : 0.003 0.037 3608 Dihedral : 6.980 163.454 2998 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.98 % Allowed : 20.21 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.16), residues: 2736 helix: 2.40 (0.12), residues: 1766 sheet: 1.62 (0.30), residues: 274 loop : -0.51 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 227 HIS 0.004 0.001 HIS G 176 PHE 0.028 0.002 PHE I 210 TYR 0.022 0.001 TYR C 158 ARG 0.009 0.000 ARG M 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 439 time to evaluate : 2.086 Fit side-chains REVERT: H 23 GLU cc_start: 0.7939 (tp30) cc_final: 0.7490 (tp30) REVERT: H 134 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8332 (mtpt) REVERT: D 133 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6835 (mtm-85) REVERT: E 126 ASP cc_start: 0.8070 (m-30) cc_final: 0.7733 (m-30) REVERT: F 35 ASP cc_start: 0.7648 (t70) cc_final: 0.7445 (t0) REVERT: F 74 MET cc_start: 0.8361 (tpp) cc_final: 0.8125 (tpt) REVERT: F 97 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7428 (mmtt) REVERT: F 126 ASP cc_start: 0.7992 (m-30) cc_final: 0.7689 (m-30) REVERT: I 30 LEU cc_start: 0.8265 (mm) cc_final: 0.8055 (pp) REVERT: I 198 ASN cc_start: 0.7485 (m110) cc_final: 0.7258 (p0) REVERT: I 241 MET cc_start: 0.8270 (tpp) cc_final: 0.7875 (mmt) REVERT: I 304 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8428 (mp) REVERT: I 389 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7479 (ptpt) REVERT: A 133 ARG cc_start: 0.7432 (mtt90) cc_final: 0.7162 (mtm-85) REVERT: B 133 ARG cc_start: 0.7277 (mtt90) cc_final: 0.6947 (mtm-85) REVERT: J 126 ASP cc_start: 0.7963 (m-30) cc_final: 0.7571 (m-30) REVERT: J 133 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7488 (mmm160) REVERT: L 50 GLN cc_start: 0.7804 (tt0) cc_final: 0.7447 (tt0) REVERT: L 72 MET cc_start: 0.6843 (mmm) cc_final: 0.6492 (mmt) REVERT: L 98 SER cc_start: 0.8201 (p) cc_final: 0.7600 (t) REVERT: M 139 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7364 (ttmt) REVERT: M 241 MET cc_start: 0.8186 (mmt) cc_final: 0.7859 (mmt) REVERT: C 24 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: C 292 ASN cc_start: 0.7122 (p0) cc_final: 0.6740 (p0) REVERT: C 389 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7681 (ttmt) outliers start: 67 outliers final: 58 residues processed: 491 average time/residue: 0.3048 time to fit residues: 234.8602 Evaluate side-chains 490 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 430 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 292 ASN Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 292 ASN Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 396 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 ASN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN M 282 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 21728 Z= 0.285 Angle : 0.832 59.199 29458 Z= 0.463 Chirality : 0.045 0.496 3548 Planarity : 0.004 0.118 3608 Dihedral : 6.993 163.358 2998 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.85 % Allowed : 20.39 % Favored : 76.76 % Cbeta Deviations : 0.08 % 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: 2.44 (0.16), residues: 2736 helix: 2.41 (0.12), residues: 1766 sheet: 1.61 (0.30), residues: 274 loop : -0.52 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 227 HIS 0.004 0.001 HIS G 176 PHE 0.028 0.002 PHE I 210 TYR 0.019 0.001 TYR C 158 ARG 0.008 0.000 ARG M 427 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 430 time to evaluate : 2.444 Fit side-chains REVERT: H 23 GLU cc_start: 0.7938 (tp30) cc_final: 0.7486 (tp30) REVERT: H 134 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8330 (mtpt) REVERT: D 133 ARG cc_start: 0.7195 (mtt90) cc_final: 0.6823 (mtm-85) REVERT: E 126 ASP cc_start: 0.8065 (m-30) cc_final: 0.7685 (m-30) REVERT: F 35 ASP cc_start: 0.7648 (t70) cc_final: 0.7442 (t0) REVERT: F 74 MET cc_start: 0.8360 (tpp) cc_final: 0.8123 (tpt) REVERT: F 97 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7430 (mmtt) REVERT: F 126 ASP cc_start: 0.7918 (m-30) cc_final: 0.7636 (m-30) REVERT: I 198 ASN cc_start: 0.7481 (m110) cc_final: 0.7255 (p0) REVERT: I 241 MET cc_start: 0.8294 (tpp) cc_final: 0.7903 (mmt) REVERT: I 304 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8438 (mp) REVERT: I 389 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7475 (ptpt) REVERT: A 110 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8456 (mtm180) REVERT: A 133 ARG cc_start: 0.7419 (mtt90) cc_final: 0.7156 (mtm-85) REVERT: B 133 ARG cc_start: 0.7264 (mtt90) cc_final: 0.6943 (mtm-85) REVERT: J 126 ASP cc_start: 0.7939 (m-30) cc_final: 0.7565 (m-30) REVERT: J 133 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7486 (mmm160) REVERT: L 50 GLN cc_start: 0.7802 (tt0) cc_final: 0.7445 (tt0) REVERT: L 72 MET cc_start: 0.6838 (mmm) cc_final: 0.6482 (mmt) REVERT: L 98 SER cc_start: 0.8199 (p) cc_final: 0.7589 (t) REVERT: M 139 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7404 (ttmt) REVERT: M 241 MET cc_start: 0.8120 (mmt) cc_final: 0.7786 (mmt) REVERT: C 24 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: C 292 ASN cc_start: 0.7122 (p0) cc_final: 0.6714 (p0) REVERT: C 304 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 389 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7679 (ttmt) outliers start: 64 outliers final: 59 residues processed: 479 average time/residue: 0.3062 time to fit residues: 230.3893 Evaluate side-chains 489 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 427 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 282 GLN Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 396 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 3.9990 chunk 229 optimal weight: 0.1980 chunk 66 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 221 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN M 282 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114514 restraints weight = 38070.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118860 restraints weight = 18062.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121778 restraints weight = 10809.293| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 21728 Z= 0.260 Angle : 0.900 59.025 29458 Z= 0.520 Chirality : 0.046 0.781 3548 Planarity : 0.004 0.122 3608 Dihedral : 7.001 163.324 2998 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.85 % Allowed : 20.39 % Favored : 76.76 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.16), residues: 2736 helix: 2.40 (0.12), residues: 1766 sheet: 1.61 (0.30), residues: 274 loop : -0.52 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 227 HIS 0.004 0.001 HIS G 176 PHE 0.028 0.002 PHE I 210 TYR 0.017 0.001 TYR C 158 ARG 0.008 0.000 ARG M 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4938.76 seconds wall clock time: 88 minutes 49.73 seconds (5329.73 seconds total)