Starting phenix.real_space_refine on Fri Mar 15 06:02:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/03_2024/7pch_13320_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/03_2024/7pch_13320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/03_2024/7pch_13320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/03_2024/7pch_13320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/03_2024/7pch_13320_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/03_2024/7pch_13320_updated.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 32 5.16 5 C 6608 2.51 5 N 1734 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Conformer: "B" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} bond proxies already assigned to first conformer: 1113 Chain: "E" Number of atoms: 2830 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2800 Classifications: {'peptide': 340} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 327} Conformer: "B" Number of residues, atoms: 340, 2800 Classifications: {'peptide': 340} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 327} bond proxies already assigned to first conformer: 2822 Chain: "C" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "D" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Conformer: "B" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} bond proxies already assigned to first conformer: 1113 Chain: "F" Number of atoms: 2830 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2800 Classifications: {'peptide': 340} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 327} Conformer: "B" Number of residues, atoms: 340, 2800 Classifications: {'peptide': 340} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 327} bond proxies already assigned to first conformer: 2822 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N ALYS B 61 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 61 " occ=0.50 residue: pdb=" N ALYS B 65 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 65 " occ=0.50 residue: pdb=" N ALYS B 82 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 82 " occ=0.50 residue: pdb=" N AGLU B 101 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 101 " occ=0.50 residue: pdb=" N ALYS E 141 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 141 " occ=0.50 residue: pdb=" N ALYS E 210 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 210 " occ=0.50 residue: pdb=" N ATYR E 214 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 214 " occ=0.50 residue: pdb=" N ALYS D 61 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 61 " occ=0.50 residue: pdb=" N ALYS D 65 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 65 " occ=0.50 residue: pdb=" N ALYS D 82 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 82 " occ=0.50 residue: pdb=" N AGLU D 101 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 101 " occ=0.50 residue: pdb=" N ALYS F 141 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS F 141 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 9.93, per 1000 atoms: 0.92 Number of scatterers: 10798 At special positions: 0 Unit cell: (101.06, 132.356, 93.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 32 16.00 O 2420 8.00 N 1734 7.00 C 6608 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 3.5 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 10 sheets defined 49.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 removed outlier: 6.134A pdb=" N ALA A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 53 through 71 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.856A pdb=" N MET A 76 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Proline residue: A 77 - end of helix No H-bonds generated for 'chain 'A' and resid 73 through 79' Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 95 through 112 removed outlier: 3.582A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 138 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.722A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 4.197A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 58 through 76 removed outlier: 3.645A pdb=" N LYS B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 5.334A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.536A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLU B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 141 Processing helix chain 'E' and resid 129 through 134 removed outlier: 4.187A pdb=" N LYS E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'E' and resid 270 through 284 Proline residue: E 281 - end of helix Processing helix chain 'E' and resid 288 through 299 Processing helix chain 'E' and resid 304 through 331 removed outlier: 4.183A pdb=" N ALA E 308 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 Processing helix chain 'E' and resid 451 through 462 removed outlier: 3.673A pdb=" N LYS E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 35 removed outlier: 6.134A pdb=" N ALA C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 53 through 71 Processing helix chain 'C' and resid 73 through 79 removed outlier: 3.856A pdb=" N MET C 76 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Proline residue: C 77 - end of helix No H-bonds generated for 'chain 'C' and resid 73 through 79' Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 95 through 112 removed outlier: 3.582A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 138 Processing helix chain 'D' and resid 5 through 17 removed outlier: 3.722A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 removed outlier: 4.197A pdb=" N GLY D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLY D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 58 through 76 removed outlier: 3.645A pdb=" N LYS D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 5.334A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.536A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS D 120 " --> pdb=" O HIS D 116 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLU D 121 " --> pdb=" O HIS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 141 Processing helix chain 'F' and resid 129 through 134 removed outlier: 4.187A pdb=" N LYS F 134 " --> pdb=" O ARG F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 Processing helix chain 'F' and resid 192 through 194 No H-bonds generated for 'chain 'F' and resid 192 through 194' Processing helix chain 'F' and resid 270 through 284 Proline residue: F 281 - end of helix Processing helix chain 'F' and resid 288 through 299 Processing helix chain 'F' and resid 304 through 331 removed outlier: 4.183A pdb=" N ALA F 308 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU F 309 " --> pdb=" O LYS F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 366 Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.673A pdb=" N LYS F 456 " --> pdb=" O GLU F 452 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 148 through 151 removed outlier: 3.610A pdb=" N ALA E 174 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG E 224 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU E 211 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N SER E 226 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 209 " --> pdb=" O SER E 226 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 153 through 156 Processing sheet with id= C, first strand: chain 'E' and resid 238 through 242 removed outlier: 3.516A pdb=" N SER E 238 " --> pdb=" O TYR E 249 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 344 through 348 removed outlier: 3.854A pdb=" N ASP E 344 " --> pdb=" O MET E 375 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 375 " --> pdb=" O ASP E 344 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE E 371 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER E 406 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE E 417 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR E 404 " --> pdb=" O ILE E 417 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 350 through 353 removed outlier: 6.246A pdb=" N HIS E 434 " --> pdb=" O TRP E 392 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TRP E 392 " --> pdb=" O HIS E 434 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 148 through 151 removed outlier: 3.610A pdb=" N ALA F 174 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG F 224 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU F 211 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N SER F 226 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE F 209 " --> pdb=" O SER F 226 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 153 through 156 Processing sheet with id= H, first strand: chain 'F' and resid 238 through 242 removed outlier: 3.516A pdb=" N SER F 238 " --> pdb=" O TYR F 249 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 344 through 348 removed outlier: 3.854A pdb=" N ASP F 344 " --> pdb=" O MET F 375 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET F 375 " --> pdb=" O ASP F 344 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE F 371 " --> pdb=" O THR F 348 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER F 406 " --> pdb=" O THR F 415 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE F 417 " --> pdb=" O THR F 404 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR F 404 " --> pdb=" O ILE F 417 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 350 through 353 removed outlier: 6.246A pdb=" N HIS F 434 " --> pdb=" O TRP F 392 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TRP F 392 " --> pdb=" O HIS F 434 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1528 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: 3.34 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3334 1.36 - 1.54: 6968 1.54 - 1.72: 184 1.72 - 1.90: 58 1.90 - 2.08: 16 Bond restraints: 10560 Sorted by residual: bond pdb=" C LEU B 88 " pdb=" O LEU B 88 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.19e-02 7.06e+03 2.61e+01 bond pdb=" C LEU D 88 " pdb=" O LEU D 88 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.19e-02 7.06e+03 2.61e+01 bond pdb=" CA SER D 89 " pdb=" CB SER D 89 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.55e-02 4.16e+03 2.13e+01 bond pdb=" CA SER B 89 " pdb=" CB SER B 89 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.55e-02 4.16e+03 2.13e+01 bond pdb=" C ARG F 447 " pdb=" O ARG F 447 " ideal model delta sigma weight residual 1.236 1.183 0.052 1.22e-02 6.72e+03 1.84e+01 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 87.55 - 105.22: 252 105.22 - 122.90: 12490 122.90 - 140.57: 1594 140.57 - 158.24: 0 158.24 - 175.91: 8 Bond angle restraints: 14344 Sorted by residual: angle pdb=" N HIS E 143 " pdb=" CA HIS E 143 " pdb=" C HIS E 143 " ideal model delta sigma weight residual 113.15 105.67 7.48 1.19e+00 7.06e-01 3.95e+01 angle pdb=" N HIS F 143 " pdb=" CA HIS F 143 " pdb=" C HIS F 143 " ideal model delta sigma weight residual 113.15 105.67 7.48 1.19e+00 7.06e-01 3.95e+01 angle pdb=" N SER E 213 " pdb=" CA SER E 213 " pdb=" C SER E 213 " ideal model delta sigma weight residual 108.99 117.44 -8.45 1.57e+00 4.06e-01 2.90e+01 angle pdb=" N SER F 213 " pdb=" CA SER F 213 " pdb=" C SER F 213 " ideal model delta sigma weight residual 108.99 117.44 -8.45 1.57e+00 4.06e-01 2.90e+01 angle pdb=" CA GLN D 127 " pdb=" C GLN D 127 " pdb=" O GLN D 127 " ideal model delta sigma weight residual 120.55 115.29 5.26 1.06e+00 8.90e-01 2.46e+01 ... (remaining 14339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5784 17.57 - 35.14: 398 35.14 - 52.70: 94 52.70 - 70.27: 26 70.27 - 87.84: 12 Dihedral angle restraints: 6314 sinusoidal: 2566 harmonic: 3748 Sorted by residual: dihedral pdb=" C2C HEM C 201 " pdb=" C3C HEM C 201 " pdb=" CAC HEM C 201 " pdb=" CBC HEM C 201 " ideal model delta sinusoidal sigma weight residual 0.00 -87.51 87.51 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2C HEM A 201 " pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " pdb=" CBC HEM A 201 " ideal model delta sinusoidal sigma weight residual -0.00 -87.51 87.51 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2B HEM B 201 " pdb=" C3B HEM B 201 " pdb=" CAB HEM B 201 " pdb=" CBB HEM B 201 " ideal model delta sinusoidal sigma weight residual 180.00 114.03 65.97 2 1.00e+01 1.00e-02 4.00e+01 ... (remaining 6311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 616 0.053 - 0.106: 396 0.106 - 0.159: 336 0.159 - 0.212: 156 0.212 - 0.265: 38 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA VAL D 54 " pdb=" N VAL D 54 " pdb=" C VAL D 54 " pdb=" CB VAL D 54 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA VAL B 54 " pdb=" N VAL B 54 " pdb=" C VAL B 54 " pdb=" CB VAL B 54 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA VAL F 237 " pdb=" N VAL F 237 " pdb=" C VAL F 237 " pdb=" CB VAL F 237 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1539 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 60 " -0.027 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C VAL B 60 " 0.095 2.00e-02 2.50e+03 pdb=" O VAL B 60 " -0.035 2.00e-02 2.50e+03 pdb=" N BLYS B 61 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 60 " 0.027 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C VAL D 60 " -0.095 2.00e-02 2.50e+03 pdb=" O VAL D 60 " 0.035 2.00e-02 2.50e+03 pdb=" N BLYS D 61 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BLYS B 61 " -0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C BLYS B 61 " 0.094 2.00e-02 2.50e+03 pdb=" O BLYS B 61 " -0.035 2.00e-02 2.50e+03 pdb=" N ALA B 62 " -0.033 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3456 2.85 - 3.37: 10250 3.37 - 3.88: 19480 3.88 - 4.39: 24063 4.39 - 4.90: 37494 Nonbonded interactions: 94743 Sorted by model distance: nonbonded pdb=" OE2 GLU D 43 " pdb=" O HOH D 301 " model vdw 2.343 2.440 nonbonded pdb=" OE2 GLU B 43 " pdb=" O HOH B 301 " model vdw 2.343 2.440 nonbonded pdb=" O THR B 84 " pdb=" O HOH B 302 " model vdw 2.452 2.440 nonbonded pdb=" O THR D 84 " pdb=" O HOH D 302 " model vdw 2.452 2.440 nonbonded pdb=" O VAL E 367 " pdb=" O HOH E 501 " model vdw 2.486 2.440 ... (remaining 94738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 60 or resid 62 through 64 or resid 66 through 81 \ or resid 83 through 100 or resid 102 through 146 or resid 201)) selection = (chain 'D' and (resid 1 through 60 or resid 62 through 64 or resid 66 through 81 \ or resid 83 through 100 or resid 102 through 146 or resid 201)) } ncs_group { reference = (chain 'E' and (resid 124 through 140 or resid 142 through 209 or resid 211 thro \ ugh 213 or resid 215 through 463)) selection = (chain 'F' and (resid 124 through 140 or resid 142 through 209 or resid 211 thro \ ugh 213 or resid 215 through 463)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 9.790 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 38.620 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.012 0.088 10560 Z= 0.821 Angle : 1.542 11.164 14344 Z= 1.142 Chirality : 0.101 0.265 1542 Planarity : 0.008 0.055 1818 Dihedral : 13.622 87.838 3898 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.55 % Allowed : 6.92 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.22 (0.23), residues: 1284 helix: 2.20 (0.21), residues: 614 sheet: 0.41 (0.43), residues: 154 loop : -0.80 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP F 392 HIS 0.004 0.001 HIS A 122 PHE 0.013 0.002 PHE F 454 TYR 0.017 0.002 TYR F 444 ARG 0.007 0.001 ARG F 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.298 Fit side-chains REVERT: A 27 GLU cc_start: 0.8732 (tt0) cc_final: 0.8409 (tt0) REVERT: B 21 ASP cc_start: 0.8833 (m-30) cc_final: 0.8175 (m-30) REVERT: B 90 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7972 (mt-10) REVERT: E 382 MET cc_start: 0.8760 (ttm) cc_final: 0.8466 (ttm) REVERT: E 396 MET cc_start: 0.8244 (mtm) cc_final: 0.7958 (mtm) REVERT: C 27 GLU cc_start: 0.8727 (tt0) cc_final: 0.8402 (tt0) REVERT: D 21 ASP cc_start: 0.8835 (m-30) cc_final: 0.8187 (m-30) REVERT: D 90 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7972 (mt-10) REVERT: F 382 MET cc_start: 0.8763 (ttm) cc_final: 0.8467 (ttm) REVERT: F 396 MET cc_start: 0.8244 (mtm) cc_final: 0.7961 (mtm) outliers start: 4 outliers final: 0 residues processed: 127 average time/residue: 1.4764 time to fit residues: 200.1586 Evaluate side-chains 83 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.0040 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 102 ASN D 77 HIS D 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10560 Z= 0.203 Angle : 0.561 9.649 14344 Z= 0.283 Chirality : 0.040 0.141 1542 Planarity : 0.004 0.032 1818 Dihedral : 7.745 80.152 1400 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.28 % Allowed : 11.66 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.10 (0.23), residues: 1284 helix: 2.92 (0.20), residues: 638 sheet: 0.36 (0.39), residues: 166 loop : -0.37 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 14 HIS 0.008 0.001 HIS E 369 PHE 0.011 0.001 PHE F 225 TYR 0.015 0.001 TYR F 310 ARG 0.009 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.399 Fit side-chains REVERT: B 7 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 104 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8319 (ttp-110) REVERT: E 276 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8453 (tm-30) REVERT: E 382 MET cc_start: 0.8672 (ttm) cc_final: 0.8434 (ttm) REVERT: E 396 MET cc_start: 0.8208 (mtm) cc_final: 0.7847 (mtt) REVERT: D 7 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8297 (mt-10) REVERT: D 104 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8317 (ttp-110) REVERT: F 276 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8456 (tm-30) REVERT: F 382 MET cc_start: 0.8676 (ttm) cc_final: 0.8440 (ttm) REVERT: F 396 MET cc_start: 0.8213 (mtm) cc_final: 0.7854 (mtt) outliers start: 12 outliers final: 6 residues processed: 102 average time/residue: 1.4782 time to fit residues: 161.5973 Evaluate side-chains 93 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain F residue 386 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN E 333 GLN C 97 ASN F 333 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10560 Z= 0.317 Angle : 0.566 8.483 14344 Z= 0.280 Chirality : 0.041 0.160 1542 Planarity : 0.004 0.033 1818 Dihedral : 6.868 80.464 1400 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.91 % Allowed : 13.57 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.41 (0.24), residues: 1284 helix: 3.11 (0.21), residues: 622 sheet: 0.48 (0.38), residues: 162 loop : 0.02 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 14 HIS 0.006 0.001 HIS E 369 PHE 0.009 0.001 PHE D 122 TYR 0.015 0.001 TYR F 310 ARG 0.003 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8137 (ttp-110) REVERT: E 276 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8529 (tm-30) REVERT: E 375 MET cc_start: 0.9255 (tpp) cc_final: 0.8992 (tpp) REVERT: E 382 MET cc_start: 0.8835 (ttm) cc_final: 0.8254 (tpp) REVERT: E 396 MET cc_start: 0.8376 (mtm) cc_final: 0.7982 (mtt) REVERT: D 7 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8277 (mt-10) REVERT: D 104 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.8130 (ttp-110) REVERT: F 276 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8526 (tm-30) REVERT: F 375 MET cc_start: 0.9255 (tpp) cc_final: 0.8991 (tpp) REVERT: F 382 MET cc_start: 0.8836 (ttm) cc_final: 0.8254 (tpp) REVERT: F 396 MET cc_start: 0.8380 (mtm) cc_final: 0.7988 (mtt) outliers start: 8 outliers final: 2 residues processed: 98 average time/residue: 1.5746 time to fit residues: 164.8772 Evaluate side-chains 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN D 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10560 Z= 0.269 Angle : 0.534 8.725 14344 Z= 0.264 Chirality : 0.040 0.143 1542 Planarity : 0.004 0.036 1818 Dihedral : 6.893 86.389 1400 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.09 % Allowed : 12.75 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.24), residues: 1284 helix: 3.05 (0.21), residues: 618 sheet: 0.21 (0.36), residues: 190 loop : 0.21 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.004 0.001 HIS E 369 PHE 0.008 0.001 PHE F 178 TYR 0.013 0.001 TYR F 310 ARG 0.002 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8397 (pp20) cc_final: 0.8139 (pp20) REVERT: E 180 ASP cc_start: 0.8881 (m-30) cc_final: 0.8626 (p0) REVERT: E 276 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8601 (tm-30) REVERT: E 382 MET cc_start: 0.8828 (ttm) cc_final: 0.8603 (ttm) REVERT: E 396 MET cc_start: 0.8382 (mtm) cc_final: 0.7949 (mtt) REVERT: D 90 GLU cc_start: 0.8401 (pp20) cc_final: 0.8142 (pp20) REVERT: F 276 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8596 (tm-30) REVERT: F 382 MET cc_start: 0.8836 (ttm) cc_final: 0.8629 (ttm) REVERT: F 396 MET cc_start: 0.8382 (mtm) cc_final: 0.7953 (mtt) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 1.4901 time to fit residues: 151.2430 Evaluate side-chains 94 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 386 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 0.0370 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10560 Z= 0.185 Angle : 0.524 9.345 14344 Z= 0.254 Chirality : 0.038 0.135 1542 Planarity : 0.004 0.048 1818 Dihedral : 6.848 87.486 1400 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.73 % Allowed : 13.57 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.24), residues: 1284 helix: 3.14 (0.21), residues: 612 sheet: 0.41 (0.37), residues: 190 loop : 0.23 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.004 0.000 HIS F 369 PHE 0.006 0.001 PHE E 418 TYR 0.011 0.001 TYR F 310 ARG 0.012 0.001 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8420 (pp20) cc_final: 0.8125 (pp20) REVERT: E 180 ASP cc_start: 0.8856 (m-30) cc_final: 0.8617 (p0) REVERT: E 276 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8426 (tm-30) REVERT: E 375 MET cc_start: 0.9056 (tpp) cc_final: 0.8648 (tpp) REVERT: E 382 MET cc_start: 0.8775 (ttm) cc_final: 0.8572 (ttm) REVERT: E 396 MET cc_start: 0.8361 (mtm) cc_final: 0.7936 (mtt) REVERT: D 90 GLU cc_start: 0.8426 (pp20) cc_final: 0.8127 (pp20) REVERT: F 180 ASP cc_start: 0.8854 (m-30) cc_final: 0.8618 (p0) REVERT: F 276 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8422 (tm-30) REVERT: F 375 MET cc_start: 0.9052 (tpp) cc_final: 0.8646 (tpp) REVERT: F 382 MET cc_start: 0.8797 (ttm) cc_final: 0.8574 (ttm) REVERT: F 396 MET cc_start: 0.8367 (mtm) cc_final: 0.7954 (mtt) outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 1.4673 time to fit residues: 149.6350 Evaluate side-chains 92 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain F residue 386 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS D 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10560 Z= 0.180 Angle : 0.524 11.581 14344 Z= 0.253 Chirality : 0.038 0.137 1542 Planarity : 0.004 0.053 1818 Dihedral : 6.857 89.261 1400 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.82 % Allowed : 13.66 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.52 (0.24), residues: 1284 helix: 3.15 (0.21), residues: 612 sheet: 0.46 (0.37), residues: 190 loop : 0.25 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 14 HIS 0.004 0.000 HIS E 369 PHE 0.007 0.001 PHE F 418 TYR 0.010 0.001 TYR F 310 ARG 0.013 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8453 (pp20) cc_final: 0.8124 (pp20) REVERT: E 180 ASP cc_start: 0.8836 (m-30) cc_final: 0.8589 (p0) REVERT: E 276 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8468 (tm-30) REVERT: E 375 MET cc_start: 0.9058 (tpp) cc_final: 0.8711 (tpp) REVERT: E 382 MET cc_start: 0.8804 (ttm) cc_final: 0.8576 (ttm) REVERT: E 396 MET cc_start: 0.8345 (mtm) cc_final: 0.7911 (mtt) REVERT: D 7 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 90 GLU cc_start: 0.8460 (pp20) cc_final: 0.8133 (pp20) REVERT: F 180 ASP cc_start: 0.8835 (m-30) cc_final: 0.8587 (p0) REVERT: F 276 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8464 (tm-30) REVERT: F 375 MET cc_start: 0.9057 (tpp) cc_final: 0.8714 (tpp) REVERT: F 396 MET cc_start: 0.8343 (mtm) cc_final: 0.7920 (mtt) outliers start: 7 outliers final: 4 residues processed: 93 average time/residue: 1.5042 time to fit residues: 150.9939 Evaluate side-chains 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10560 Z= 0.192 Angle : 0.523 11.555 14344 Z= 0.253 Chirality : 0.038 0.133 1542 Planarity : 0.004 0.048 1818 Dihedral : 6.830 89.793 1400 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.46 % Allowed : 13.84 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.24), residues: 1284 helix: 3.16 (0.21), residues: 612 sheet: 0.37 (0.37), residues: 192 loop : 0.24 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.003 0.000 HIS F 369 PHE 0.008 0.001 PHE F 418 TYR 0.011 0.001 TYR F 310 ARG 0.012 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8475 (pp20) cc_final: 0.8152 (pp20) REVERT: E 180 ASP cc_start: 0.8851 (m-30) cc_final: 0.8597 (p0) REVERT: E 276 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8458 (tm-30) REVERT: E 375 MET cc_start: 0.9097 (tpp) cc_final: 0.8827 (tpp) REVERT: E 396 MET cc_start: 0.8342 (mtm) cc_final: 0.7993 (mtt) REVERT: D 7 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8265 (mt-10) REVERT: D 90 GLU cc_start: 0.8482 (pp20) cc_final: 0.8157 (pp20) REVERT: F 180 ASP cc_start: 0.8851 (m-30) cc_final: 0.8597 (p0) REVERT: F 276 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8456 (tm-30) REVERT: F 375 MET cc_start: 0.9087 (tpp) cc_final: 0.8822 (tpp) REVERT: F 382 MET cc_start: 0.8893 (ttm) cc_final: 0.8572 (ttm) REVERT: F 396 MET cc_start: 0.8343 (mtm) cc_final: 0.7989 (mtt) outliers start: 3 outliers final: 2 residues processed: 89 average time/residue: 1.5349 time to fit residues: 146.2428 Evaluate side-chains 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10560 Z= 0.265 Angle : 0.556 11.913 14344 Z= 0.269 Chirality : 0.039 0.126 1542 Planarity : 0.004 0.054 1818 Dihedral : 6.890 89.478 1400 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.46 % Allowed : 14.39 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.24), residues: 1284 helix: 3.10 (0.21), residues: 612 sheet: 0.26 (0.37), residues: 192 loop : 0.26 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.004 0.001 HIS E 369 PHE 0.007 0.001 PHE B 122 TYR 0.013 0.001 TYR F 310 ARG 0.014 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8362 (m-40) cc_final: 0.8159 (m-40) REVERT: B 90 GLU cc_start: 0.8459 (pp20) cc_final: 0.8119 (pp20) REVERT: E 180 ASP cc_start: 0.8868 (m-30) cc_final: 0.8614 (p0) REVERT: E 276 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8470 (tm-30) REVERT: E 375 MET cc_start: 0.9135 (tpp) cc_final: 0.8874 (tpp) REVERT: E 382 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8630 (ttm) REVERT: E 396 MET cc_start: 0.8323 (mtm) cc_final: 0.7881 (mtt) REVERT: D 90 GLU cc_start: 0.8462 (pp20) cc_final: 0.8127 (pp20) REVERT: F 180 ASP cc_start: 0.8866 (m-30) cc_final: 0.8614 (p0) REVERT: F 276 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8466 (tm-30) REVERT: F 375 MET cc_start: 0.9125 (tpp) cc_final: 0.8868 (tpp) REVERT: F 382 MET cc_start: 0.8899 (ttm) cc_final: 0.8642 (ttm) REVERT: F 396 MET cc_start: 0.8320 (mtm) cc_final: 0.7878 (mtt) outliers start: 3 outliers final: 4 residues processed: 89 average time/residue: 1.5730 time to fit residues: 149.7795 Evaluate side-chains 93 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain E residue 382 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10560 Z= 0.265 Angle : 0.542 11.601 14344 Z= 0.263 Chirality : 0.039 0.124 1542 Planarity : 0.004 0.049 1818 Dihedral : 6.846 87.671 1400 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.46 % Allowed : 14.30 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.24), residues: 1284 helix: 3.03 (0.21), residues: 612 sheet: 0.43 (0.39), residues: 186 loop : 0.20 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.003 0.001 HIS F 369 PHE 0.008 0.001 PHE E 418 TYR 0.012 0.001 TYR F 310 ARG 0.015 0.001 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 90 GLU cc_start: 0.8444 (pp20) cc_final: 0.8092 (pp20) REVERT: E 180 ASP cc_start: 0.8881 (m-30) cc_final: 0.8625 (p0) REVERT: E 276 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8472 (tm-30) REVERT: E 375 MET cc_start: 0.9127 (tpp) cc_final: 0.8877 (tpp) REVERT: E 382 MET cc_start: 0.8927 (ttm) cc_final: 0.8632 (ttm) REVERT: E 396 MET cc_start: 0.8315 (mtm) cc_final: 0.7888 (mtt) REVERT: D 90 GLU cc_start: 0.8437 (pp20) cc_final: 0.8087 (pp20) REVERT: F 180 ASP cc_start: 0.8879 (m-30) cc_final: 0.8624 (p0) REVERT: F 276 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8471 (tm-30) REVERT: F 375 MET cc_start: 0.9120 (tpp) cc_final: 0.8872 (tpp) REVERT: F 382 MET cc_start: 0.8916 (ttm) cc_final: 0.8650 (ttm) REVERT: F 396 MET cc_start: 0.8352 (mtm) cc_final: 0.7912 (mtt) outliers start: 3 outliers final: 4 residues processed: 90 average time/residue: 1.5658 time to fit residues: 150.6179 Evaluate side-chains 94 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10560 Z= 0.204 Angle : 0.545 11.948 14344 Z= 0.266 Chirality : 0.039 0.131 1542 Planarity : 0.004 0.068 1818 Dihedral : 6.785 85.978 1400 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.36 % Allowed : 14.48 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.36 (0.24), residues: 1284 helix: 3.01 (0.21), residues: 612 sheet: 0.31 (0.38), residues: 192 loop : 0.22 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.003 0.000 HIS F 369 PHE 0.008 0.001 PHE F 418 TYR 0.011 0.001 TYR F 310 ARG 0.014 0.001 ARG D 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 90 GLU cc_start: 0.8421 (pp20) cc_final: 0.8059 (pp20) REVERT: E 180 ASP cc_start: 0.8853 (m-30) cc_final: 0.8603 (p0) REVERT: E 276 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8462 (tm-30) REVERT: E 375 MET cc_start: 0.9085 (tpp) cc_final: 0.8838 (tpp) REVERT: E 382 MET cc_start: 0.8904 (ttm) cc_final: 0.8655 (ttm) REVERT: D 90 GLU cc_start: 0.8427 (pp20) cc_final: 0.8065 (pp20) REVERT: F 180 ASP cc_start: 0.8854 (m-30) cc_final: 0.8602 (p0) REVERT: F 276 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8454 (tm-30) REVERT: F 375 MET cc_start: 0.9081 (tpp) cc_final: 0.8835 (tpp) REVERT: F 382 MET cc_start: 0.8893 (ttm) cc_final: 0.8638 (ttm) REVERT: F 396 MET cc_start: 0.8320 (mtm) cc_final: 0.7887 (mtt) outliers start: 2 outliers final: 3 residues processed: 90 average time/residue: 1.6447 time to fit residues: 158.1561 Evaluate side-chains 91 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 23 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.0010 chunk 86 optimal weight: 0.8980 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.036339 restraints weight = 236496.869| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 7.53 r_work: 0.2314 rms_B_bonded: 7.04 restraints_weight: 2.0000 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2327 r_free = 0.2327 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2323 r_free = 0.2323 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10560 Z= 0.246 Angle : 0.542 11.897 14344 Z= 0.264 Chirality : 0.039 0.136 1542 Planarity : 0.004 0.063 1818 Dihedral : 6.769 85.874 1400 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.36 % Allowed : 14.39 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.24), residues: 1284 helix: 3.05 (0.21), residues: 612 sheet: 0.43 (0.39), residues: 186 loop : 0.19 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.003 0.001 HIS F 369 PHE 0.007 0.001 PHE E 418 TYR 0.011 0.001 TYR F 310 ARG 0.015 0.001 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3657.65 seconds wall clock time: 65 minutes 40.36 seconds (3940.36 seconds total)