Starting phenix.real_space_refine on Sun Jun 15 00:23:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frx_29410/06_2025/8frx_29410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frx_29410/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8frx_29410/06_2025/8frx_29410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frx_29410/06_2025/8frx_29410.map" model { file = "/net/cci-nas-00/data/ceres_data/8frx_29410/06_2025/8frx_29410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frx_29410/06_2025/8frx_29410.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D Time building chain proxies: 7.42, per 1000 atoms: 0.45 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 C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 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: 3.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.50 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: 4.57 Time building geometry restraints manager: 4.61 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 1.150 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.730 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.018 0.001 TRP C 456 HIS 0.001 0.000 HIS E 158 PHE 0.018 0.001 PHE C 199 TYR 0.018 0.001 TYR B 67 ARG 0.003 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 15) link_NAG-ASN : angle 1.46558 ( 45) hydrogen bonds : bond 0.12754 ( 815) hydrogen bonds : angle 5.14897 ( 2355) SS BOND : bond 0.00037 ( 5) SS BOND : angle 0.10363 ( 10) covalent geometry : bond 0.00415 (17140) covalent geometry : angle 0.76961 (23435) *********************** 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 : 2.023 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: 1.1012 time to fit residues: 172.5076 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 : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.097787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063284 restraints weight = 33895.351| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.50 r_work: 0.2779 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17160 Z= 0.180 Angle : 0.599 11.147 23490 Z= 0.295 Chirality : 0.045 0.162 2755 Planarity : 0.004 0.031 2840 Dihedral : 5.610 58.289 2645 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.65 % Allowed : 7.21 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1955 helix: 2.29 (0.19), residues: 775 sheet: -0.50 (0.25), residues: 400 loop : -0.88 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 320 HIS 0.003 0.001 HIS C 309 PHE 0.009 0.001 PHE C 254 TYR 0.023 0.001 TYR B 67 ARG 0.009 0.001 ARG D 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 15) link_NAG-ASN : angle 1.55506 ( 45) hydrogen bonds : bond 0.04655 ( 815) hydrogen bonds : angle 4.11606 ( 2355) SS BOND : bond 0.00056 ( 5) SS BOND : angle 0.47193 ( 10) covalent geometry : bond 0.00433 (17140) covalent geometry : angle 0.59553 (23435) *********************** 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 124 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 HIS cc_start: 0.7101 (m90) cc_final: 0.6848 (m-70) REVERT: B 322 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8368 (mmp80) REVERT: B 419 MET cc_start: 0.7882 (mmm) cc_final: 0.7611 (mmm) REVERT: C 411 HIS cc_start: 0.7123 (m90) cc_final: 0.6877 (m-70) REVERT: D 411 HIS cc_start: 0.7041 (m90) cc_final: 0.6750 (m90) REVERT: D 414 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7630 (mm-30) outliers start: 12 outliers final: 1 residues processed: 120 average time/residue: 1.4557 time to fit residues: 201.1808 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 : 1.501 ------------------------------------------------------------------------------- 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 3 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.098892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.064756 restraints weight = 33593.934| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.51 r_work: 0.2805 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17160 Z= 0.106 Angle : 0.544 13.134 23490 Z= 0.262 Chirality : 0.043 0.147 2755 Planarity : 0.003 0.029 2840 Dihedral : 5.295 54.955 2645 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.03 % Allowed : 7.48 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1955 helix: 2.68 (0.19), residues: 750 sheet: -0.49 (0.25), residues: 400 loop : -0.85 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 320 HIS 0.002 0.000 HIS C 18 PHE 0.010 0.001 PHE B 233 TYR 0.015 0.001 TYR B 67 ARG 0.008 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 15) link_NAG-ASN : angle 1.44948 ( 45) hydrogen bonds : bond 0.04142 ( 815) hydrogen bonds : angle 3.88446 ( 2355) SS BOND : bond 0.00007 ( 5) SS BOND : angle 0.03106 ( 10) covalent geometry : bond 0.00229 (17140) covalent geometry : angle 0.54054 (23435) *********************** 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 121 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 HIS cc_start: 0.7155 (m90) cc_final: 0.6955 (m-70) REVERT: B 108 LYS cc_start: 0.8852 (mmmt) cc_final: 0.8374 (mtmm) REVERT: B 322 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8436 (mmp80) REVERT: B 419 MET cc_start: 0.7803 (mmm) cc_final: 0.7596 (mmm) REVERT: C 324 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8218 (tt) REVERT: C 411 HIS cc_start: 0.7179 (m90) cc_final: 0.6949 (m-70) REVERT: D 324 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8262 (tt) REVERT: D 411 HIS cc_start: 0.7144 (m90) cc_final: 0.6840 (m90) REVERT: E 324 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8168 (tt) outliers start: 19 outliers final: 7 residues processed: 116 average time/residue: 1.0231 time to fit residues: 137.7133 Evaluate side-chains 103 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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 109 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.098631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.064039 restraints weight = 33537.138| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.56 r_work: 0.2776 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17160 Z= 0.107 Angle : 0.525 10.727 23490 Z= 0.256 Chirality : 0.043 0.145 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.253 55.511 2645 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.63 % Allowed : 7.97 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1955 helix: 2.51 (0.19), residues: 780 sheet: -0.61 (0.24), residues: 420 loop : -0.81 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 320 HIS 0.002 0.000 HIS C 18 PHE 0.010 0.001 PHE B 233 TYR 0.015 0.001 TYR E 67 ARG 0.010 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 15) link_NAG-ASN : angle 1.46514 ( 45) hydrogen bonds : bond 0.04031 ( 815) hydrogen bonds : angle 3.76927 ( 2355) SS BOND : bond 0.00012 ( 5) SS BOND : angle 0.05679 ( 10) covalent geometry : bond 0.00238 (17140) covalent geometry : angle 0.52149 (23435) *********************** 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: 30 poor density : 103 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: A 411 HIS cc_start: 0.7119 (m90) cc_final: 0.6885 (m-70) REVERT: B 108 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8329 (mtmm) REVERT: B 315 ARG cc_start: 0.7211 (tpt170) cc_final: 0.6765 (tpt170) REVERT: B 322 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8411 (mmp80) REVERT: B 419 MET cc_start: 0.7738 (mmm) cc_final: 0.7522 (mmm) REVERT: C 324 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8206 (tt) REVERT: C 411 HIS cc_start: 0.7177 (m90) cc_final: 0.6945 (m-70) REVERT: D 324 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8297 (tt) REVERT: D 411 HIS cc_start: 0.7147 (m90) cc_final: 0.6842 (m90) outliers start: 30 outliers final: 14 residues processed: 129 average time/residue: 0.9376 time to fit residues: 141.9633 Evaluate side-chains 115 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 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 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 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 332 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 58 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.099477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.065023 restraints weight = 33823.385| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.58 r_work: 0.2795 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17160 Z= 0.094 Angle : 0.509 14.681 23490 Z= 0.246 Chirality : 0.042 0.145 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.138 54.592 2645 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.57 % Allowed : 9.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1955 helix: 2.59 (0.19), residues: 780 sheet: -0.59 (0.24), residues: 420 loop : -0.77 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 320 HIS 0.002 0.000 HIS E 323 PHE 0.008 0.001 PHE E 233 TYR 0.012 0.001 TYR E 67 ARG 0.006 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 15) link_NAG-ASN : angle 1.38402 ( 45) hydrogen bonds : bond 0.03773 ( 815) hydrogen bonds : angle 3.67338 ( 2355) SS BOND : bond 0.00036 ( 5) SS BOND : angle 0.10234 ( 10) covalent geometry : bond 0.00195 (17140) covalent geometry : angle 0.50557 (23435) *********************** 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 129 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9323 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: A 411 HIS cc_start: 0.7035 (m90) cc_final: 0.6835 (m-70) REVERT: B 108 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8368 (mtmm) REVERT: B 322 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8382 (mmp80) REVERT: B 419 MET cc_start: 0.7713 (mmm) cc_final: 0.7461 (mmm) REVERT: C 324 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8087 (tt) REVERT: C 411 HIS cc_start: 0.7187 (m90) cc_final: 0.6936 (m-70) REVERT: D 324 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8244 (tt) REVERT: D 411 HIS cc_start: 0.7092 (m90) cc_final: 0.6797 (m-70) REVERT: E 333 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7767 (mt) outliers start: 29 outliers final: 16 residues processed: 125 average time/residue: 1.2476 time to fit residues: 186.9411 Evaluate side-chains 115 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 3.058 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 26 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 77 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.0670 chunk 188 optimal weight: 0.2980 chunk 123 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.099988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.065461 restraints weight = 33703.127| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.58 r_work: 0.2806 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17160 Z= 0.092 Angle : 0.523 14.702 23490 Z= 0.247 Chirality : 0.042 0.165 2755 Planarity : 0.003 0.027 2840 Dihedral : 5.093 54.734 2645 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.41 % Allowed : 10.30 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1955 helix: 2.58 (0.19), residues: 785 sheet: -0.60 (0.24), residues: 420 loop : -0.70 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 320 HIS 0.001 0.000 HIS C 18 PHE 0.016 0.001 PHE B 233 TYR 0.012 0.001 TYR E 67 ARG 0.008 0.000 ARG E 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 15) link_NAG-ASN : angle 1.37234 ( 45) hydrogen bonds : bond 0.03635 ( 815) hydrogen bonds : angle 3.61520 ( 2355) SS BOND : bond 0.00039 ( 5) SS BOND : angle 0.11426 ( 10) covalent geometry : bond 0.00190 (17140) covalent geometry : angle 0.52033 (23435) *********************** 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 126 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: A 324 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8055 (tt) REVERT: A 411 HIS cc_start: 0.7024 (m90) cc_final: 0.6782 (m-70) REVERT: B 108 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8412 (mtmm) REVERT: B 419 MET cc_start: 0.7684 (mmm) cc_final: 0.7430 (mmm) REVERT: C 324 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8068 (tt) REVERT: C 411 HIS cc_start: 0.7234 (m90) cc_final: 0.6975 (m-70) REVERT: D 324 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8234 (tt) REVERT: D 411 HIS cc_start: 0.7129 (m90) cc_final: 0.6831 (m90) REVERT: E 333 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7838 (mt) outliers start: 26 outliers final: 17 residues processed: 125 average time/residue: 0.8912 time to fit residues: 130.4604 Evaluate side-chains 114 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 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 317 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.098750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.064038 restraints weight = 33710.785| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.58 r_work: 0.2774 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17160 Z= 0.120 Angle : 0.553 14.908 23490 Z= 0.264 Chirality : 0.043 0.179 2755 Planarity : 0.003 0.081 2840 Dihedral : 5.214 56.072 2645 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.46 % Allowed : 11.17 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1955 helix: 2.50 (0.19), residues: 780 sheet: -0.56 (0.24), residues: 420 loop : -0.70 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 320 HIS 0.002 0.000 HIS C 18 PHE 0.013 0.001 PHE E 233 TYR 0.016 0.001 TYR E 67 ARG 0.014 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.53413 ( 45) hydrogen bonds : bond 0.03927 ( 815) hydrogen bonds : angle 3.68139 ( 2355) SS BOND : bond 0.00013 ( 5) SS BOND : angle 0.15096 ( 10) covalent geometry : bond 0.00276 (17140) covalent geometry : angle 0.54941 (23435) *********************** 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 129 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8308 (mtmm) REVERT: A 116 TYR cc_start: 0.9370 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: A 324 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8046 (tt) REVERT: A 411 HIS cc_start: 0.7055 (m90) cc_final: 0.6803 (m-70) REVERT: B 322 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8391 (mmp80) REVERT: B 419 MET cc_start: 0.7711 (mmm) cc_final: 0.7461 (mmm) REVERT: C 324 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8114 (tt) REVERT: C 411 HIS cc_start: 0.7234 (m90) cc_final: 0.6981 (m-70) REVERT: D 324 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8249 (tt) REVERT: D 411 HIS cc_start: 0.7125 (m90) cc_final: 0.6842 (m90) REVERT: E 333 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7893 (mt) outliers start: 27 outliers final: 16 residues processed: 129 average time/residue: 0.8657 time to fit residues: 131.8586 Evaluate side-chains 114 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 159 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.095853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.061562 restraints weight = 34029.295| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.52 r_work: 0.2732 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 17160 Z= 0.236 Angle : 0.664 16.088 23490 Z= 0.320 Chirality : 0.047 0.172 2755 Planarity : 0.004 0.029 2840 Dihedral : 5.713 58.713 2645 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.68 % Allowed : 11.76 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1955 helix: 2.29 (0.19), residues: 775 sheet: -0.29 (0.24), residues: 400 loop : -1.03 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 456 HIS 0.004 0.001 HIS C 18 PHE 0.013 0.001 PHE B 233 TYR 0.028 0.002 TYR D 67 ARG 0.016 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 15) link_NAG-ASN : angle 2.02889 ( 45) hydrogen bonds : bond 0.05226 ( 815) hydrogen bonds : angle 4.04313 ( 2355) SS BOND : bond 0.00088 ( 5) SS BOND : angle 0.68791 ( 10) covalent geometry : bond 0.00575 (17140) covalent geometry : angle 0.65906 (23435) *********************** 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: 31 poor density : 94 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9423 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: A 324 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 411 HIS cc_start: 0.7361 (m90) cc_final: 0.7097 (m-70) REVERT: B 108 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8509 (mtmm) REVERT: B 322 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8328 (mmp80) REVERT: C 411 HIS cc_start: 0.7323 (m90) cc_final: 0.7018 (m-70) REVERT: D 91 ASP cc_start: 0.9033 (p0) cc_final: 0.8745 (p0) REVERT: D 324 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8417 (tt) REVERT: D 411 HIS cc_start: 0.7230 (m90) cc_final: 0.6910 (m90) REVERT: E 324 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8146 (tt) outliers start: 31 outliers final: 19 residues processed: 121 average time/residue: 0.8535 time to fit residues: 121.7678 Evaluate side-chains 114 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 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 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 324 LEU 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 76 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 124 optimal weight: 0.0570 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 E 125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.063756 restraints weight = 33527.021| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.57 r_work: 0.2771 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1887 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= 0.106 Angle : 0.579 15.026 23490 Z= 0.273 Chirality : 0.043 0.171 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.274 54.847 2645 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.36 % Allowed : 12.25 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1955 helix: 2.47 (0.19), residues: 780 sheet: -0.60 (0.24), residues: 420 loop : -0.84 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 456 HIS 0.002 0.000 HIS B 158 PHE 0.009 0.001 PHE D 233 TYR 0.012 0.001 TYR E 67 ARG 0.009 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 15) link_NAG-ASN : angle 1.54910 ( 45) hydrogen bonds : bond 0.04254 ( 815) hydrogen bonds : angle 3.79864 ( 2355) SS BOND : bond 0.00008 ( 5) SS BOND : angle 0.13589 ( 10) covalent geometry : bond 0.00222 (17140) covalent geometry : angle 0.57583 (23435) *********************** 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 123 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: A 324 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8117 (tt) REVERT: A 411 HIS cc_start: 0.7166 (m90) cc_final: 0.6924 (m-70) REVERT: B 108 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8342 (mtmm) REVERT: B 116 TYR cc_start: 0.9359 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: C 324 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8133 (tt) REVERT: C 411 HIS cc_start: 0.7258 (m90) cc_final: 0.6987 (m-70) REVERT: D 91 ASP cc_start: 0.8964 (p0) cc_final: 0.8649 (p0) REVERT: D 324 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8311 (tt) REVERT: D 411 HIS cc_start: 0.7224 (m90) cc_final: 0.6931 (m90) REVERT: E 315 ARG cc_start: 0.8858 (mtp180) cc_final: 0.8611 (tpt90) REVERT: E 324 LEU cc_start: 0.8287 (tm) cc_final: 0.8025 (tt) outliers start: 25 outliers final: 19 residues processed: 123 average time/residue: 0.8418 time to fit residues: 123.3611 Evaluate side-chains 117 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 179 optimal weight: 0.0970 chunk 113 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 0.3980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.098528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.063887 restraints weight = 33588.799| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.58 r_work: 0.2771 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17160 Z= 0.109 Angle : 0.584 15.092 23490 Z= 0.273 Chirality : 0.043 0.160 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.238 55.484 2645 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1955 helix: 2.49 (0.19), residues: 780 sheet: -0.60 (0.24), residues: 420 loop : -0.81 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 456 HIS 0.002 0.000 HIS C 18 PHE 0.010 0.001 PHE B 233 TYR 0.014 0.001 TYR E 67 ARG 0.009 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 15) link_NAG-ASN : angle 1.54910 ( 45) hydrogen bonds : bond 0.04064 ( 815) hydrogen bonds : angle 3.72947 ( 2355) SS BOND : bond 0.00008 ( 5) SS BOND : angle 0.04239 ( 10) covalent geometry : bond 0.00244 (17140) covalent geometry : angle 0.58074 (23435) ********************** 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 120 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9385 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: A 324 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7993 (tt) REVERT: A 411 HIS cc_start: 0.7112 (m90) cc_final: 0.6857 (m-70) REVERT: B 108 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8351 (mtmm) REVERT: B 116 TYR cc_start: 0.9386 (OUTLIER) cc_final: 0.8940 (m-10) REVERT: C 315 ARG cc_start: 0.6883 (tpt170) cc_final: 0.6447 (tpm170) REVERT: C 324 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8094 (tp) REVERT: C 411 HIS cc_start: 0.7272 (m90) cc_final: 0.6983 (m-70) REVERT: D 91 ASP cc_start: 0.8966 (p0) cc_final: 0.8670 (p0) REVERT: D 324 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8222 (tt) REVERT: D 411 HIS cc_start: 0.7186 (m90) cc_final: 0.6899 (m90) outliers start: 26 outliers final: 19 residues processed: 117 average time/residue: 0.9572 time to fit residues: 135.0895 Evaluate side-chains 115 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 2.202 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 135 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.098427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.063821 restraints weight = 33557.742| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.58 r_work: 0.2769 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17160 Z= 0.116 Angle : 0.581 14.866 23490 Z= 0.274 Chirality : 0.043 0.158 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.236 55.409 2645 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.41 % Allowed : 12.25 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1955 helix: 2.47 (0.19), residues: 780 sheet: -0.58 (0.24), residues: 420 loop : -0.81 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 456 HIS 0.002 0.000 HIS C 18 PHE 0.011 0.001 PHE D 233 TYR 0.015 0.001 TYR E 67 ARG 0.011 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 15) link_NAG-ASN : angle 1.56594 ( 45) hydrogen bonds : bond 0.04060 ( 815) hydrogen bonds : angle 3.73167 ( 2355) SS BOND : bond 0.00011 ( 5) SS BOND : angle 0.06473 ( 10) covalent geometry : bond 0.00265 (17140) covalent geometry : angle 0.57720 (23435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12351.92 seconds wall clock time: 214 minutes 31.07 seconds (12871.07 seconds total)