Starting phenix.real_space_refine on Sat Sep 28 17:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/09_2024/8dzg_27797.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/09_2024/8dzg_27797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/09_2024/8dzg_27797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/09_2024/8dzg_27797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/09_2024/8dzg_27797.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/09_2024/8dzg_27797.cif" } resolution = 3.1 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= 0.002 sd= 0.077 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 12 5.49 5 Mg 6 5.21 5 S 84 5.16 5 C 12396 2.51 5 N 3486 2.21 5 O 3768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19758 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2249 SG CYS A 403 91.228 129.664 31.801 1.00 76.41 S ATOM 2269 SG CYS A 406 94.765 130.815 30.837 1.00 85.65 S ATOM 2553 SG CYS A 445 92.667 132.874 33.325 1.00 94.65 S ATOM 2559 SG CYS A 446 94.089 129.607 34.341 1.00 90.08 S Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.45, per 1000 atoms: 0.38 Number of scatterers: 19758 At special positions: 0 Unit cell: (147.96, 143.64, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 84 16.00 P 12 15.00 Mg 6 11.99 O 3768 8.00 N 3486 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 446 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 445 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 403 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 446 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 445 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 406 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 403 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 446 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 445 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 406 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 403 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 446 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 445 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 406 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 403 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 446 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 445 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 406 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 403 " pdb=" ZN F 603 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 446 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 445 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 406 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 403 " Number of angles added : 36 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 44.6% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.644A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.616A pdb=" N LEU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.513A pdb=" N ILE A 519 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 265 through 281 removed outlier: 3.544A pdb=" N THR B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.615A pdb=" N LEU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP B 386 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 490 through 502 Processing helix chain 'B' and resid 505 through 513 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.512A pdb=" N ILE B 519 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 534 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'C' and resid 153 through 166 Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 341 through 353 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.616A pdb=" N LEU C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 386 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 421 through 429 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 474 through 485 Processing helix chain 'C' and resid 490 through 502 Processing helix chain 'C' and resid 505 through 513 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.512A pdb=" N ILE C 519 " --> pdb=" O ILE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 534 Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 328 Processing helix chain 'D' and resid 341 through 353 Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 380 through 386 removed outlier: 3.616A pdb=" N LEU D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 421 through 429 Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 474 through 485 Processing helix chain 'D' and resid 490 through 502 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.513A pdb=" N ILE D 519 " --> pdb=" O ILE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 534 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 328 Processing helix chain 'E' and resid 341 through 353 Processing helix chain 'E' and resid 369 through 378 Processing helix chain 'E' and resid 380 through 386 removed outlier: 3.616A pdb=" N LEU E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP E 386 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'E' and resid 421 through 429 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 474 through 485 Processing helix chain 'E' and resid 490 through 502 Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 515 through 519 removed outlier: 3.512A pdb=" N ILE E 519 " --> pdb=" O ILE E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 534 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 238 through 251 Processing helix chain 'F' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR F 269 " --> pdb=" O GLY F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 328 Processing helix chain 'F' and resid 341 through 353 Processing helix chain 'F' and resid 369 through 378 Processing helix chain 'F' and resid 380 through 386 removed outlier: 3.615A pdb=" N LEU F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP F 386 " --> pdb=" O PHE F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 417 Processing helix chain 'F' and resid 421 through 429 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 474 through 485 Processing helix chain 'F' and resid 490 through 502 Processing helix chain 'F' and resid 505 through 513 Processing helix chain 'F' and resid 515 through 519 removed outlier: 3.512A pdb=" N ILE F 519 " --> pdb=" O ILE F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 534 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 152 removed outlier: 6.711A pdb=" N ILE A 137 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN A 150 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA A 135 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 125 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR A 213 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 204 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 215 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 202 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG A 217 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 200 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 219 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU A 304 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER A 289 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 361 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY A 254 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR A 360 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN A 256 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 362 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 258 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 255 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 392 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 144 through 152 removed outlier: 6.712A pdb=" N ILE B 137 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN B 150 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 135 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 125 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR B 213 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 204 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 215 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 202 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG B 217 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 200 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 219 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU B 304 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER B 289 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 361 " --> pdb=" O PRO B 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 254 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR B 360 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B 256 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU B 362 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 258 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 255 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 392 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 152 removed outlier: 6.712A pdb=" N ILE C 137 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN C 150 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 135 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP C 125 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR C 213 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE C 204 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C 215 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 202 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 217 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 200 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 219 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU C 304 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER C 289 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER C 361 " --> pdb=" O PRO C 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY C 254 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR C 360 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN C 256 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU C 362 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE C 258 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 255 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C 392 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 144 through 152 removed outlier: 6.711A pdb=" N ILE D 137 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN D 150 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA D 135 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 125 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR D 213 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE D 204 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE D 215 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU D 202 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG D 217 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL D 200 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 219 " --> pdb=" O GLN D 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU D 304 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER D 289 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER D 361 " --> pdb=" O PRO D 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY D 254 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR D 360 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN D 256 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU D 362 " --> pdb=" O ASN D 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE D 258 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE D 255 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 392 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 144 through 152 removed outlier: 6.712A pdb=" N ILE E 137 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN E 150 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA E 135 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP E 125 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR E 213 " --> pdb=" O PHE E 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 204 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 215 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU E 202 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG E 217 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL E 200 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU E 219 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU E 304 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER E 289 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER E 361 " --> pdb=" O PRO E 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY E 254 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR E 360 " --> pdb=" O GLY E 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN E 256 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU E 362 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE E 258 " --> pdb=" O LEU E 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE E 255 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY E 392 " --> pdb=" O ILE E 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 144 through 152 removed outlier: 6.712A pdb=" N ILE F 137 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN F 150 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA F 135 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP F 125 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR F 213 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE F 204 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE F 215 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU F 202 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG F 217 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL F 200 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU F 219 " --> pdb=" O GLN F 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU F 304 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER F 289 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER F 361 " --> pdb=" O PRO F 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY F 254 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR F 360 " --> pdb=" O GLY F 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN F 256 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU F 362 " --> pdb=" O ASN F 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE F 258 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE F 255 " --> pdb=" O ILE F 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY F 392 " --> pdb=" O ILE F 255 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2808 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: 6.55 Time building geometry restraints manager: 7.01 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: 6624 1.34 - 1.46: 3258 1.46 - 1.58: 10050 1.58 - 1.69: 24 1.69 - 1.81: 132 Bond restraints: 20088 Sorted by residual: bond pdb=" C1' ADP F 602 " pdb=" C2' ADP F 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP D 602 " pdb=" C2' ADP D 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP E 602 " pdb=" C2' ADP E 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP B 602 " pdb=" C2' ADP B 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP A 602 " pdb=" C2' ADP A 602 " ideal model delta sigma weight residual 1.524 1.290 0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 20083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 26861 2.38 - 4.77: 247 4.77 - 7.15: 48 7.15 - 9.53: 18 9.53 - 11.91: 36 Bond angle restraints: 27210 Sorted by residual: angle pdb=" C SER E 170 " pdb=" N ASP E 171 " pdb=" CA ASP E 171 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C SER B 170 " pdb=" N ASP B 171 " pdb=" CA ASP B 171 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER F 170 " pdb=" N ASP F 171 " pdb=" CA ASP F 171 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER A 170 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.20e+01 ... (remaining 27205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 11774 32.91 - 65.82: 436 65.82 - 98.73: 24 98.73 - 131.64: 6 131.64 - 164.54: 6 Dihedral angle restraints: 12246 sinusoidal: 4914 harmonic: 7332 Sorted by residual: dihedral pdb=" C2' ADP F 602 " pdb=" C1' ADP F 602 " pdb=" N9 ADP F 602 " pdb=" C4 ADP F 602 " ideal model delta sinusoidal sigma weight residual 91.55 -73.00 164.54 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C2' ADP E 602 " pdb=" C1' ADP E 602 " pdb=" N9 ADP E 602 " pdb=" C4 ADP E 602 " ideal model delta sinusoidal sigma weight residual 91.55 -72.99 164.53 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C2' ADP C 602 " pdb=" C1' ADP C 602 " pdb=" N9 ADP C 602 " pdb=" C4 ADP C 602 " ideal model delta sinusoidal sigma weight residual 91.55 -72.98 164.52 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 12243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1790 0.027 - 0.055: 758 0.055 - 0.082: 320 0.082 - 0.110: 133 0.110 - 0.137: 119 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA ILE E 258 " pdb=" N ILE E 258 " pdb=" C ILE E 258 " pdb=" CB ILE E 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE A 258 " pdb=" N ILE A 258 " pdb=" C ILE A 258 " pdb=" CB ILE A 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 3117 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 526 " -0.012 2.00e-02 2.50e+03 1.55e-02 4.82e+00 pdb=" CG TYR F 526 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 526 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR F 526 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR F 526 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 526 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 526 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 526 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 193 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 194 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 194 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 194 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 526 " -0.011 2.00e-02 2.50e+03 1.54e-02 4.74e+00 pdb=" CG TYR E 526 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 526 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR E 526 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR E 526 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 526 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 526 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 526 " 0.001 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 162 2.64 - 3.21: 16546 3.21 - 3.77: 28979 3.77 - 4.34: 39696 4.34 - 4.90: 68339 Nonbonded interactions: 153722 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O2B ADP D 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ADP C 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2B ADP A 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2B ADP B 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG E 601 " pdb=" O2B ADP E 602 " model vdw 2.076 2.170 ... (remaining 153717 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' selection = chain 'F' } 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: 1.610 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: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 46.910 Find NCS groups from input model: 0.760 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.008 0.235 20088 Z= 0.525 Angle : 0.733 11.913 27210 Z= 0.355 Chirality : 0.044 0.137 3120 Planarity : 0.005 0.054 3486 Dihedral : 16.805 164.544 7506 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.29 % Allowed : 12.39 % Favored : 87.32 % 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: -0.15 (0.16), residues: 2496 helix: 0.78 (0.15), residues: 1104 sheet: 1.42 (0.21), residues: 546 loop : -2.41 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 359 HIS 0.004 0.001 HIS E 127 PHE 0.010 0.001 PHE D 382 TYR 0.038 0.001 TYR F 526 ARG 0.002 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 2.095 Fit side-chains REVERT: A 463 ASP cc_start: 0.7240 (m-30) cc_final: 0.6944 (m-30) REVERT: C 338 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: C 489 MET cc_start: 0.8396 (ttp) cc_final: 0.8130 (ttp) REVERT: D 463 ASP cc_start: 0.7313 (m-30) cc_final: 0.6964 (m-30) REVERT: F 489 MET cc_start: 0.8395 (ttp) cc_final: 0.8134 (ttp) outliers start: 6 outliers final: 0 residues processed: 161 average time/residue: 0.3503 time to fit residues: 86.3724 Evaluate side-chains 137 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 363 HIS B 205 ASN B 363 HIS C 205 ASN D 205 ASN D 363 HIS E 205 ASN E 363 HIS F 205 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20088 Z= 0.239 Angle : 0.589 7.388 27210 Z= 0.290 Chirality : 0.044 0.148 3120 Planarity : 0.004 0.047 3486 Dihedral : 10.594 161.356 2823 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 2.16 % Allowed : 12.30 % Favored : 85.54 % 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: 0.40 (0.16), residues: 2496 helix: 1.56 (0.16), residues: 1110 sheet: 1.42 (0.21), residues: 546 loop : -2.45 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 496 HIS 0.004 0.001 HIS F 239 PHE 0.009 0.001 PHE F 204 TYR 0.019 0.001 TYR C 526 ARG 0.003 0.000 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 2.105 Fit side-chains REVERT: A 346 ASN cc_start: 0.7073 (m-40) cc_final: 0.6839 (m-40) REVERT: A 526 TYR cc_start: 0.7945 (t80) cc_final: 0.7558 (t80) REVERT: B 166 ASN cc_start: 0.7836 (m-40) cc_final: 0.7415 (m110) REVERT: B 500 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 166 ASN cc_start: 0.7498 (m-40) cc_final: 0.7266 (m-40) REVERT: C 318 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: C 507 MET cc_start: 0.7262 (mpp) cc_final: 0.7004 (mpp) REVERT: D 346 ASN cc_start: 0.7010 (m-40) cc_final: 0.6791 (m-40) REVERT: D 526 TYR cc_start: 0.7946 (t80) cc_final: 0.7556 (t80) REVERT: E 166 ASN cc_start: 0.7836 (m-40) cc_final: 0.7406 (m110) REVERT: E 500 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8125 (mp) REVERT: F 166 ASN cc_start: 0.7505 (m-40) cc_final: 0.7262 (m-40) REVERT: F 318 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: F 507 MET cc_start: 0.7261 (mpp) cc_final: 0.7007 (mpp) outliers start: 45 outliers final: 22 residues processed: 177 average time/residue: 0.3001 time to fit residues: 85.4848 Evaluate side-chains 161 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20088 Z= 0.272 Angle : 0.597 8.656 27210 Z= 0.297 Chirality : 0.045 0.161 3120 Planarity : 0.005 0.079 3486 Dihedral : 10.120 156.765 2820 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.25 % Favored : 94.51 % Rotamer: Outliers : 2.16 % Allowed : 14.60 % Favored : 83.24 % 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: 0.51 (0.17), residues: 2496 helix: 1.89 (0.16), residues: 1110 sheet: 1.14 (0.21), residues: 552 loop : -2.54 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 359 HIS 0.004 0.001 HIS F 239 PHE 0.010 0.001 PHE F 204 TYR 0.014 0.001 TYR B 526 ARG 0.002 0.000 ARG E 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 167 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8137 (tt0) cc_final: 0.7852 (tt0) REVERT: A 526 TYR cc_start: 0.7973 (t80) cc_final: 0.7442 (t80) REVERT: B 166 ASN cc_start: 0.7689 (m-40) cc_final: 0.7320 (m110) REVERT: B 262 THR cc_start: 0.8853 (t) cc_final: 0.8559 (t) REVERT: C 166 ASN cc_start: 0.7486 (m-40) cc_final: 0.7148 (m110) REVERT: C 507 MET cc_start: 0.7258 (mpp) cc_final: 0.6954 (mpp) REVERT: C 526 TYR cc_start: 0.7918 (t80) cc_final: 0.7628 (t80) REVERT: C 529 SER cc_start: 0.7823 (m) cc_final: 0.7340 (p) REVERT: D 526 TYR cc_start: 0.7976 (t80) cc_final: 0.7460 (t80) REVERT: E 166 ASN cc_start: 0.7683 (m-40) cc_final: 0.7310 (m110) REVERT: E 262 THR cc_start: 0.8853 (t) cc_final: 0.8561 (t) REVERT: F 166 ASN cc_start: 0.7473 (m-40) cc_final: 0.7134 (m110) REVERT: F 507 MET cc_start: 0.7260 (mpp) cc_final: 0.6959 (mpp) REVERT: F 526 TYR cc_start: 0.7944 (t80) cc_final: 0.7658 (t80) REVERT: F 529 SER cc_start: 0.7840 (m) cc_final: 0.7367 (p) outliers start: 45 outliers final: 38 residues processed: 202 average time/residue: 0.2908 time to fit residues: 94.7075 Evaluate side-chains 192 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 218 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN B 198 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN E 198 GLN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20088 Z= 0.199 Angle : 0.550 7.139 27210 Z= 0.272 Chirality : 0.043 0.150 3120 Planarity : 0.005 0.071 3486 Dihedral : 9.730 152.969 2820 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 2.31 % Allowed : 16.19 % Favored : 81.51 % 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: 0.67 (0.17), residues: 2496 helix: 2.09 (0.16), residues: 1116 sheet: 1.08 (0.21), residues: 558 loop : -2.51 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 496 HIS 0.004 0.001 HIS B 127 PHE 0.008 0.001 PHE F 204 TYR 0.013 0.001 TYR E 526 ARG 0.002 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 151 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8124 (tt0) cc_final: 0.7829 (tt0) REVERT: A 526 TYR cc_start: 0.7946 (t80) cc_final: 0.7445 (t80) REVERT: B 166 ASN cc_start: 0.7665 (m-40) cc_final: 0.7353 (m110) REVERT: B 262 THR cc_start: 0.8833 (t) cc_final: 0.8540 (t) REVERT: C 166 ASN cc_start: 0.7445 (m-40) cc_final: 0.7188 (m110) REVERT: C 507 MET cc_start: 0.7234 (mpp) cc_final: 0.6901 (mpp) REVERT: C 526 TYR cc_start: 0.7943 (t80) cc_final: 0.7699 (t80) REVERT: C 529 SER cc_start: 0.7829 (m) cc_final: 0.7322 (p) REVERT: D 526 TYR cc_start: 0.7926 (t80) cc_final: 0.7425 (t80) REVERT: E 166 ASN cc_start: 0.7659 (m-40) cc_final: 0.7344 (m110) REVERT: E 262 THR cc_start: 0.8831 (t) cc_final: 0.8538 (t) REVERT: F 166 ASN cc_start: 0.7338 (m-40) cc_final: 0.7052 (m110) REVERT: F 507 MET cc_start: 0.7240 (mpp) cc_final: 0.6907 (mpp) REVERT: F 526 TYR cc_start: 0.7944 (t80) cc_final: 0.7701 (t80) REVERT: F 529 SER cc_start: 0.7851 (m) cc_final: 0.7363 (p) outliers start: 48 outliers final: 36 residues processed: 191 average time/residue: 0.2847 time to fit residues: 88.2443 Evaluate side-chains 182 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 501 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20088 Z= 0.369 Angle : 0.640 7.975 27210 Z= 0.319 Chirality : 0.047 0.162 3120 Planarity : 0.005 0.094 3486 Dihedral : 10.120 157.922 2820 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.01 % Favored : 93.75 % Rotamer: Outliers : 3.22 % Allowed : 16.23 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: 0.41 (0.17), residues: 2496 helix: 1.87 (0.16), residues: 1116 sheet: 0.88 (0.21), residues: 546 loop : -2.53 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 359 HIS 0.005 0.001 HIS F 239 PHE 0.013 0.002 PHE E 204 TYR 0.015 0.001 TYR E 526 ARG 0.003 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 159 time to evaluate : 2.045 Fit side-chains REVERT: A 338 GLU cc_start: 0.8186 (tt0) cc_final: 0.7921 (tt0) REVERT: A 464 SER cc_start: 0.7555 (OUTLIER) cc_final: 0.7294 (p) REVERT: A 526 TYR cc_start: 0.7996 (t80) cc_final: 0.7551 (t80) REVERT: B 262 THR cc_start: 0.8902 (t) cc_final: 0.8594 (t) REVERT: B 500 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 166 ASN cc_start: 0.7368 (m-40) cc_final: 0.7075 (m110) REVERT: C 450 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: C 507 MET cc_start: 0.7341 (mpp) cc_final: 0.7007 (mpp) REVERT: D 464 SER cc_start: 0.7558 (OUTLIER) cc_final: 0.7295 (p) REVERT: D 526 TYR cc_start: 0.7970 (t80) cc_final: 0.7521 (t80) REVERT: E 262 THR cc_start: 0.8900 (t) cc_final: 0.8594 (t) REVERT: E 500 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8167 (mp) REVERT: F 166 ASN cc_start: 0.7371 (m-40) cc_final: 0.7076 (m110) REVERT: F 450 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: F 507 MET cc_start: 0.7348 (mpp) cc_final: 0.6999 (mpp) REVERT: F 526 TYR cc_start: 0.7946 (t80) cc_final: 0.7704 (t80) REVERT: F 529 SER cc_start: 0.7803 (m) cc_final: 0.7304 (p) outliers start: 67 outliers final: 52 residues processed: 215 average time/residue: 0.2886 time to fit residues: 100.6243 Evaluate side-chains 215 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 157 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain E residue 501 SER Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 450 TYR Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 3.9990 chunk 219 optimal weight: 0.0980 chunk 48 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 243 optimal weight: 0.0870 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 20088 Z= 0.159 Angle : 0.532 6.780 27210 Z= 0.263 Chirality : 0.042 0.144 3120 Planarity : 0.005 0.083 3486 Dihedral : 9.486 150.073 2820 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 2.07 % Allowed : 18.64 % Favored : 79.30 % 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: 0.72 (0.17), residues: 2496 helix: 2.27 (0.16), residues: 1116 sheet: 0.98 (0.21), residues: 558 loop : -2.62 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 496 HIS 0.003 0.001 HIS B 127 PHE 0.007 0.001 PHE B 382 TYR 0.025 0.001 TYR C 526 ARG 0.001 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 157 time to evaluate : 2.347 Fit side-chains REVERT: A 338 GLU cc_start: 0.8133 (tt0) cc_final: 0.7852 (tt0) REVERT: A 526 TYR cc_start: 0.7940 (t80) cc_final: 0.7518 (t80) REVERT: B 262 THR cc_start: 0.8828 (t) cc_final: 0.8536 (t) REVERT: D 526 TYR cc_start: 0.7936 (t80) cc_final: 0.7529 (t80) REVERT: E 262 THR cc_start: 0.8824 (t) cc_final: 0.8535 (t) REVERT: F 166 ASN cc_start: 0.7148 (m-40) cc_final: 0.6864 (m110) outliers start: 43 outliers final: 34 residues processed: 192 average time/residue: 0.2939 time to fit residues: 90.0124 Evaluate side-chains 188 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2088 > 50: distance: 49 - 87: 28.274 distance: 58 - 94: 26.556 distance: 81 - 87: 25.972 distance: 87 - 88: 38.072 distance: 88 - 89: 56.557 distance: 88 - 91: 32.833 distance: 89 - 90: 17.806 distance: 89 - 94: 32.502 distance: 91 - 92: 39.200 distance: 94 - 95: 29.664 distance: 95 - 96: 4.976 distance: 95 - 98: 30.481 distance: 96 - 97: 5.768 distance: 96 - 100: 19.849 distance: 98 - 99: 29.407 distance: 100 - 101: 4.696 distance: 101 - 102: 11.085 distance: 101 - 104: 19.073 distance: 102 - 103: 8.584 distance: 102 - 108: 28.172 distance: 104 - 105: 16.553 distance: 105 - 106: 36.319 distance: 105 - 107: 28.306 distance: 108 - 109: 28.791 distance: 109 - 110: 21.110 distance: 109 - 112: 15.386 distance: 110 - 111: 39.209 distance: 110 - 118: 19.867 distance: 112 - 113: 41.967 distance: 113 - 114: 47.492 distance: 113 - 115: 46.692 distance: 114 - 116: 50.520 distance: 115 - 117: 45.850 distance: 116 - 117: 41.903 distance: 118 - 119: 47.701 distance: 119 - 120: 37.499 distance: 120 - 121: 36.514 distance: 120 - 122: 58.858 distance: 122 - 123: 19.754 distance: 123 - 124: 28.604 distance: 123 - 126: 16.286 distance: 124 - 125: 11.122 distance: 124 - 130: 16.278 distance: 126 - 127: 18.585 distance: 127 - 128: 37.172 distance: 128 - 129: 34.560 distance: 130 - 131: 41.159 distance: 131 - 132: 21.106 distance: 131 - 134: 32.865 distance: 132 - 133: 30.851 distance: 132 - 135: 24.305 distance: 133 - 161: 29.666 distance: 135 - 136: 43.227 distance: 136 - 139: 20.790 distance: 137 - 138: 27.788 distance: 137 - 143: 25.452 distance: 138 - 168: 29.481 distance: 139 - 140: 22.108 distance: 140 - 141: 19.207 distance: 140 - 142: 3.009 distance: 143 - 144: 13.912 distance: 144 - 145: 41.439 distance: 144 - 147: 25.267 distance: 145 - 146: 10.812 distance: 145 - 152: 44.063 distance: 146 - 173: 27.762 distance: 147 - 148: 19.294 distance: 148 - 149: 13.103 distance: 149 - 150: 21.765 distance: 150 - 151: 17.475 distance: 152 - 153: 37.505 distance: 153 - 154: 13.846 distance: 153 - 156: 13.281 distance: 154 - 155: 15.825 distance: 154 - 161: 16.520 distance: 155 - 181: 18.760 distance: 156 - 157: 12.139 distance: 157 - 158: 13.337 distance: 158 - 159: 5.782 distance: 158 - 160: 12.433