Starting phenix.real_space_refine (version: dev) on Sun Feb 19 22:33:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/02_2023/7pch_13320_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/02_2023/7pch_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_13320/02_2023/7pch_13320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/02_2023/7pch_13320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/02_2023/7pch_13320_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/02_2023/7pch_13320_updated.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 9.79, per 1000 atoms: 0.91 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: 4.82 Conformation dependent library (CDL) restraints added in 2.4 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: 1.55 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: 3.19 Time building geometry restraints manager: 4.80 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 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. 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: 4.790 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: 11.150 Check model and map are aligned: 0.160 Process input model: 34.890 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 % 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 *********************** 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 : 1.333 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 127 average time/residue: 1.5049 time to fit residues: 204.7027 Evaluate side-chains 81 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7121 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 0.0040 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 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: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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: 0.8334 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10560 Z= 0.199 Angle : 0.556 9.892 14344 Z= 0.281 Chirality : 0.040 0.144 1542 Planarity : 0.004 0.030 1818 Dihedral : 7.853 82.307 1400 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer Outliers : 1.09 % 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: 2.14 (0.23), residues: 1284 helix: 2.95 (0.20), residues: 638 sheet: 0.41 (0.39), residues: 162 loop : -0.36 (0.26), residues: 484 *********************** 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 104 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.247 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 100 average time/residue: 1.5821 time to fit residues: 169.3564 Evaluate side-chains 92 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2380 time to fit residues: 3.0551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 93 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN C 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.092 10560 Z= 0.407 Angle : 0.615 8.811 14344 Z= 0.305 Chirality : 0.043 0.165 1542 Planarity : 0.004 0.032 1818 Dihedral : 6.990 79.646 1400 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 1.46 % 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: 2.28 (0.24), residues: 1284 helix: 2.97 (0.21), residues: 620 sheet: 0.48 (0.39), residues: 162 loop : 0.02 (0.27), residues: 502 *********************** 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 109 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 103 average time/residue: 1.5342 time to fit residues: 169.3580 Evaluate side-chains 91 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.2636 time to fit residues: 2.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 108 ASN D 102 ASN D 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 10560 Z= 0.277 Angle : 0.543 8.768 14344 Z= 0.268 Chirality : 0.040 0.144 1542 Planarity : 0.004 0.036 1818 Dihedral : 6.955 86.937 1400 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 1.64 % 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: 2.33 (0.24), residues: 1284 helix: 2.98 (0.21), residues: 618 sheet: 0.22 (0.37), residues: 190 loop : 0.21 (0.28), residues: 476 *********************** 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 103 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 95 average time/residue: 1.5776 time to fit residues: 160.8350 Evaluate side-chains 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.2980 time to fit residues: 2.6592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8490 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10560 Z= 0.194 Angle : 0.539 11.173 14344 Z= 0.260 Chirality : 0.039 0.141 1542 Planarity : 0.004 0.037 1818 Dihedral : 6.901 87.863 1400 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 0.91 % 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: 0.37 (0.37), residues: 190 loop : 0.21 (0.28), residues: 482 *********************** 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 94 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 1.5878 time to fit residues: 153.6708 Evaluate side-chains 86 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.2505 time to fit residues: 2.4234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN B 146 HIS D 108 ASN D 146 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 10560 Z= 0.286 Angle : 0.568 11.225 14344 Z= 0.275 Chirality : 0.040 0.137 1542 Planarity : 0.004 0.046 1818 Dihedral : 6.952 87.750 1400 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 0.73 % 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: 3.10 (0.21), residues: 600 sheet: 0.46 (0.38), residues: 184 loop : 0.15 (0.27), residues: 500 *********************** 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 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 1.5610 time to fit residues: 144.3251 Evaluate side-chains 86 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.2550 time to fit residues: 2.4528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10560 Z= 0.215 Angle : 0.541 10.995 14344 Z= 0.260 Chirality : 0.039 0.123 1542 Planarity : 0.004 0.048 1818 Dihedral : 6.919 89.832 1400 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.73 % 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: 2.30 (0.24), residues: 1284 helix: 3.06 (0.21), residues: 600 sheet: 0.24 (0.38), residues: 192 loop : 0.15 (0.27), residues: 492 *********************** 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 87 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 83 average time/residue: 1.4875 time to fit residues: 132.8559 Evaluate side-chains 82 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.7618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10560 Z= 0.245 Angle : 0.566 11.419 14344 Z= 0.270 Chirality : 0.039 0.125 1542 Planarity : 0.004 0.054 1818 Dihedral : 6.927 89.484 1400 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 0.55 % 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: 2.35 (0.24), residues: 1284 helix: 3.01 (0.21), residues: 612 sheet: 0.38 (0.39), residues: 186 loop : 0.16 (0.27), residues: 486 *********************** 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 88 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 86 average time/residue: 1.5556 time to fit residues: 144.0314 Evaluate side-chains 88 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 2 average time/residue: 1.7418 time to fit residues: 5.4768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 0.0030 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10560 Z= 0.195 Angle : 0.544 10.980 14344 Z= 0.260 Chirality : 0.039 0.124 1542 Planarity : 0.004 0.042 1818 Dihedral : 6.823 87.221 1400 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 0.55 % 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: 2.34 (0.24), residues: 1284 helix: 2.98 (0.21), residues: 612 sheet: 0.44 (0.40), residues: 186 loop : 0.17 (0.28), residues: 486 *********************** 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 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 88 average time/residue: 1.5934 time to fit residues: 150.6451 Evaluate side-chains 84 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.8492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8507 moved from start: 0.4081 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= 0.206 Angle : 0.554 11.387 14344 Z= 0.270 Chirality : 0.039 0.162 1542 Planarity : 0.004 0.057 1818 Dihedral : 6.805 86.437 1400 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.46 % 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: 2.33 (0.24), residues: 1284 helix: 2.96 (0.21), residues: 612 sheet: 0.44 (0.40), residues: 186 loop : 0.17 (0.28), residues: 486 ********************** 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 87 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 86 average time/residue: 1.6136 time to fit residues: 148.5694 Evaluate side-chains 85 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.2326 time to fit residues: 1.9695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.0170 chunk 86 optimal weight: 0.9980 overall best weight: 1.3020 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.057628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.036301 restraints weight = 229287.175| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 7.55 r_work: 0.2250 rms_B_bonded: 7.05 restraints_weight: 2.0000 r_work (final): 0.2250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 10560 Z= 0.240 Angle : 0.579 12.114 14344 Z= 0.279 Chirality : 0.040 0.144 1542 Planarity : 0.005 0.059 1818 Dihedral : 6.809 86.035 1400 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 0.64 % 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: 2.33 (0.24), residues: 1284 helix: 2.95 (0.21), residues: 612 sheet: 0.43 (0.40), residues: 186 loop : 0.19 (0.28), residues: 486 =============================================================================== Job complete usr+sys time: 3513.11 seconds wall clock time: 64 minutes 22.11 seconds (3862.11 seconds total)