Starting phenix.real_space_refine on Mon Nov 18 15:01:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/11_2024/8frx_29410.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/11_2024/8frx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/11_2024/8frx_29410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/11_2024/8frx_29410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/11_2024/8frx_29410.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/11_2024/8frx_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-5513/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: 7.78, per 1000 atoms: 0.47 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 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: 4.18 Conformation dependent library (CDL) restraints added in 2.1 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: 1.55 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: 5.08 Time building geometry restraints manager: 4.69 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: 9369 15.70 - 31.40: 739 31.40 - 47.09: 215 47.09 - 62.79: 30 62.79 - 78.49: 15 Dihedral angle restraints: 10368 sinusoidal: 4473 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 10365 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: 2.03 - 2.60: 69 2.60 - 3.18: 13529 3.18 - 3.75: 25190 3.75 - 4.33: 33754 4.33 - 4.90: 56770 Nonbonded interactions: 129312 Sorted by model distance: nonbonded pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " model vdw 2.032 3.760 nonbonded pdb=" OH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 2.253 3.040 ... (remaining 129307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.930 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.960 ------------------------------------------------------------------------------- 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 17140 Z= 0.271 Angle : 0.770 10.049 23435 Z= 0.440 Chirality : 0.050 0.309 2755 Planarity : 0.004 0.042 2840 Dihedral : 12.616 78.488 6525 Min Nonbonded Distance : 2.031 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 *********************** 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 : 1.938 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: 1.1424 time to fit residues: 178.1486 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 : 2.244 ------------------------------------------------------------------------------- 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: 2.9990 chunk 113 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 E 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17140 Z= 0.259 Angle : 0.583 10.846 23435 Z= 0.289 Chirality : 0.044 0.163 2755 Planarity : 0.004 0.031 2840 Dihedral : 5.550 57.491 2645 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.65 % Allowed : 6.88 % Favored : 92.47 % 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: 0.70 (0.20), residues: 1955 helix: 2.31 (0.19), residues: 775 sheet: -0.56 (0.25), residues: 400 loop : -0.86 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 320 HIS 0.003 0.001 HIS C 309 PHE 0.008 0.001 PHE C 254 TYR 0.021 0.001 TYR B 67 ARG 0.008 0.001 ARG D 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 HIS cc_start: 0.7111 (m90) cc_final: 0.6858 (m-70) REVERT: B 322 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8150 (mmp80) REVERT: B 419 MET cc_start: 0.7645 (mmm) cc_final: 0.7415 (mmm) REVERT: D 411 HIS cc_start: 0.6983 (m90) cc_final: 0.6724 (m90) REVERT: D 414 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7624 (mm-30) outliers start: 12 outliers final: 1 residues processed: 121 average time/residue: 1.1473 time to fit residues: 158.7339 Evaluate side-chains 92 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 157 optimal weight: 0.0370 chunk 175 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 E 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17140 Z= 0.132 Angle : 0.527 12.745 23435 Z= 0.255 Chirality : 0.042 0.148 2755 Planarity : 0.003 0.030 2840 Dihedral : 5.208 54.363 2645 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.92 % Allowed : 7.43 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.20), residues: 1955 helix: 2.66 (0.20), residues: 755 sheet: -0.77 (0.24), residues: 420 loop : -0.68 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 320 HIS 0.001 0.000 HIS A 323 PHE 0.012 0.001 PHE B 233 TYR 0.012 0.001 TYR E 67 ARG 0.008 0.000 ARG B 328 *********************** 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 119 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 HIS cc_start: 0.7060 (m90) cc_final: 0.6802 (m-70) REVERT: B 322 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8127 (mmp80) REVERT: C 324 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8309 (tt) REVERT: D 324 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8368 (tt) REVERT: D 411 HIS cc_start: 0.7149 (m90) cc_final: 0.6846 (m90) REVERT: E 324 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8229 (tt) outliers start: 17 outliers final: 7 residues processed: 113 average time/residue: 1.0185 time to fit residues: 133.7703 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 : 1.970 ------------------------------------------------------------------------------- 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 175 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN E 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17140 Z= 0.227 Angle : 0.545 10.768 23435 Z= 0.268 Chirality : 0.043 0.147 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.366 56.716 2645 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.63 % Allowed : 8.13 % Favored : 90.24 % 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: 0.78 (0.20), residues: 1955 helix: 2.44 (0.19), residues: 780 sheet: -0.64 (0.24), residues: 420 loop : -0.83 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 320 HIS 0.002 0.001 HIS C 18 PHE 0.011 0.001 PHE B 233 TYR 0.020 0.001 TYR B 67 ARG 0.008 0.000 ARG D 328 *********************** 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 : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: A 411 HIS cc_start: 0.7178 (m90) cc_final: 0.6944 (m-70) REVERT: B 315 ARG cc_start: 0.7209 (tpt170) cc_final: 0.6645 (tpt170) REVERT: B 322 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8029 (mmp80) REVERT: C 324 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8297 (tt) REVERT: D 324 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8454 (tt) REVERT: D 411 HIS cc_start: 0.7169 (m90) cc_final: 0.6860 (m90) REVERT: E 324 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8279 (tt) outliers start: 30 outliers final: 14 residues processed: 128 average time/residue: 1.0233 time to fit residues: 153.0573 Evaluate side-chains 110 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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 317 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.2980 chunk 169 optimal weight: 0.0040 chunk 47 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17140 Z= 0.126 Angle : 0.519 14.714 23435 Z= 0.249 Chirality : 0.042 0.147 2755 Planarity : 0.003 0.028 2840 Dihedral : 5.142 54.254 2645 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.46 % Allowed : 9.16 % Favored : 89.38 % 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: 2.57 (0.19), residues: 780 sheet: -0.61 (0.24), residues: 420 loop : -0.79 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 320 HIS 0.001 0.000 HIS E 323 PHE 0.009 0.001 PHE B 233 TYR 0.012 0.001 TYR E 67 ARG 0.009 0.000 ARG B 328 *********************** 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 124 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 HIS cc_start: 0.7060 (m90) cc_final: 0.6858 (m-70) REVERT: B 322 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7993 (mmp80) REVERT: C 324 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8348 (tt) REVERT: D 324 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8409 (tt) REVERT: D 411 HIS cc_start: 0.7130 (m90) cc_final: 0.6833 (m-70) outliers start: 27 outliers final: 12 residues processed: 120 average time/residue: 0.8990 time to fit residues: 127.6234 Evaluate side-chains 109 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 308 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU 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 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 0.0470 chunk 188 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17140 Z= 0.197 Angle : 0.540 14.337 23435 Z= 0.262 Chirality : 0.043 0.164 2755 Planarity : 0.003 0.078 2840 Dihedral : 5.278 56.339 2645 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.46 % Allowed : 10.24 % 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: 0.84 (0.20), residues: 1955 helix: 2.50 (0.19), residues: 780 sheet: -0.58 (0.24), residues: 420 loop : -0.83 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 320 HIS 0.002 0.001 HIS C 18 PHE 0.011 0.001 PHE B 233 TYR 0.017 0.001 TYR B 67 ARG 0.013 0.000 ARG C 315 *********************** 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 124 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: A 324 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8336 (tt) REVERT: A 411 HIS cc_start: 0.7098 (m90) cc_final: 0.6856 (m-70) REVERT: B 322 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8004 (mmp80) REVERT: C 324 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8307 (tt) REVERT: D 91 ASP cc_start: 0.8038 (p0) cc_final: 0.7804 (p0) REVERT: D 324 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8426 (tt) REVERT: D 411 HIS cc_start: 0.7139 (m90) cc_final: 0.6861 (m90) outliers start: 27 outliers final: 17 residues processed: 121 average time/residue: 0.9404 time to fit residues: 133.2447 Evaluate side-chains 113 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17140 Z= 0.234 Angle : 0.576 15.020 23435 Z= 0.277 Chirality : 0.044 0.172 2755 Planarity : 0.003 0.072 2840 Dihedral : 5.361 56.559 2645 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.57 % Allowed : 11.06 % 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: 0.78 (0.20), residues: 1955 helix: 2.41 (0.19), residues: 780 sheet: -0.58 (0.24), residues: 420 loop : -0.84 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 456 HIS 0.002 0.001 HIS C 18 PHE 0.010 0.001 PHE B 233 TYR 0.019 0.001 TYR B 67 ARG 0.015 0.000 ARG A 315 *********************** 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 130 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: A 324 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 411 HIS cc_start: 0.7170 (m90) cc_final: 0.6930 (m-70) REVERT: B 322 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7988 (mmp80) REVERT: C 324 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8375 (tt) REVERT: D 91 ASP cc_start: 0.8075 (p0) cc_final: 0.7839 (p0) REVERT: D 411 HIS cc_start: 0.7197 (m90) cc_final: 0.6904 (m90) outliers start: 29 outliers final: 17 residues processed: 125 average time/residue: 0.9431 time to fit residues: 138.4352 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 : 1.691 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 0.2980 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17140 Z= 0.168 Angle : 0.565 15.349 23435 Z= 0.268 Chirality : 0.043 0.154 2755 Planarity : 0.003 0.027 2840 Dihedral : 5.258 55.395 2645 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.46 % Allowed : 11.92 % Favored : 86.61 % 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: 0.82 (0.20), residues: 1955 helix: 2.49 (0.19), residues: 780 sheet: -0.60 (0.24), residues: 420 loop : -0.83 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 456 HIS 0.002 0.000 HIS C 18 PHE 0.012 0.001 PHE D 233 TYR 0.015 0.001 TYR E 67 ARG 0.010 0.000 ARG B 328 *********************** 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: 27 poor density : 98 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 324 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 411 HIS cc_start: 0.7126 (m90) cc_final: 0.6894 (m-70) REVERT: B 116 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: B 322 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7999 (mmp80) REVERT: C 324 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8364 (tt) REVERT: D 91 ASP cc_start: 0.8061 (p0) cc_final: 0.7824 (p0) REVERT: D 324 LEU cc_start: 0.8497 (tm) cc_final: 0.8296 (tt) REVERT: D 411 HIS cc_start: 0.7192 (m90) cc_final: 0.6901 (m90) outliers start: 27 outliers final: 18 residues processed: 124 average time/residue: 0.8920 time to fit residues: 130.4816 Evaluate side-chains 117 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 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 C residue 433 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17140 Z= 0.233 Angle : 0.591 14.340 23435 Z= 0.283 Chirality : 0.044 0.156 2755 Planarity : 0.003 0.027 2840 Dihedral : 5.400 56.874 2645 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.30 % Allowed : 12.30 % 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: 0.74 (0.20), residues: 1955 helix: 2.47 (0.19), residues: 775 sheet: -0.58 (0.24), residues: 420 loop : -0.97 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 456 HIS 0.003 0.001 HIS C 18 PHE 0.012 0.001 PHE D 233 TYR 0.020 0.001 TYR E 67 ARG 0.009 0.000 ARG B 328 *********************** 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 114 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: A 324 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8290 (tt) REVERT: A 411 HIS cc_start: 0.7156 (m90) cc_final: 0.6914 (m-70) REVERT: B 116 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: B 322 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7998 (mmp80) REVERT: C 324 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8390 (tt) REVERT: D 91 ASP cc_start: 0.8073 (p0) cc_final: 0.7848 (p0) REVERT: D 324 LEU cc_start: 0.8479 (tm) cc_final: 0.8247 (tt) REVERT: D 411 HIS cc_start: 0.7191 (m90) cc_final: 0.6915 (m90) outliers start: 24 outliers final: 19 residues processed: 113 average time/residue: 0.9637 time to fit residues: 127.8590 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 : 2.032 ------------------------------------------------------------------------------- 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 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 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 433 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 178 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17140 Z= 0.210 Angle : 0.584 14.202 23435 Z= 0.279 Chirality : 0.044 0.154 2755 Planarity : 0.003 0.029 2840 Dihedral : 5.341 55.939 2645 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.36 % Allowed : 12.41 % Favored : 86.23 % 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: 0.73 (0.20), residues: 1955 helix: 2.47 (0.19), residues: 775 sheet: -0.60 (0.24), residues: 420 loop : -0.97 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 456 HIS 0.002 0.001 HIS C 18 PHE 0.013 0.001 PHE B 233 TYR 0.016 0.001 TYR E 67 ARG 0.008 0.000 ARG B 328 ********************** 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 118 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: A 315 ARG cc_start: 0.6821 (tpt170) cc_final: 0.6432 (tpm170) REVERT: A 324 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 411 HIS cc_start: 0.7163 (m90) cc_final: 0.6916 (m-70) REVERT: B 116 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: B 322 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7968 (mmp80) REVERT: C 324 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8386 (tt) REVERT: D 91 ASP cc_start: 0.8068 (p0) cc_final: 0.7835 (p0) REVERT: D 324 LEU cc_start: 0.8492 (tm) cc_final: 0.8247 (tt) REVERT: D 411 HIS cc_start: 0.7194 (m90) cc_final: 0.6916 (m90) outliers start: 25 outliers final: 20 residues processed: 117 average time/residue: 0.9947 time to fit residues: 138.2582 Evaluate side-chains 116 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 136 optimal weight: 0.0770 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.098150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.063644 restraints weight = 33838.125| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.58 r_work: 0.2765 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17140 Z= 0.161 Angle : 0.576 16.246 23435 Z= 0.271 Chirality : 0.043 0.154 2755 Planarity : 0.003 0.027 2840 Dihedral : 5.253 55.295 2645 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.36 % Allowed : 12.41 % Favored : 86.23 % 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: 0.79 (0.20), residues: 1955 helix: 2.45 (0.19), residues: 780 sheet: -0.60 (0.24), residues: 420 loop : -0.85 (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 0.015 0.001 PHE D 233 TYR 0.014 0.001 TYR E 67 ARG 0.008 0.000 ARG B 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4233.85 seconds wall clock time: 77 minutes 26.52 seconds (4646.52 seconds total)