Starting phenix.real_space_refine on Sun Aug 24 03:41:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frx_29410/08_2025/8frx_29410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frx_29410/08_2025/8frx_29410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8frx_29410/08_2025/8frx_29410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frx_29410/08_2025/8frx_29410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8frx_29410/08_2025/8frx_29410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frx_29410/08_2025/8frx_29410.map" } resolution = 2.7 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 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= 0.003 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10985 2.51 5 N 2705 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16670 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D, E Time building chain proxies: 3.32, per 1000 atoms: 0.20 Number of scatterers: 16670 At special positions: 0 Unit cell: (94.6, 95.7, 172.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2930 8.00 N 2705 7.00 C 10985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 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=0, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 82 " " NAG A 503 " - " ASN A 148 " " NAG A 504 " - " ASN A 164 " " NAG B 502 " - " ASN B 82 " " NAG B 503 " - " ASN B 148 " " NAG B 504 " - " ASN B 164 " " NAG C 502 " - " ASN C 82 " " NAG C 503 " - " ASN C 148 " " NAG C 504 " - " ASN C 164 " " NAG D 502 " - " ASN D 82 " " NAG D 503 " - " ASN D 148 " " NAG D 504 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 901.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 43.5% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.795A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.690A pdb=" N PHE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 271 removed outlier: 4.237A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.908A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 325 through 332 removed outlier: 3.933A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 461 removed outlier: 4.060A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.795A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.690A pdb=" N PHE B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 271 removed outlier: 4.237A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.908A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.932A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 461 removed outlier: 4.061A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 removed outlier: 3.794A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.690A pdb=" N PHE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 271 removed outlier: 4.236A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.908A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 325 through 332 removed outlier: 3.933A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 461 removed outlier: 4.059A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 21 removed outlier: 3.794A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.690A pdb=" N PHE D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 271 removed outlier: 4.237A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.908A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 325 through 332 removed outlier: 3.933A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 461 removed outlier: 4.059A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 21 removed outlier: 3.795A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'E' and resid 228 through 242 removed outlier: 3.690A pdb=" N PHE E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 removed outlier: 4.237A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.908A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 325 through 332 removed outlier: 3.933A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 461 removed outlier: 4.060A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.083A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N GLU A 71 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 13.360A pdb=" N THR A 38 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR A 207 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU A 198 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 89 removed outlier: 7.083A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N GLU B 71 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 13.361A pdb=" N THR B 38 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR B 207 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU B 198 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU B 209 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE B 196 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 89 removed outlier: 7.082A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N GLU C 71 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 13.359A pdb=" N THR C 38 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR C 207 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU C 198 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU C 209 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE C 196 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS C 211 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR C 213 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 192 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C 215 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 89 removed outlier: 7.082A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY D 121 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N GLU D 71 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 13.360A pdb=" N THR D 38 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR D 207 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU D 198 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU D 209 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE D 196 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS D 211 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR D 213 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL D 192 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D 215 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 89 removed outlier: 7.082A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY E 121 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N GLU E 71 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 13.360A pdb=" N THR E 38 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2355 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: 3.04 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5065 1.34 - 1.46: 3908 1.46 - 1.58: 8092 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 17140 Sorted by residual: bond pdb=" C12 Y82 B 501 " pdb=" N4 Y82 B 501 " ideal model delta sigma weight residual 1.464 1.547 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C12 Y82 D 501 " pdb=" N4 Y82 D 501 " ideal model delta sigma weight residual 1.464 1.547 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C12 Y82 C 501 " pdb=" N4 Y82 C 501 " ideal model delta sigma weight residual 1.464 1.547 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C12 Y82 E 501 " pdb=" N4 Y82 E 501 " ideal model delta sigma weight residual 1.464 1.547 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C12 Y82 A 501 " pdb=" N4 Y82 A 501 " ideal model delta sigma weight residual 1.464 1.547 -0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 17135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 22737 2.01 - 4.02: 578 4.02 - 6.03: 76 6.03 - 8.04: 24 8.04 - 10.05: 20 Bond angle restraints: 23435 Sorted by residual: angle pdb=" N ILE C 203 " pdb=" CA ILE C 203 " pdb=" C ILE C 203 " ideal model delta sigma weight residual 110.36 119.33 -8.97 1.05e+00 9.07e-01 7.30e+01 angle pdb=" N ILE B 203 " pdb=" CA ILE B 203 " pdb=" C ILE B 203 " ideal model delta sigma weight residual 110.36 119.33 -8.97 1.05e+00 9.07e-01 7.29e+01 angle pdb=" N ILE A 203 " pdb=" CA ILE A 203 " pdb=" C ILE A 203 " ideal model delta sigma weight residual 110.36 119.32 -8.96 1.05e+00 9.07e-01 7.28e+01 angle pdb=" N ILE E 203 " pdb=" CA ILE E 203 " pdb=" C ILE E 203 " ideal model delta sigma weight residual 110.36 119.31 -8.95 1.05e+00 9.07e-01 7.27e+01 angle pdb=" N ILE D 203 " pdb=" CA ILE D 203 " pdb=" C ILE D 203 " ideal model delta sigma weight residual 110.36 119.28 -8.92 1.05e+00 9.07e-01 7.22e+01 ... (remaining 23430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 9377 15.70 - 31.40: 743 31.40 - 47.09: 215 47.09 - 62.79: 30 62.79 - 78.49: 15 Dihedral angle restraints: 10380 sinusoidal: 4485 harmonic: 5895 Sorted by residual: dihedral pdb=" CG ARG B 424 " pdb=" CD ARG B 424 " pdb=" NE ARG B 424 " pdb=" CZ ARG B 424 " ideal model delta sinusoidal sigma weight residual 90.00 132.98 -42.98 2 1.50e+01 4.44e-03 9.92e+00 dihedral pdb=" CG ARG A 424 " pdb=" CD ARG A 424 " pdb=" NE ARG A 424 " pdb=" CZ ARG A 424 " ideal model delta sinusoidal sigma weight residual 90.00 132.98 -42.98 2 1.50e+01 4.44e-03 9.91e+00 dihedral pdb=" CG ARG E 424 " pdb=" CD ARG E 424 " pdb=" NE ARG E 424 " pdb=" CZ ARG E 424 " ideal model delta sinusoidal sigma weight residual 90.00 132.95 -42.95 2 1.50e+01 4.44e-03 9.91e+00 ... (remaining 10377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2293 0.062 - 0.124: 406 0.124 - 0.185: 46 0.185 - 0.247: 2 0.247 - 0.309: 8 Chirality restraints: 2755 Sorted by residual: chirality pdb=" C15 Y82 C 501 " pdb=" C11 Y82 C 501 " pdb=" C14 Y82 C 501 " pdb=" C16 Y82 C 501 " both_signs ideal model delta sigma weight residual False 2.87 3.18 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C15 Y82 B 501 " pdb=" C11 Y82 B 501 " pdb=" C14 Y82 B 501 " pdb=" C16 Y82 B 501 " both_signs ideal model delta sigma weight residual False 2.87 3.18 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C15 Y82 D 501 " pdb=" C11 Y82 D 501 " pdb=" C14 Y82 D 501 " pdb=" C16 Y82 D 501 " both_signs ideal model delta sigma weight residual False 2.87 3.18 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2752 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 280 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 281 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 280 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 281 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 280 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 281 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 281 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 281 " -0.024 5.00e-02 4.00e+02 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3245 2.78 - 3.31: 15102 3.31 - 3.84: 27212 3.84 - 4.37: 30126 4.37 - 4.90: 53615 Nonbonded interactions: 129300 Sorted by model distance: nonbonded pdb=" OH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 2.253 3.040 ... (remaining 129295 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.004 0.083 17160 Z= 0.231 Angle : 0.771 10.049 23490 Z= 0.440 Chirality : 0.050 0.309 2755 Planarity : 0.004 0.042 2840 Dihedral : 12.616 78.488 6525 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.20), residues: 1955 helix: 1.92 (0.20), residues: 775 sheet: -0.62 (0.25), residues: 425 loop : -1.31 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.018 0.001 TYR B 67 PHE 0.018 0.001 PHE C 199 TRP 0.018 0.001 TRP C 456 HIS 0.001 0.000 HIS E 158 Details of bonding type rmsd covalent geometry : bond 0.00415 (17140) covalent geometry : angle 0.76961 (23435) SS BOND : bond 0.00037 ( 5) SS BOND : angle 0.10363 ( 10) hydrogen bonds : bond 0.12754 ( 815) hydrogen bonds : angle 5.14897 ( 2355) link_NAG-ASN : bond 0.00062 ( 15) link_NAG-ASN : angle 1.46558 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.5562 time to fit residues: 85.7715 Evaluate side-chains 84 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN C 125 ASN D 125 ASN E 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.063392 restraints weight = 34068.050| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.52 r_work: 0.2781 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17160 Z= 0.181 Angle : 0.598 11.092 23490 Z= 0.295 Chirality : 0.044 0.161 2755 Planarity : 0.004 0.031 2840 Dihedral : 5.602 58.076 2645 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.65 % Allowed : 6.99 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1955 helix: 2.29 (0.19), residues: 775 sheet: -0.50 (0.25), residues: 400 loop : -0.89 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 328 TYR 0.022 0.001 TYR B 67 PHE 0.009 0.001 PHE C 254 TRP 0.018 0.002 TRP A 320 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00438 (17140) covalent geometry : angle 0.59512 (23435) SS BOND : bond 0.00048 ( 5) SS BOND : angle 0.46471 ( 10) hydrogen bonds : bond 0.04646 ( 815) hydrogen bonds : angle 4.11961 ( 2355) link_NAG-ASN : bond 0.00164 ( 15) link_NAG-ASN : angle 1.57157 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 HIS cc_start: 0.7135 (m90) cc_final: 0.6838 (m-70) REVERT: B 322 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8385 (mmp80) REVERT: B 419 MET cc_start: 0.7887 (mmm) cc_final: 0.7611 (mmm) REVERT: C 411 HIS cc_start: 0.7119 (m90) cc_final: 0.6910 (m-70) REVERT: D 411 HIS cc_start: 0.7027 (m90) cc_final: 0.6725 (m90) REVERT: D 414 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7645 (mm-30) outliers start: 12 outliers final: 1 residues processed: 121 average time/residue: 0.5551 time to fit residues: 75.9365 Evaluate side-chains 95 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain D residue 332 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN C 125 ASN C 183 ASN D 125 ASN E 125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.098946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.064510 restraints weight = 34171.570| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.55 r_work: 0.2804 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17160 Z= 0.106 Angle : 0.540 12.791 23490 Z= 0.261 Chirality : 0.042 0.147 2755 Planarity : 0.003 0.030 2840 Dihedral : 5.276 54.784 2645 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.03 % Allowed : 7.32 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1955 helix: 2.65 (0.19), residues: 750 sheet: -0.68 (0.24), residues: 420 loop : -0.78 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 328 TYR 0.014 0.001 TYR D 67 PHE 0.011 0.001 PHE B 233 TRP 0.018 0.001 TRP A 320 HIS 0.001 0.000 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00232 (17140) covalent geometry : angle 0.53678 (23435) SS BOND : bond 0.00010 ( 5) SS BOND : angle 0.02689 ( 10) hydrogen bonds : bond 0.04113 ( 815) hydrogen bonds : angle 3.87267 ( 2355) link_NAG-ASN : bond 0.00111 ( 15) link_NAG-ASN : angle 1.43767 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 HIS cc_start: 0.7154 (m90) cc_final: 0.6902 (m-70) REVERT: B 108 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8390 (mtmm) REVERT: B 322 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8428 (mmp80) REVERT: B 419 MET cc_start: 0.7800 (mmm) cc_final: 0.7589 (mmm) REVERT: C 324 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8223 (tt) REVERT: C 411 HIS cc_start: 0.7159 (m90) cc_final: 0.6907 (m-70) REVERT: D 324 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8250 (tt) REVERT: D 411 HIS cc_start: 0.7138 (m90) cc_final: 0.6836 (m90) REVERT: E 324 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8172 (tt) outliers start: 19 outliers final: 7 residues processed: 118 average time/residue: 0.5081 time to fit residues: 68.8155 Evaluate side-chains 105 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 17 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 179 optimal weight: 0.0020 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN B 183 ASN C 125 ASN D 125 ASN E 125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.062031 restraints weight = 34083.537| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.50 r_work: 0.2737 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 17160 Z= 0.227 Angle : 0.612 10.798 23490 Z= 0.303 Chirality : 0.046 0.152 2755 Planarity : 0.004 0.030 2840 Dihedral : 5.659 58.482 2645 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.73 % Allowed : 9.21 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1955 helix: 2.35 (0.19), residues: 775 sheet: -0.35 (0.25), residues: 400 loop : -1.05 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 328 TYR 0.025 0.001 TYR D 67 PHE 0.012 0.001 PHE B 233 TRP 0.020 0.002 TRP D 320 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00551 (17140) covalent geometry : angle 0.60706 (23435) SS BOND : bond 0.00074 ( 5) SS BOND : angle 0.60649 ( 10) hydrogen bonds : bond 0.05065 ( 815) hydrogen bonds : angle 4.00705 ( 2355) link_NAG-ASN : bond 0.00289 ( 15) link_NAG-ASN : angle 1.88557 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9405 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: A 411 HIS cc_start: 0.7299 (m90) cc_final: 0.7055 (m-70) REVERT: B 322 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8388 (mmp80) REVERT: C 324 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8210 (tt) REVERT: C 411 HIS cc_start: 0.7191 (m90) cc_final: 0.6934 (m-70) REVERT: D 324 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8290 (tt) REVERT: D 411 HIS cc_start: 0.7199 (m90) cc_final: 0.6874 (m90) REVERT: E 324 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8183 (tt) outliers start: 32 outliers final: 16 residues processed: 127 average time/residue: 0.4549 time to fit residues: 67.1463 Evaluate side-chains 111 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 165 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.063832 restraints weight = 33601.552| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.48 r_work: 0.2784 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17160 Z= 0.113 Angle : 0.536 13.883 23490 Z= 0.261 Chirality : 0.043 0.146 2755 Planarity : 0.003 0.030 2840 Dihedral : 5.296 54.858 2645 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.95 % Allowed : 10.24 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.20), residues: 1955 helix: 2.47 (0.19), residues: 780 sheet: -0.58 (0.24), residues: 420 loop : -0.94 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 328 TYR 0.013 0.001 TYR B 67 PHE 0.011 0.001 PHE D 233 TRP 0.022 0.001 TRP D 320 HIS 0.002 0.000 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00251 (17140) covalent geometry : angle 0.53250 (23435) SS BOND : bond 0.00021 ( 5) SS BOND : angle 0.05842 ( 10) hydrogen bonds : bond 0.04329 ( 815) hydrogen bonds : angle 3.82171 ( 2355) link_NAG-ASN : bond 0.00092 ( 15) link_NAG-ASN : angle 1.53393 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9359 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: A 324 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 411 HIS cc_start: 0.7186 (m90) cc_final: 0.6924 (m-70) REVERT: B 108 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8437 (mtmm) REVERT: B 116 TYR cc_start: 0.9390 (OUTLIER) cc_final: 0.8846 (m-80) REVERT: B 322 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8334 (mmp80) REVERT: C 324 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8188 (tt) REVERT: C 411 HIS cc_start: 0.7260 (m90) cc_final: 0.7023 (m-70) REVERT: D 324 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8334 (tt) REVERT: D 411 HIS cc_start: 0.7220 (m90) cc_final: 0.6912 (m90) REVERT: E 333 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7880 (mt) outliers start: 36 outliers final: 18 residues processed: 133 average time/residue: 0.4545 time to fit residues: 70.1028 Evaluate side-chains 122 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 114 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 151 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 187 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.098446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063979 restraints weight = 33754.389| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.58 r_work: 0.2772 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17160 Z= 0.103 Angle : 0.546 14.292 23490 Z= 0.261 Chirality : 0.043 0.144 2755 Planarity : 0.003 0.029 2840 Dihedral : 5.235 55.153 2645 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.68 % Allowed : 11.33 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1955 helix: 2.49 (0.19), residues: 780 sheet: -0.59 (0.24), residues: 420 loop : -0.79 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 328 TYR 0.013 0.001 TYR E 67 PHE 0.011 0.001 PHE E 233 TRP 0.024 0.001 TRP D 320 HIS 0.001 0.000 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00220 (17140) covalent geometry : angle 0.54238 (23435) SS BOND : bond 0.00023 ( 5) SS BOND : angle 0.05943 ( 10) hydrogen bonds : bond 0.04097 ( 815) hydrogen bonds : angle 3.72420 ( 2355) link_NAG-ASN : bond 0.00070 ( 15) link_NAG-ASN : angle 1.49102 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9359 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: A 324 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 411 HIS cc_start: 0.7155 (m90) cc_final: 0.6919 (m-70) REVERT: B 108 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8409 (mtmm) REVERT: B 116 TYR cc_start: 0.9377 (OUTLIER) cc_final: 0.8829 (m-80) REVERT: B 315 ARG cc_start: 0.7062 (tpt170) cc_final: 0.6832 (tpt170) REVERT: C 324 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8146 (tt) REVERT: C 411 HIS cc_start: 0.7238 (m90) cc_final: 0.6977 (m-70) REVERT: D 324 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8254 (tt) REVERT: D 411 HIS cc_start: 0.7174 (m90) cc_final: 0.6874 (m90) REVERT: E 333 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7858 (mt) outliers start: 31 outliers final: 16 residues processed: 129 average time/residue: 0.4130 time to fit residues: 62.6238 Evaluate side-chains 118 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 2.9990 chunk 168 optimal weight: 0.0970 chunk 86 optimal weight: 0.2980 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 0.0060 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.098899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.064362 restraints weight = 33613.180| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.57 r_work: 0.2783 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17160 Z= 0.099 Angle : 0.549 15.177 23490 Z= 0.260 Chirality : 0.042 0.148 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.176 54.784 2645 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.46 % Allowed : 11.82 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.20), residues: 1955 helix: 2.59 (0.19), residues: 775 sheet: -0.59 (0.24), residues: 420 loop : -0.78 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 328 TYR 0.012 0.001 TYR E 67 PHE 0.016 0.001 PHE B 233 TRP 0.025 0.001 TRP C 456 HIS 0.002 0.000 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00212 (17140) covalent geometry : angle 0.54566 (23435) SS BOND : bond 0.00035 ( 5) SS BOND : angle 0.09518 ( 10) hydrogen bonds : bond 0.03908 ( 815) hydrogen bonds : angle 3.66589 ( 2355) link_NAG-ASN : bond 0.00091 ( 15) link_NAG-ASN : angle 1.44985 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8278 (mtmm) REVERT: A 116 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: A 324 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8035 (tt) REVERT: A 411 HIS cc_start: 0.7083 (m90) cc_final: 0.6838 (m-70) REVERT: B 108 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8420 (mtmm) REVERT: B 116 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: C 324 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8163 (tt) REVERT: C 411 HIS cc_start: 0.7211 (m90) cc_final: 0.6932 (m-70) REVERT: D 324 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8220 (tt) REVERT: D 411 HIS cc_start: 0.7154 (m90) cc_final: 0.6853 (m90) REVERT: E 333 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8004 (mt) outliers start: 27 outliers final: 20 residues processed: 131 average time/residue: 0.4197 time to fit residues: 64.4638 Evaluate side-chains 123 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 23 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.098206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.063495 restraints weight = 33805.463| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.58 r_work: 0.2762 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17160 Z= 0.122 Angle : 0.571 15.172 23490 Z= 0.270 Chirality : 0.043 0.152 2755 Planarity : 0.003 0.027 2840 Dihedral : 5.259 55.945 2645 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.41 % Allowed : 12.30 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.20), residues: 1955 helix: 2.53 (0.19), residues: 775 sheet: -0.56 (0.24), residues: 420 loop : -0.82 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 328 TYR 0.016 0.001 TYR E 67 PHE 0.011 0.001 PHE E 233 TRP 0.027 0.002 TRP A 456 HIS 0.002 0.000 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00281 (17140) covalent geometry : angle 0.56769 (23435) SS BOND : bond 0.00016 ( 5) SS BOND : angle 0.12036 ( 10) hydrogen bonds : bond 0.04084 ( 815) hydrogen bonds : angle 3.70685 ( 2355) link_NAG-ASN : bond 0.00063 ( 15) link_NAG-ASN : angle 1.56623 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9382 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: A 324 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8044 (tt) REVERT: A 411 HIS cc_start: 0.7100 (m90) cc_final: 0.6850 (m-70) REVERT: B 108 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8395 (mtmm) REVERT: B 116 TYR cc_start: 0.9402 (OUTLIER) cc_final: 0.8897 (m-10) REVERT: C 324 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 411 HIS cc_start: 0.7257 (m90) cc_final: 0.6998 (m-70) REVERT: D 91 ASP cc_start: 0.8967 (p0) cc_final: 0.8650 (p0) REVERT: D 324 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8211 (tt) REVERT: D 411 HIS cc_start: 0.7177 (m90) cc_final: 0.6866 (m90) outliers start: 26 outliers final: 20 residues processed: 123 average time/residue: 0.4394 time to fit residues: 63.1221 Evaluate side-chains 120 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 6 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 156 optimal weight: 0.0040 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.099205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064712 restraints weight = 33575.367| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.57 r_work: 0.2792 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17160 Z= 0.098 Angle : 0.557 14.091 23490 Z= 0.264 Chirality : 0.042 0.145 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.134 54.366 2645 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.46 % Allowed : 12.41 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1955 helix: 2.59 (0.19), residues: 775 sheet: -0.59 (0.24), residues: 420 loop : -0.74 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 328 TYR 0.011 0.001 TYR E 67 PHE 0.010 0.001 PHE E 233 TRP 0.029 0.002 TRP C 456 HIS 0.001 0.000 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00211 (17140) covalent geometry : angle 0.55455 (23435) SS BOND : bond 0.00046 ( 5) SS BOND : angle 0.14751 ( 10) hydrogen bonds : bond 0.03766 ( 815) hydrogen bonds : angle 3.63028 ( 2355) link_NAG-ASN : bond 0.00123 ( 15) link_NAG-ASN : angle 1.43190 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9359 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: A 324 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8028 (tt) REVERT: A 411 HIS cc_start: 0.7065 (m90) cc_final: 0.6825 (m-70) REVERT: B 108 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8411 (mtmm) REVERT: B 116 TYR cc_start: 0.9381 (OUTLIER) cc_final: 0.8831 (m-10) REVERT: C 324 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8147 (tt) REVERT: C 411 HIS cc_start: 0.7270 (m90) cc_final: 0.7013 (m-70) REVERT: D 91 ASP cc_start: 0.8957 (p0) cc_final: 0.8637 (p0) REVERT: D 197 LYS cc_start: 0.8652 (tttm) cc_final: 0.8313 (tppt) REVERT: D 324 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8223 (tt) REVERT: D 411 HIS cc_start: 0.7144 (m90) cc_final: 0.6848 (m90) REVERT: E 333 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8036 (mt) outliers start: 27 outliers final: 20 residues processed: 125 average time/residue: 0.4129 time to fit residues: 60.0321 Evaluate side-chains 122 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 133 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.097896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.063420 restraints weight = 33427.549| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.56 r_work: 0.2757 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17160 Z= 0.131 Angle : 0.606 16.498 23490 Z= 0.285 Chirality : 0.043 0.162 2755 Planarity : 0.003 0.035 2840 Dihedral : 5.288 56.412 2645 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.36 % Allowed : 12.79 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.20), residues: 1955 helix: 2.51 (0.19), residues: 775 sheet: -0.55 (0.24), residues: 420 loop : -0.80 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 328 TYR 0.018 0.001 TYR E 67 PHE 0.011 0.001 PHE E 233 TRP 0.031 0.002 TRP A 456 HIS 0.002 0.000 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00308 (17140) covalent geometry : angle 0.60253 (23435) SS BOND : bond 0.00011 ( 5) SS BOND : angle 0.18731 ( 10) hydrogen bonds : bond 0.04113 ( 815) hydrogen bonds : angle 3.71027 ( 2355) link_NAG-ASN : bond 0.00095 ( 15) link_NAG-ASN : angle 1.61855 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9397 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: A 324 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7979 (tt) REVERT: A 411 HIS cc_start: 0.7070 (m90) cc_final: 0.6851 (m-70) REVERT: B 116 TYR cc_start: 0.9412 (OUTLIER) cc_final: 0.8846 (m-80) REVERT: C 324 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 411 HIS cc_start: 0.7243 (m90) cc_final: 0.6951 (m-70) REVERT: D 91 ASP cc_start: 0.8972 (p0) cc_final: 0.8659 (p0) REVERT: D 324 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8193 (tt) REVERT: D 411 HIS cc_start: 0.7177 (m90) cc_final: 0.6868 (m90) outliers start: 25 outliers final: 20 residues processed: 119 average time/residue: 0.4014 time to fit residues: 56.1721 Evaluate side-chains 120 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 50 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN D 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.062614 restraints weight = 33482.825| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.56 r_work: 0.2742 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17160 Z= 0.154 Angle : 0.617 15.464 23490 Z= 0.293 Chirality : 0.044 0.160 2755 Planarity : 0.003 0.033 2840 Dihedral : 5.397 56.517 2645 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.36 % Allowed : 12.90 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.20), residues: 1955 helix: 2.44 (0.19), residues: 775 sheet: -0.56 (0.24), residues: 420 loop : -0.91 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 328 TYR 0.019 0.001 TYR D 67 PHE 0.014 0.001 PHE D 233 TRP 0.032 0.002 TRP A 456 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00369 (17140) covalent geometry : angle 0.61351 (23435) SS BOND : bond 0.00014 ( 5) SS BOND : angle 0.25880 ( 10) hydrogen bonds : bond 0.04453 ( 815) hydrogen bonds : angle 3.81575 ( 2355) link_NAG-ASN : bond 0.00114 ( 15) link_NAG-ASN : angle 1.72450 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5659.37 seconds wall clock time: 97 minutes 25.33 seconds (5845.33 seconds total)