Starting phenix.real_space_refine on Wed Sep 25 18:30:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/09_2024/7pch_13320.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/09_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_13320/09_2024/7pch_13320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/09_2024/7pch_13320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/09_2024/7pch_13320.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pch_13320/09_2024/7pch_13320.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 11 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: "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: "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} Restraints were copied for chains: C, D, F 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: 10.57, per 1000 atoms: 0.98 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 - 3.00 Amino acid : True - 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: 3.14 Conformation dependent library (CDL) restraints added in 2.7 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... Secondary structure from input PDB file: 48 helices and 10 sheets defined 53.9% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.655A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 removed outlier: 4.219A pdb=" N LYS A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 19 through 35 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 42 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 77 removed outlier: 3.571A pdb=" N ALYS B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 95 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 99 through 119 removed outlier: 3.636A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'E' and resid 128 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 163 through 169 Processing helix chain 'E' and resid 269 through 285 Proline residue: E 281 - end of helix Processing helix chain 'E' and resid 287 through 300 removed outlier: 4.572A pdb=" N ASP E 300 " --> pdb=" O ASN E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 332 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 361 through 365 Processing helix chain 'E' and resid 451 through 463 removed outlier: 3.673A pdb=" N LYS E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.655A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 139 removed outlier: 4.219A pdb=" N LYS C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 19 through 35 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 42 Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 57 through 77 removed outlier: 3.571A pdb=" N ALYS D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 95 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 99 through 119 removed outlier: 3.636A pdb=" N PHE D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 142 Processing helix chain 'F' and resid 128 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 163 through 169 Processing helix chain 'F' and resid 269 through 285 Proline residue: F 281 - end of helix Processing helix chain 'F' and resid 287 through 300 removed outlier: 4.572A pdb=" N ASP F 300 " --> pdb=" O ASN F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 332 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 361 through 365 Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.673A pdb=" N LYS F 456 " --> pdb=" O GLU F 452 " (cutoff:3.500A) Processing sheet with id=AA1, 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: 7.071A pdb=" N VAL E 171 " --> pdb=" O GLN E 190 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN E 190 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLY E 188 " --> pdb=" O PRO E 173 " (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=AA2, first strand: chain 'E' and resid 153 through 156 removed outlier: 11.269A pdb=" N MET E 254 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL E 237 " --> pdb=" O MET E 254 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N PHE E 256 " --> pdb=" O LYS E 235 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N LYS E 235 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLN E 258 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA E 233 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR E 231 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS E 241 " --> pdb=" O TRP E 195 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP E 195 " --> pdb=" O HIS E 241 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL E 200 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 153 through 156 removed outlier: 11.269A pdb=" N MET E 254 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL E 237 " --> pdb=" O MET E 254 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N PHE E 256 " --> pdb=" O LYS E 235 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N LYS E 235 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLN E 258 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA E 233 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR E 231 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 238 " --> pdb=" O TYR E 249 " (cutoff:3.500A) Processing sheet with id=AA4, 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: 5.988A pdb=" N GLU E 385 " --> pdb=" O PRO E 370 " (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=AA5, first strand: chain 'E' and resid 350 through 353 removed outlier: 7.274A pdb=" N ASP E 428 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL E 397 " --> pdb=" O ASP E 428 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 430 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE E 395 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS E 432 " --> pdb=" O LYS E 393 " (cutoff:3.500A) Processing sheet with id=AA6, 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: 7.071A pdb=" N VAL F 171 " --> pdb=" O GLN F 190 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN F 190 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLY F 188 " --> pdb=" O PRO F 173 " (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=AA7, first strand: chain 'F' and resid 153 through 156 removed outlier: 11.269A pdb=" N MET F 254 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL F 237 " --> pdb=" O MET F 254 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N PHE F 256 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N LYS F 235 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLN F 258 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA F 233 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR F 231 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS F 241 " --> pdb=" O TRP F 195 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP F 195 " --> pdb=" O HIS F 241 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL F 200 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 153 through 156 removed outlier: 11.269A pdb=" N MET F 254 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL F 237 " --> pdb=" O MET F 254 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N PHE F 256 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N LYS F 235 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLN F 258 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA F 233 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR F 231 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 238 " --> pdb=" O TYR F 249 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 5.988A pdb=" N GLU F 385 " --> pdb=" O PRO F 370 " (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=AB1, first strand: chain 'F' and resid 350 through 353 removed outlier: 7.274A pdb=" N ASP F 428 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL F 397 " --> pdb=" O ASP F 428 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE F 430 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE F 395 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS F 432 " --> pdb=" O LYS F 393 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1714 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: 3.36 Time building geometry restraints manager: 3.57 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: 0.00 - 2.23: 12108 2.23 - 4.47: 2110 4.47 - 6.70: 106 6.70 - 8.93: 8 8.93 - 11.16: 12 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: 3426 2.85 - 3.37: 10214 3.37 - 3.88: 19380 3.88 - 4.39: 23989 4.39 - 4.90: 37494 Nonbonded interactions: 94503 Sorted by model distance: nonbonded pdb=" OE2 GLU D 43 " pdb=" O HOH D 301 " model vdw 2.343 3.040 nonbonded pdb=" OE2 GLU B 43 " pdb=" O HOH B 301 " model vdw 2.343 3.040 nonbonded pdb=" O THR B 84 " pdb=" O HOH B 302 " model vdw 2.452 3.040 nonbonded pdb=" O THR D 84 " pdb=" O HOH D 302 " model vdw 2.452 3.040 nonbonded pdb=" O VAL E 367 " pdb=" O HOH E 501 " model vdw 2.486 3.040 ... (remaining 94498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 32.590 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.620 ------------------------------------------------------------------------------- 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= 0.823 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 : 1.286 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: 1.5215 time to fit residues: 206.2984 Evaluate side-chains 83 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7873 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10560 Z= 0.210 Angle : 0.586 9.739 14344 Z= 0.301 Chirality : 0.041 0.150 1542 Planarity : 0.004 0.035 1818 Dihedral : 7.930 81.795 1400 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.28 % Allowed : 11.84 % Favored : 86.89 % 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: 2.06 (0.23), residues: 1284 helix: 2.84 (0.20), residues: 628 sheet: 0.64 (0.42), residues: 158 loop : -0.34 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 14 HIS 0.007 0.001 HIS E 369 PHE 0.008 0.001 PHE F 178 TYR 0.015 0.001 TYR F 310 ARG 0.006 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 : 1.295 Fit side-chains REVERT: A 27 GLU cc_start: 0.8775 (tt0) cc_final: 0.8378 (tt0) REVERT: B 7 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8295 (mt-10) REVERT: B 104 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8334 (ttp-110) REVERT: E 276 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8486 (tm-30) REVERT: E 382 MET cc_start: 0.8725 (ttm) cc_final: 0.8500 (ttm) REVERT: E 396 MET cc_start: 0.8300 (mtm) cc_final: 0.7927 (mtt) REVERT: C 27 GLU cc_start: 0.8771 (tt0) cc_final: 0.8371 (tt0) REVERT: D 7 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8299 (mt-10) REVERT: D 104 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8331 (ttp-110) REVERT: F 276 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8481 (tm-30) REVERT: F 382 MET cc_start: 0.8733 (ttm) cc_final: 0.8508 (ttm) REVERT: F 396 MET cc_start: 0.8300 (mtm) cc_final: 0.7929 (mtt) outliers start: 12 outliers final: 2 residues processed: 100 average time/residue: 1.3692 time to fit residues: 147.5801 Evaluate side-chains 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 333 GLN C 97 ASN F 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10560 Z= 0.243 Angle : 0.553 9.268 14344 Z= 0.279 Chirality : 0.040 0.158 1542 Planarity : 0.004 0.035 1818 Dihedral : 6.913 85.598 1400 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.64 % Allowed : 11.84 % Favored : 86.52 % 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: 2.34 (0.24), residues: 1284 helix: 2.98 (0.21), residues: 626 sheet: 0.68 (0.40), residues: 162 loop : -0.02 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 14 HIS 0.004 0.001 HIS E 369 PHE 0.008 0.001 PHE F 164 TYR 0.014 0.001 TYR F 310 ARG 0.002 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 112 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.909 Fit side-chains REVERT: A 27 GLU cc_start: 0.8815 (tt0) cc_final: 0.8534 (tt0) REVERT: B 104 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8278 (ttp-110) REVERT: E 276 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8522 (tm-30) REVERT: E 375 MET cc_start: 0.9189 (tpp) cc_final: 0.8901 (tpp) REVERT: E 382 MET cc_start: 0.8802 (ttm) cc_final: 0.8582 (ttm) REVERT: E 396 MET cc_start: 0.8456 (mtm) cc_final: 0.8112 (mtt) REVERT: C 27 GLU cc_start: 0.8811 (tt0) cc_final: 0.8531 (tt0) REVERT: D 104 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8274 (ttp-110) REVERT: F 276 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8520 (tm-30) REVERT: F 375 MET cc_start: 0.9187 (tpp) cc_final: 0.8899 (tpp) REVERT: F 382 MET cc_start: 0.8804 (ttm) cc_final: 0.8585 (ttm) REVERT: F 396 MET cc_start: 0.8439 (mtm) cc_final: 0.8095 (mtt) outliers start: 16 outliers final: 4 residues processed: 100 average time/residue: 1.3266 time to fit residues: 141.3654 Evaluate side-chains 93 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.7972 moved from start: 0.3164 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= 0.196 Angle : 0.539 8.620 14344 Z= 0.269 Chirality : 0.039 0.142 1542 Planarity : 0.004 0.038 1818 Dihedral : 6.947 86.903 1400 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.46 % Allowed : 11.38 % Favored : 87.16 % 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: 2.35 (0.24), residues: 1284 helix: 2.92 (0.21), residues: 624 sheet: 0.72 (0.41), residues: 166 loop : 0.09 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.004 0.001 HIS F 369 PHE 0.007 0.001 PHE F 225 TYR 0.012 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 108 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8277 (ttp-110) REVERT: E 276 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8385 (tm-30) REVERT: E 375 MET cc_start: 0.9224 (tpp) cc_final: 0.8945 (tpp) REVERT: E 382 MET cc_start: 0.8794 (ttm) cc_final: 0.8584 (ttm) REVERT: E 396 MET cc_start: 0.8452 (mtm) cc_final: 0.8072 (mtt) REVERT: D 104 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8277 (ttp-110) REVERT: F 276 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8378 (tm-30) REVERT: F 375 MET cc_start: 0.9223 (tpp) cc_final: 0.8945 (tpp) REVERT: F 382 MET cc_start: 0.8803 (ttm) cc_final: 0.8597 (ttm) REVERT: F 396 MET cc_start: 0.8453 (mtm) cc_final: 0.8070 (mtt) outliers start: 14 outliers final: 2 residues processed: 100 average time/residue: 1.4242 time to fit residues: 153.1671 Evaluate side-chains 89 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.0010 overall best weight: 1.3590 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10560 Z= 0.239 Angle : 0.561 9.374 14344 Z= 0.279 Chirality : 0.040 0.142 1542 Planarity : 0.004 0.037 1818 Dihedral : 7.005 87.345 1400 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.46 % Allowed : 11.75 % Favored : 86.79 % 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: 3.00 (0.21), residues: 614 sheet: 0.62 (0.40), residues: 162 loop : 0.15 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 14 HIS 0.003 0.001 HIS A 20 PHE 0.007 0.001 PHE F 164 TYR 0.012 0.001 TYR F 310 ARG 0.002 0.000 ARG D 104 *********************** 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 107 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9224 (t0) cc_final: 0.8985 (t0) REVERT: B 26 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: B 104 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8274 (ttp-110) REVERT: E 276 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8407 (tm-30) REVERT: E 396 MET cc_start: 0.8465 (mtm) cc_final: 0.8053 (mtt) REVERT: C 78 ASN cc_start: 0.9219 (t0) cc_final: 0.8983 (t0) REVERT: D 104 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8273 (ttp-110) REVERT: F 276 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8411 (tm-30) REVERT: F 396 MET cc_start: 0.8479 (mtm) cc_final: 0.8064 (mtt) outliers start: 14 outliers final: 2 residues processed: 97 average time/residue: 1.5026 time to fit residues: 156.2289 Evaluate side-chains 89 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 119 optimal weight: 7.9990 chunk 99 optimal weight: 0.0020 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10560 Z= 0.181 Angle : 0.578 9.995 14344 Z= 0.283 Chirality : 0.039 0.137 1542 Planarity : 0.004 0.046 1818 Dihedral : 7.041 89.608 1400 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.73 % Allowed : 13.30 % Favored : 85.97 % 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: 2.98 (0.21), residues: 616 sheet: 0.66 (0.40), residues: 166 loop : 0.12 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 14 HIS 0.003 0.000 HIS F 369 PHE 0.008 0.001 PHE F 418 TYR 0.012 0.001 TYR F 444 ARG 0.015 0.001 ARG F 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 94 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8783 (m-30) cc_final: 0.8540 (p0) REVERT: A 78 ASN cc_start: 0.9232 (t0) cc_final: 0.8971 (t0) REVERT: B 26 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: E 124 MET cc_start: 0.7305 (ppp) cc_final: 0.7059 (ppp) REVERT: E 276 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8380 (tm-30) REVERT: E 375 MET cc_start: 0.8901 (tpp) cc_final: 0.8472 (tpp) REVERT: E 382 MET cc_start: 0.8834 (ttm) cc_final: 0.8546 (ttm) REVERT: E 396 MET cc_start: 0.8414 (mtm) cc_final: 0.8028 (mtt) REVERT: C 6 ASP cc_start: 0.8791 (m-30) cc_final: 0.8542 (p0) REVERT: C 78 ASN cc_start: 0.9229 (t0) cc_final: 0.8974 (t0) REVERT: F 124 MET cc_start: 0.7309 (ppp) cc_final: 0.7065 (ppp) REVERT: F 276 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8385 (tm-30) REVERT: F 375 MET cc_start: 0.8898 (tpp) cc_final: 0.8468 (tpp) REVERT: F 382 MET cc_start: 0.8831 (ttm) cc_final: 0.8513 (ttm) REVERT: F 396 MET cc_start: 0.8443 (mtm) cc_final: 0.8065 (mtt) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 1.5179 time to fit residues: 146.5307 Evaluate side-chains 91 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10560 Z= 0.220 Angle : 0.588 12.178 14344 Z= 0.287 Chirality : 0.039 0.143 1542 Planarity : 0.004 0.045 1818 Dihedral : 7.040 89.902 1400 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.82 % Allowed : 13.30 % Favored : 85.88 % 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: 2.46 (0.24), residues: 1284 helix: 3.03 (0.21), residues: 618 sheet: 0.41 (0.38), residues: 192 loop : 0.31 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.003 0.001 HIS E 369 PHE 0.008 0.001 PHE F 418 TYR 0.011 0.001 TYR F 310 ARG 0.013 0.001 ARG D 104 *********************** 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 93 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8816 (m-30) cc_final: 0.8554 (p0) REVERT: A 78 ASN cc_start: 0.9247 (t0) cc_final: 0.9003 (t0) REVERT: E 276 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8390 (tm-30) REVERT: E 375 MET cc_start: 0.8983 (tpp) cc_final: 0.8563 (tpp) REVERT: E 382 MET cc_start: 0.8837 (ttm) cc_final: 0.8522 (ttm) REVERT: E 396 MET cc_start: 0.8453 (mtm) cc_final: 0.8064 (mtt) REVERT: C 6 ASP cc_start: 0.8821 (m-30) cc_final: 0.8557 (p0) REVERT: C 78 ASN cc_start: 0.9243 (t0) cc_final: 0.8997 (t0) REVERT: F 276 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8391 (tm-30) REVERT: F 375 MET cc_start: 0.8975 (tpp) cc_final: 0.8553 (tpp) REVERT: F 382 MET cc_start: 0.8789 (ttm) cc_final: 0.8507 (ttm) REVERT: F 396 MET cc_start: 0.8455 (mtm) cc_final: 0.8105 (mtt) outliers start: 7 outliers final: 2 residues processed: 88 average time/residue: 1.4672 time to fit residues: 138.6661 Evaluate side-chains 88 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8019 moved from start: 0.3887 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= 0.203 Angle : 0.585 11.989 14344 Z= 0.286 Chirality : 0.039 0.123 1542 Planarity : 0.004 0.049 1818 Dihedral : 6.974 89.330 1400 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.36 % Allowed : 13.75 % Favored : 85.88 % 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: 2.47 (0.24), residues: 1284 helix: 3.04 (0.21), residues: 618 sheet: 0.48 (0.39), residues: 186 loop : 0.28 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.003 0.001 HIS D 146 PHE 0.008 0.001 PHE F 418 TYR 0.010 0.001 TYR F 310 ARG 0.010 0.001 ARG D 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 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8809 (m-30) cc_final: 0.8561 (p0) REVERT: A 78 ASN cc_start: 0.9255 (t0) cc_final: 0.9042 (t0) REVERT: B 90 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7870 (pp20) REVERT: E 124 MET cc_start: 0.7330 (ppp) cc_final: 0.7098 (ppp) REVERT: E 276 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8423 (tm-30) REVERT: E 375 MET cc_start: 0.8986 (tpp) cc_final: 0.8711 (tpp) REVERT: E 382 MET cc_start: 0.8849 (ttm) cc_final: 0.8557 (ttm) REVERT: E 396 MET cc_start: 0.8439 (mtm) cc_final: 0.8037 (mtt) REVERT: C 6 ASP cc_start: 0.8814 (m-30) cc_final: 0.8563 (p0) REVERT: C 78 ASN cc_start: 0.9249 (t0) cc_final: 0.9036 (t0) REVERT: F 124 MET cc_start: 0.7335 (ppp) cc_final: 0.7106 (ppp) REVERT: F 276 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8423 (tm-30) REVERT: F 375 MET cc_start: 0.8988 (tpp) cc_final: 0.8714 (tpp) REVERT: F 382 MET cc_start: 0.8776 (ttm) cc_final: 0.8505 (ttm) REVERT: F 396 MET cc_start: 0.8448 (mtm) cc_final: 0.8044 (mtt) outliers start: 2 outliers final: 4 residues processed: 88 average time/residue: 1.5714 time to fit residues: 148.2645 Evaluate side-chains 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- 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: 0.8035 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 0.056 10560 Z= 0.244 Angle : 0.595 11.720 14344 Z= 0.292 Chirality : 0.039 0.129 1542 Planarity : 0.004 0.044 1818 Dihedral : 6.965 89.646 1400 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.55 % Allowed : 13.66 % Favored : 85.79 % 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: 2.54 (0.24), residues: 1284 helix: 3.12 (0.21), residues: 614 sheet: 0.48 (0.40), residues: 186 loop : 0.31 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.003 0.001 HIS D 146 PHE 0.008 0.001 PHE F 418 TYR 0.011 0.001 TYR F 310 ARG 0.009 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 90 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7878 (pp20) REVERT: E 276 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8411 (tm-30) REVERT: E 375 MET cc_start: 0.8997 (tpp) cc_final: 0.8730 (tpp) REVERT: E 382 MET cc_start: 0.8870 (ttm) cc_final: 0.8567 (ttm) REVERT: E 396 MET cc_start: 0.8471 (mtm) cc_final: 0.8064 (mtt) REVERT: D 90 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7882 (pp20) REVERT: F 276 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8407 (tm-30) REVERT: F 375 MET cc_start: 0.9005 (tpp) cc_final: 0.8745 (tpp) REVERT: F 382 MET cc_start: 0.8794 (ttm) cc_final: 0.8515 (ttm) REVERT: F 396 MET cc_start: 0.8475 (mtm) cc_final: 0.8041 (mtt) outliers start: 4 outliers final: 2 residues processed: 86 average time/residue: 1.5329 time to fit residues: 141.2981 Evaluate side-chains 88 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP 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: 1.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3984 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= 0.239 Angle : 0.605 11.997 14344 Z= 0.298 Chirality : 0.040 0.127 1542 Planarity : 0.004 0.043 1818 Dihedral : 6.922 89.309 1400 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.55 % Allowed : 13.93 % 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: 2.54 (0.24), residues: 1284 helix: 3.12 (0.21), residues: 614 sheet: 0.48 (0.40), residues: 186 loop : 0.32 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.003 0.001 HIS E 369 PHE 0.007 0.001 PHE F 418 TYR 0.011 0.001 TYR F 310 ARG 0.009 0.001 ARG F 403 ********************** 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 88 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8852 (m-30) cc_final: 0.8467 (p0) REVERT: B 90 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7859 (pp20) REVERT: E 124 MET cc_start: 0.7344 (ppp) cc_final: 0.7098 (ppp) REVERT: E 276 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8410 (tm-30) REVERT: E 375 MET cc_start: 0.8986 (tpp) cc_final: 0.8727 (tpp) REVERT: E 382 MET cc_start: 0.8858 (ttm) cc_final: 0.8590 (ttm) REVERT: E 396 MET cc_start: 0.8485 (mtm) cc_final: 0.8040 (mtt) REVERT: C 6 ASP cc_start: 0.8857 (m-30) cc_final: 0.8468 (p0) REVERT: D 90 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7874 (pp20) REVERT: F 124 MET cc_start: 0.7347 (ppp) cc_final: 0.7104 (ppp) REVERT: F 276 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8403 (tm-30) REVERT: F 375 MET cc_start: 0.8998 (tpp) cc_final: 0.8750 (tpp) REVERT: F 382 MET cc_start: 0.8807 (ttm) cc_final: 0.8523 (ttm) REVERT: F 396 MET cc_start: 0.8498 (mtm) cc_final: 0.8037 (mtt) outliers start: 2 outliers final: 2 residues processed: 86 average time/residue: 1.5309 time to fit residues: 141.0320 Evaluate side-chains 88 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP 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 104 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.057924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.036724 restraints weight = 234497.039| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 7.73 r_work: 0.2353 rms_B_bonded: 7.03 restraints_weight: 2.0000 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2368 r_free = 0.2368 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2364 r_free = 0.2364 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.4039 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= 0.213 Angle : 0.595 11.823 14344 Z= 0.294 Chirality : 0.039 0.142 1542 Planarity : 0.004 0.040 1818 Dihedral : 6.837 88.251 1400 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.55 % Allowed : 13.93 % 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: 2.50 (0.24), residues: 1284 helix: 3.09 (0.21), residues: 616 sheet: 0.45 (0.40), residues: 186 loop : 0.28 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.003 0.000 HIS B 146 PHE 0.008 0.001 PHE F 418 TYR 0.010 0.001 TYR F 310 ARG 0.009 0.001 ARG F 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3548.32 seconds wall clock time: 66 minutes 31.72 seconds (3991.72 seconds total)