Starting phenix.real_space_refine on Sat Sep 12 12:54:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5u6p_8512/09_2026/5u6p_8512.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u6p_8512/09_2026/5u6p_8512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2026/5u6p_8512.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2026/5u6p_8512.cif" model { file = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2026/5u6p_8512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2026/5u6p_8512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2026/5u6p_8512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2026/5u6p_8512.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 C 10156 2.51 5 N 2688 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15640 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3793 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain breaks: 2 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 5, 'PHE:plan': 2, 'GLU:plan': 13, 'TRP:plan': 1, 'ASP:plan': 13, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 174 Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 3.86, per 1000 atoms: 0.25 Number of scatterers: 15640 At special positions: 0 Unit cell: (123.5, 123.5, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 4 15.00 O 2676 8.00 N 2688 7.00 C 10156 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: 1.44 Conformation dependent library (CDL) restraints added in 548.1 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3992 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 79.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.640A pdb=" N PHE A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 167 Proline residue: A 161 - end of helix removed outlier: 3.534A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.934A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.646A pdb=" N LYS A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.509A pdb=" N ASP A 225 " --> pdb=" O TRP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.810A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 290 Processing helix chain 'A' and resid 292 through 323 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.518A pdb=" N ASN A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.674A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.570A pdb=" N ASN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.939A pdb=" N ALA A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.661A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.678A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.934A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 167 Proline residue: B 161 - end of helix removed outlier: 3.534A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.935A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.648A pdb=" N LYS B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.508A pdb=" N ASP B 225 " --> pdb=" O TRP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.811A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 270 through 290 Processing helix chain 'B' and resid 292 through 323 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.519A pdb=" N ASN B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.675A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.572A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.939A pdb=" N ALA B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.663A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 491 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.678A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.932A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 167 Proline residue: C 161 - end of helix removed outlier: 3.533A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.935A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.648A pdb=" N LYS C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 removed outlier: 3.509A pdb=" N ASP C 225 " --> pdb=" O TRP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.810A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 Processing helix chain 'C' and resid 270 through 290 Processing helix chain 'C' and resid 292 through 323 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.519A pdb=" N ASN C 334 " --> pdb=" O TRP C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.676A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.571A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.939A pdb=" N ALA C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 491 removed outlier: 3.662A pdb=" N LYS C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 491 " --> pdb=" O MET C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 546 Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.679A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 595 removed outlier: 3.933A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'D' and resid 95 through 103 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 167 Proline residue: D 161 - end of helix removed outlier: 3.534A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 removed outlier: 3.935A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.648A pdb=" N LYS D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.507A pdb=" N ASP D 225 " --> pdb=" O TRP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.811A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 Processing helix chain 'D' and resid 270 through 290 Processing helix chain 'D' and resid 292 through 323 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 335 removed outlier: 3.518A pdb=" N ASN D 334 " --> pdb=" O TRP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.679A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.571A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.940A pdb=" N ALA D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 491 removed outlier: 3.662A pdb=" N LYS D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 491 " --> pdb=" O MET D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.677A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 595 removed outlier: 3.932A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 608 Processing helix chain 'H' and resid 2 through 19 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.688A pdb=" N TYR A 562 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE A 515 " --> pdb=" O TYR A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.751A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 492 through 496 Processing sheet with id=AA5, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.690A pdb=" N TYR B 562 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE B 515 " --> pdb=" O TYR B 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.752A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 492 through 496 Processing sheet with id=AA8, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.689A pdb=" N TYR C 562 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE C 515 " --> pdb=" O TYR C 562 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.750A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 492 through 496 Processing sheet with id=AB2, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.688A pdb=" N TYR D 562 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE D 515 " --> pdb=" O TYR D 562 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.751A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) 1184 hydrogen bonds defined for protein. 3468 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: 2.82 Time building geometry restraints manager: 1.79 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: 4708 1.34 - 1.46: 2376 1.46 - 1.57: 8720 1.57 - 1.69: 8 1.69 - 1.81: 204 Bond restraints: 16016 Sorted by residual: bond pdb=" CA ILE C 160 " pdb=" CB ILE C 160 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.35e+01 bond pdb=" CA ILE B 160 " pdb=" CB ILE B 160 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.34e+01 bond pdb=" CA ILE D 160 " pdb=" CB ILE D 160 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.27e+01 bond pdb=" CA ILE A 160 " pdb=" CB ILE A 160 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.19e+01 bond pdb=" C SER C 346 " pdb=" O SER C 346 " ideal model delta sigma weight residual 1.236 1.275 -0.039 1.15e-02 7.56e+03 1.15e+01 ... (remaining 16011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17623 1.97 - 3.94: 3999 3.94 - 5.91: 154 5.91 - 7.88: 8 7.88 - 9.85: 16 Bond angle restraints: 21800 Sorted by residual: angle pdb=" O ILE D 160 " pdb=" C ILE D 160 " pdb=" N PRO D 161 " ideal model delta sigma weight residual 120.42 124.84 -4.42 6.40e-01 2.44e+00 4.77e+01 angle pdb=" O ILE A 160 " pdb=" C ILE A 160 " pdb=" N PRO A 161 " ideal model delta sigma weight residual 120.42 124.81 -4.39 6.40e-01 2.44e+00 4.70e+01 angle pdb=" O ILE C 160 " pdb=" C ILE C 160 " pdb=" N PRO C 161 " ideal model delta sigma weight residual 120.42 124.79 -4.37 6.40e-01 2.44e+00 4.66e+01 angle pdb=" O ILE B 160 " pdb=" C ILE B 160 " pdb=" N PRO B 161 " ideal model delta sigma weight residual 120.42 124.79 -4.37 6.40e-01 2.44e+00 4.66e+01 angle pdb=" O THR D 173 " pdb=" C THR D 173 " pdb=" N PRO D 174 " ideal model delta sigma weight residual 120.38 125.11 -4.73 7.90e-01 1.60e+00 3.59e+01 ... (remaining 21795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 9308 31.61 - 63.21: 64 63.21 - 94.82: 0 94.82 - 126.43: 0 126.43 - 158.03: 8 Dihedral angle restraints: 9380 sinusoidal: 3224 harmonic: 6156 Sorted by residual: dihedral pdb=" C5' CMP D 901 " pdb=" O5' CMP D 901 " pdb=" P CMP D 901 " pdb=" O1P CMP D 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.97 -158.03 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' CMP C 901 " pdb=" O5' CMP C 901 " pdb=" P CMP C 901 " pdb=" O1P CMP C 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.98 -158.02 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' CMP B 901 " pdb=" O5' CMP B 901 " pdb=" P CMP B 901 " pdb=" O1P CMP B 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.99 -158.01 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1589 0.057 - 0.114: 593 0.114 - 0.171: 225 0.171 - 0.228: 51 0.228 - 0.285: 26 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CA HIS D 279 " pdb=" N HIS D 279 " pdb=" C HIS D 279 " pdb=" CB HIS D 279 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA HIS B 279 " pdb=" N HIS B 279 " pdb=" C HIS B 279 " pdb=" CB HIS B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PHE C 186 " pdb=" N PHE C 186 " pdb=" C PHE C 186 " pdb=" CB PHE C 186 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2481 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO D 320 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 319 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 320 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 319 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 320 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " 0.059 5.00e-02 4.00e+02 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5775 2.90 - 3.40: 16994 3.40 - 3.90: 25277 3.90 - 4.40: 28759 4.40 - 4.90: 45760 Nonbonded interactions: 122565 Sorted by model distance: nonbonded pdb=" O LYS C 261 " pdb=" OG SER C 264 " model vdw 2.399 3.040 nonbonded pdb=" O LYS D 261 " pdb=" OG SER D 264 " model vdw 2.399 3.040 nonbonded pdb=" O LYS A 261 " pdb=" OG SER A 264 " model vdw 2.399 3.040 nonbonded pdb=" O LYS B 261 " pdb=" OG SER B 264 " model vdw 2.400 3.040 nonbonded pdb=" O ASP C 225 " pdb=" OG SER C 228 " model vdw 2.447 3.040 ... (remaining 122560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 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 : 0.007 0.044 16016 Z= 0.516 Angle : 1.419 9.850 21800 Z= 1.080 Chirality : 0.073 0.285 2484 Planarity : 0.006 0.112 2748 Dihedral : 11.924 158.034 5388 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.17), residues: 1992 helix: 1.89 (0.12), residues: 1380 sheet: 0.47 (0.47), residues: 100 loop : -1.97 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 112 TYR 0.027 0.002 TYR C 411 PHE 0.027 0.002 PHE A 569 TRP 0.030 0.002 TRP D 281 HIS 0.008 0.002 HIS D 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.52 (16016) covalent geometry : angle 1.41904 / 1.08 (21800) hydrogen bonds : bond 0.19194 / 13.62 ( 1160) hydrogen bonds : angle 5.71463 / 4.22 ( 3468) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8142 (mt) cc_final: 0.7785 (tt) REVERT: A 234 TYR cc_start: 0.6663 (m-80) cc_final: 0.5665 (t80) REVERT: A 236 PHE cc_start: 0.8369 (t80) cc_final: 0.8137 (t80) REVERT: A 439 TYR cc_start: 0.6267 (m-80) cc_final: 0.6007 (m-80) REVERT: B 135 ILE cc_start: 0.8309 (mt) cc_final: 0.8069 (tt) REVERT: B 152 MET cc_start: 0.6683 (mmm) cc_final: 0.6314 (tpt) REVERT: B 234 TYR cc_start: 0.6469 (m-80) cc_final: 0.5524 (t80) REVERT: B 445 ASP cc_start: 0.6626 (t0) cc_final: 0.6413 (p0) REVERT: B 482 ASN cc_start: 0.8055 (m110) cc_final: 0.7673 (t0) REVERT: B 485 THR cc_start: 0.8331 (m) cc_final: 0.8108 (p) REVERT: C 135 ILE cc_start: 0.8233 (mt) cc_final: 0.7939 (tt) REVERT: C 152 MET cc_start: 0.6730 (mmm) cc_final: 0.6341 (tpt) REVERT: C 217 TYR cc_start: 0.6281 (t80) cc_final: 0.6046 (t80) REVERT: C 234 TYR cc_start: 0.6468 (m-80) cc_final: 0.5654 (t80) REVERT: C 287 MET cc_start: 0.6196 (mmm) cc_final: 0.5872 (mmt) REVERT: C 336 MET cc_start: 0.7088 (ptm) cc_final: 0.6883 (ptp) REVERT: C 445 ASP cc_start: 0.6820 (t0) cc_final: 0.6513 (p0) REVERT: D 135 ILE cc_start: 0.8345 (mt) cc_final: 0.8092 (tt) REVERT: D 152 MET cc_start: 0.6796 (mmm) cc_final: 0.6433 (tpt) REVERT: D 217 TYR cc_start: 0.5843 (t80) cc_final: 0.5615 (t80) REVERT: D 233 ASP cc_start: 0.6993 (p0) cc_final: 0.6099 (p0) REVERT: D 234 TYR cc_start: 0.6374 (m-80) cc_final: 0.5615 (t80) REVERT: D 336 MET cc_start: 0.7020 (ptm) cc_final: 0.6819 (ptp) REVERT: D 445 ASP cc_start: 0.6655 (t0) cc_final: 0.6452 (p0) REVERT: D 482 ASN cc_start: 0.7800 (m110) cc_final: 0.7434 (m-40) REVERT: D 485 THR cc_start: 0.8419 (m) cc_final: 0.8207 (p) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.1121 time to fit residues: 87.4401 Evaluate side-chains 338 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN A 421 HIS B 398 GLN B 421 HIS C 179 ASN C 398 GLN D 398 GLN D 421 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.094695 restraints weight = 30542.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097429 restraints weight = 14560.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099154 restraints weight = 9384.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099950 restraints weight = 7377.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100651 restraints weight = 6566.301| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16016 Z= 0.158 Angle : 0.617 7.916 21800 Z= 0.315 Chirality : 0.042 0.155 2484 Planarity : 0.005 0.067 2748 Dihedral : 9.150 141.856 2304 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.41 % Allowed : 10.37 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.19), residues: 1992 helix: 3.03 (0.13), residues: 1420 sheet: 0.06 (0.45), residues: 96 loop : -1.78 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 112 TYR 0.021 0.001 TYR D 411 PHE 0.031 0.002 PHE D 186 TRP 0.055 0.003 TRP A 281 HIS 0.006 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (16016) covalent geometry : angle 0.61740 / 0.31 (21800) hydrogen bonds : bond 0.05099 / 3.54 ( 1160) hydrogen bonds : angle 4.37696 / 3.28 ( 3468) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 399 time to evaluate : 0.489 Fit side-chains REVERT: A 234 TYR cc_start: 0.7650 (m-80) cc_final: 0.6170 (t80) REVERT: A 236 PHE cc_start: 0.8453 (t80) cc_final: 0.8190 (t80) REVERT: A 289 TYR cc_start: 0.6711 (m-80) cc_final: 0.6300 (m-10) REVERT: A 386 TYR cc_start: 0.8878 (t80) cc_final: 0.8599 (t80) REVERT: A 388 MET cc_start: 0.8103 (mmm) cc_final: 0.7865 (mmm) REVERT: A 419 SER cc_start: 0.9320 (t) cc_final: 0.9094 (p) REVERT: A 439 TYR cc_start: 0.9077 (m-80) cc_final: 0.8751 (m-80) REVERT: B 140 ASP cc_start: 0.7788 (m-30) cc_final: 0.7375 (t0) REVERT: B 149 MET cc_start: 0.8556 (tpp) cc_final: 0.8330 (tpp) REVERT: B 234 TYR cc_start: 0.7537 (m-80) cc_final: 0.5977 (t80) REVERT: B 281 TRP cc_start: 0.8049 (m100) cc_final: 0.7751 (m100) REVERT: B 380 ILE cc_start: 0.9551 (mm) cc_final: 0.9349 (mm) REVERT: C 234 TYR cc_start: 0.7495 (m-80) cc_final: 0.6149 (t80) REVERT: C 281 TRP cc_start: 0.8022 (m100) cc_final: 0.7713 (m100) REVERT: D 234 TYR cc_start: 0.7460 (m-80) cc_final: 0.6012 (t80) REVERT: D 281 TRP cc_start: 0.7903 (m100) cc_final: 0.7692 (m100) outliers start: 34 outliers final: 15 residues processed: 408 average time/residue: 0.0914 time to fit residues: 60.0553 Evaluate side-chains 355 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 340 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 74 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 187 optimal weight: 0.5980 chunk 200 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 0.0570 chunk 144 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN C 300 ASN C 421 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.095880 restraints weight = 31010.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098733 restraints weight = 14605.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100531 restraints weight = 9313.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101371 restraints weight = 7201.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101973 restraints weight = 6341.115| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16016 Z= 0.118 Angle : 0.576 8.227 21800 Z= 0.278 Chirality : 0.039 0.139 2484 Planarity : 0.004 0.052 2748 Dihedral : 8.824 140.718 2304 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.63 % Allowed : 13.14 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.19), residues: 1992 helix: 2.92 (0.13), residues: 1432 sheet: 0.39 (0.50), residues: 96 loop : -1.63 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 112 TYR 0.025 0.001 TYR A 217 PHE 0.017 0.001 PHE B 569 TRP 0.047 0.002 TRP A 281 HIS 0.014 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (16016) covalent geometry : angle 0.57582 / 0.28 (21800) hydrogen bonds : bond 0.04095 / 2.83 ( 1160) hydrogen bonds : angle 4.13004 / 3.06 ( 3468) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 360 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 234 TYR cc_start: 0.7826 (m-80) cc_final: 0.6143 (t80) REVERT: A 236 PHE cc_start: 0.8459 (t80) cc_final: 0.8205 (t80) REVERT: A 281 TRP cc_start: 0.7711 (m100) cc_final: 0.7510 (m100) REVERT: A 289 TYR cc_start: 0.7078 (m-80) cc_final: 0.6669 (m-10) REVERT: A 353 MET cc_start: 0.8154 (ttm) cc_final: 0.7889 (mtp) REVERT: A 386 TYR cc_start: 0.8855 (t80) cc_final: 0.8552 (t80) REVERT: A 419 SER cc_start: 0.9265 (t) cc_final: 0.8974 (p) REVERT: A 517 HIS cc_start: 0.7811 (m-70) cc_final: 0.7547 (m90) REVERT: B 225 ASP cc_start: 0.8161 (m-30) cc_final: 0.7575 (m-30) REVERT: B 234 TYR cc_start: 0.7588 (m-80) cc_final: 0.5985 (t80) REVERT: B 281 TRP cc_start: 0.8004 (m100) cc_final: 0.7764 (m100) REVERT: B 569 PHE cc_start: 0.8596 (t80) cc_final: 0.8055 (t80) REVERT: C 189 ASP cc_start: 0.8683 (t0) cc_final: 0.8383 (t0) REVERT: C 225 ASP cc_start: 0.8021 (m-30) cc_final: 0.7761 (m-30) REVERT: C 234 TYR cc_start: 0.7594 (m-80) cc_final: 0.6118 (t80) REVERT: C 281 TRP cc_start: 0.7880 (m100) cc_final: 0.7654 (m100) REVERT: D 225 ASP cc_start: 0.8165 (m-30) cc_final: 0.7659 (m-30) REVERT: D 234 TYR cc_start: 0.7497 (m-80) cc_final: 0.6000 (t80) REVERT: D 281 TRP cc_start: 0.7975 (m100) cc_final: 0.7681 (m100) REVERT: D 436 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7460 (mt-10) outliers start: 23 outliers final: 12 residues processed: 367 average time/residue: 0.0868 time to fit residues: 51.4734 Evaluate side-chains 337 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 324 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 436 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 118 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 154 optimal weight: 0.0870 chunk 193 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 300 ASN B 300 ASN B 517 HIS C 107 ASN C 300 ASN C 517 HIS D 300 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095439 restraints weight = 30721.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098319 restraints weight = 14696.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100060 restraints weight = 9372.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100956 restraints weight = 7270.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101614 restraints weight = 6395.410| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16016 Z= 0.112 Angle : 0.558 10.774 21800 Z= 0.266 Chirality : 0.038 0.145 2484 Planarity : 0.004 0.059 2748 Dihedral : 8.660 135.259 2304 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.20 % Allowed : 14.49 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.19), residues: 1992 helix: 2.94 (0.13), residues: 1420 sheet: 0.57 (0.53), residues: 96 loop : -1.35 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 560 TYR 0.022 0.001 TYR A 217 PHE 0.016 0.001 PHE C 569 TRP 0.030 0.002 TRP A 281 HIS 0.013 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16016) covalent geometry : angle 0.55845 / 0.27 (21800) hydrogen bonds : bond 0.03795 / 2.62 ( 1160) hydrogen bonds : angle 4.02302 / 2.99 ( 3468) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 355 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 TYR cc_start: 0.7675 (m-80) cc_final: 0.6136 (t80) REVERT: A 236 PHE cc_start: 0.8417 (t80) cc_final: 0.8163 (t80) REVERT: A 289 TYR cc_start: 0.7184 (m-80) cc_final: 0.6727 (m-10) REVERT: A 353 MET cc_start: 0.8186 (ttm) cc_final: 0.7872 (mtp) REVERT: A 419 SER cc_start: 0.9162 (t) cc_final: 0.8905 (p) REVERT: A 436 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7454 (mt-10) REVERT: A 494 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 517 HIS cc_start: 0.7808 (m-70) cc_final: 0.7537 (m90) REVERT: B 225 ASP cc_start: 0.8470 (m-30) cc_final: 0.7982 (m-30) REVERT: B 234 TYR cc_start: 0.7567 (m-80) cc_final: 0.6063 (t80) REVERT: B 281 TRP cc_start: 0.7970 (m100) cc_final: 0.7703 (m100) REVERT: B 512 MET cc_start: 0.8117 (ptp) cc_final: 0.7848 (ptp) REVERT: B 569 PHE cc_start: 0.8580 (t80) cc_final: 0.8081 (t80) REVERT: C 189 ASP cc_start: 0.8880 (t0) cc_final: 0.8645 (t0) REVERT: C 225 ASP cc_start: 0.8289 (m-30) cc_final: 0.8086 (m-30) REVERT: C 234 TYR cc_start: 0.7576 (m-80) cc_final: 0.6144 (t80) REVERT: C 281 TRP cc_start: 0.7892 (m100) cc_final: 0.7627 (m100) REVERT: C 419 SER cc_start: 0.9176 (t) cc_final: 0.8949 (t) REVERT: D 225 ASP cc_start: 0.8422 (m-30) cc_final: 0.7958 (m-30) REVERT: D 234 TYR cc_start: 0.7508 (m-80) cc_final: 0.6099 (t80) REVERT: D 281 TRP cc_start: 0.7894 (m100) cc_final: 0.7568 (m100) REVERT: D 287 MET cc_start: 0.7868 (tpt) cc_final: 0.7335 (tpp) REVERT: D 388 MET cc_start: 0.8404 (mmm) cc_final: 0.8197 (mmm) REVERT: D 436 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7456 (tt0) outliers start: 31 outliers final: 25 residues processed: 368 average time/residue: 0.0938 time to fit residues: 55.5709 Evaluate side-chains 354 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 328 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 436 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.0470 chunk 148 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 106 optimal weight: 8.9990 chunk 152 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 300 ASN C 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.093820 restraints weight = 30805.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096564 restraints weight = 15026.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098302 restraints weight = 9693.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099109 restraints weight = 7564.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099794 restraints weight = 6678.482| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16016 Z= 0.135 Angle : 0.560 11.863 21800 Z= 0.269 Chirality : 0.039 0.157 2484 Planarity : 0.004 0.048 2748 Dihedral : 8.659 135.128 2304 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.06 % Allowed : 15.27 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.19), residues: 1992 helix: 2.94 (0.13), residues: 1420 sheet: 0.66 (0.54), residues: 96 loop : -1.23 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 560 TYR 0.019 0.001 TYR D 411 PHE 0.023 0.001 PHE A 143 TRP 0.054 0.002 TRP A 281 HIS 0.012 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (16016) covalent geometry : angle 0.56021 / 0.27 (21800) hydrogen bonds : bond 0.03833 / 2.65 ( 1160) hydrogen bonds : angle 4.03207 / 3.00 ( 3468) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 344 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7846 (p0) cc_final: 0.7388 (p0) REVERT: A 234 TYR cc_start: 0.7735 (m-80) cc_final: 0.6063 (t80) REVERT: A 236 PHE cc_start: 0.8450 (t80) cc_final: 0.8200 (t80) REVERT: A 289 TYR cc_start: 0.7420 (m-80) cc_final: 0.7006 (m-10) REVERT: A 353 MET cc_start: 0.8153 (ttm) cc_final: 0.7811 (mtp) REVERT: A 419 SER cc_start: 0.9267 (t) cc_final: 0.9010 (p) REVERT: A 494 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8128 (mt-10) REVERT: A 517 HIS cc_start: 0.7749 (m-70) cc_final: 0.7485 (m90) REVERT: B 225 ASP cc_start: 0.8597 (m-30) cc_final: 0.8263 (m-30) REVERT: B 234 TYR cc_start: 0.7702 (m-80) cc_final: 0.6180 (t80) REVERT: B 281 TRP cc_start: 0.8202 (m100) cc_final: 0.7828 (m100) REVERT: B 380 ILE cc_start: 0.9553 (mm) cc_final: 0.9260 (tt) REVERT: B 569 PHE cc_start: 0.8676 (t80) cc_final: 0.8265 (t80) REVERT: C 189 ASP cc_start: 0.8692 (t0) cc_final: 0.8464 (t0) REVERT: C 234 TYR cc_start: 0.7741 (m-80) cc_final: 0.6160 (t80) REVERT: C 281 TRP cc_start: 0.8025 (m100) cc_final: 0.7738 (m100) REVERT: C 388 MET cc_start: 0.8405 (mmm) cc_final: 0.8205 (mmm) REVERT: D 225 ASP cc_start: 0.8586 (m-30) cc_final: 0.8281 (m-30) REVERT: D 234 TYR cc_start: 0.7709 (m-80) cc_final: 0.6153 (t80) REVERT: D 281 TRP cc_start: 0.7991 (m100) cc_final: 0.7607 (m100) REVERT: D 287 MET cc_start: 0.7644 (tpt) cc_final: 0.7162 (tpp) outliers start: 29 outliers final: 26 residues processed: 357 average time/residue: 0.0958 time to fit residues: 54.6868 Evaluate side-chains 350 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN B 300 ASN C 408 GLN D 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.094452 restraints weight = 30764.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095696 restraints weight = 15980.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096557 restraints weight = 10934.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096818 restraints weight = 8905.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096943 restraints weight = 8378.545| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16016 Z= 0.153 Angle : 0.569 11.012 21800 Z= 0.272 Chirality : 0.038 0.149 2484 Planarity : 0.004 0.043 2748 Dihedral : 8.688 135.696 2304 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.84 % Allowed : 15.34 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.19), residues: 1992 helix: 2.86 (0.13), residues: 1424 sheet: 0.63 (0.53), residues: 96 loop : -1.08 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 112 TYR 0.020 0.001 TYR B 411 PHE 0.016 0.001 PHE B 226 TRP 0.067 0.002 TRP A 281 HIS 0.003 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (16016) covalent geometry : angle 0.56894 / 0.27 (21800) hydrogen bonds : bond 0.03861 / 2.67 ( 1160) hydrogen bonds : angle 4.02818 / 2.99 ( 3468) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 189 ASP cc_start: 0.9064 (t0) cc_final: 0.8665 (t0) REVERT: A 234 TYR cc_start: 0.7998 (m-80) cc_final: 0.6208 (t80) REVERT: A 236 PHE cc_start: 0.8724 (t80) cc_final: 0.8438 (t80) REVERT: A 353 MET cc_start: 0.8164 (ttm) cc_final: 0.7807 (mtp) REVERT: A 419 SER cc_start: 0.9285 (t) cc_final: 0.9047 (p) REVERT: A 494 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8130 (mt-10) REVERT: A 517 HIS cc_start: 0.7806 (m-70) cc_final: 0.7517 (m90) REVERT: B 225 ASP cc_start: 0.8387 (m-30) cc_final: 0.8128 (m-30) REVERT: B 234 TYR cc_start: 0.7956 (m-80) cc_final: 0.6169 (t80) REVERT: B 281 TRP cc_start: 0.8243 (m100) cc_final: 0.7796 (m100) REVERT: B 380 ILE cc_start: 0.9553 (mm) cc_final: 0.9257 (tt) REVERT: B 419 SER cc_start: 0.9297 (t) cc_final: 0.8990 (p) REVERT: B 569 PHE cc_start: 0.8710 (t80) cc_final: 0.8301 (t80) REVERT: C 140 ASP cc_start: 0.7993 (m-30) cc_final: 0.7570 (t0) REVERT: C 189 ASP cc_start: 0.8834 (t0) cc_final: 0.8538 (t0) REVERT: C 234 TYR cc_start: 0.7936 (m-80) cc_final: 0.6159 (t80) REVERT: C 281 TRP cc_start: 0.8074 (m100) cc_final: 0.7753 (m100) REVERT: C 287 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7419 (tpt) REVERT: D 225 ASP cc_start: 0.8568 (m-30) cc_final: 0.8270 (m-30) REVERT: D 234 TYR cc_start: 0.7929 (m-80) cc_final: 0.6158 (t80) REVERT: D 281 TRP cc_start: 0.8078 (m100) cc_final: 0.7652 (m100) REVERT: D 287 MET cc_start: 0.7727 (tpt) cc_final: 0.7233 (tpp) REVERT: D 436 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7453 (mt-10) outliers start: 40 outliers final: 32 residues processed: 336 average time/residue: 0.0913 time to fit residues: 50.3581 Evaluate side-chains 344 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 385 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 136 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 ASN B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.094491 restraints weight = 30646.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097359 restraints weight = 14811.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099141 restraints weight = 9495.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099949 restraints weight = 7365.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100410 restraints weight = 6495.070| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16016 Z= 0.111 Angle : 0.546 8.566 21800 Z= 0.259 Chirality : 0.038 0.149 2484 Planarity : 0.003 0.039 2748 Dihedral : 8.654 135.882 2304 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.42 % Allowed : 17.40 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.19), residues: 1992 helix: 2.85 (0.13), residues: 1424 sheet: 0.58 (0.53), residues: 96 loop : -1.12 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 112 TYR 0.017 0.001 TYR A 411 PHE 0.013 0.001 PHE A 226 TRP 0.060 0.002 TRP A 281 HIS 0.004 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (16016) covalent geometry : angle 0.54611 / 0.26 (21800) hydrogen bonds : bond 0.03542 / 2.44 ( 1160) hydrogen bonds : angle 3.92511 / 2.90 ( 3468) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 350 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8228 (m-80) cc_final: 0.8016 (m-80) REVERT: A 233 ASP cc_start: 0.7928 (p0) cc_final: 0.7543 (p0) REVERT: A 234 TYR cc_start: 0.7859 (m-80) cc_final: 0.6274 (t80) REVERT: A 236 PHE cc_start: 0.8505 (t80) cc_final: 0.8247 (t80) REVERT: A 281 TRP cc_start: 0.6895 (m100) cc_final: 0.6633 (m100) REVERT: A 353 MET cc_start: 0.7996 (ttm) cc_final: 0.7642 (mtp) REVERT: A 419 SER cc_start: 0.9266 (t) cc_final: 0.9017 (p) REVERT: A 517 HIS cc_start: 0.7803 (m-70) cc_final: 0.7543 (m90) REVERT: B 189 ASP cc_start: 0.8691 (t0) cc_final: 0.8491 (t0) REVERT: B 225 ASP cc_start: 0.8296 (m-30) cc_final: 0.8036 (m-30) REVERT: B 234 TYR cc_start: 0.7785 (m-80) cc_final: 0.6168 (t80) REVERT: B 281 TRP cc_start: 0.7998 (m100) cc_final: 0.7637 (m100) REVERT: B 380 ILE cc_start: 0.9530 (mm) cc_final: 0.9236 (tt) REVERT: B 512 MET cc_start: 0.8140 (ptp) cc_final: 0.7859 (ptp) REVERT: B 569 PHE cc_start: 0.8642 (t80) cc_final: 0.8151 (t80) REVERT: C 189 ASP cc_start: 0.8695 (t0) cc_final: 0.8283 (t0) REVERT: C 234 TYR cc_start: 0.7805 (m-80) cc_final: 0.6143 (t80) REVERT: C 236 PHE cc_start: 0.8375 (t80) cc_final: 0.8127 (t80) REVERT: C 353 MET cc_start: 0.8265 (ttm) cc_final: 0.7924 (mtp) REVERT: C 418 MET cc_start: 0.8610 (mmt) cc_final: 0.8323 (mmt) REVERT: C 512 MET cc_start: 0.8146 (ptp) cc_final: 0.7872 (ptp) REVERT: C 569 PHE cc_start: 0.8790 (t80) cc_final: 0.8283 (t80) REVERT: D 225 ASP cc_start: 0.8533 (m-30) cc_final: 0.8273 (m-30) REVERT: D 234 TYR cc_start: 0.7868 (m-80) cc_final: 0.6160 (t80) REVERT: D 281 TRP cc_start: 0.8017 (m100) cc_final: 0.7681 (m100) REVERT: D 436 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7332 (mt-10) REVERT: D 569 PHE cc_start: 0.8760 (t80) cc_final: 0.8253 (t80) outliers start: 20 outliers final: 14 residues processed: 361 average time/residue: 0.0877 time to fit residues: 52.0740 Evaluate side-chains 344 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 330 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 175 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 159 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 516 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.095164 restraints weight = 30845.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097955 restraints weight = 15023.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099683 restraints weight = 9669.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100502 restraints weight = 7550.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100774 restraints weight = 6662.264| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 16016 Z= 0.111 Angle : 0.562 11.841 21800 Z= 0.265 Chirality : 0.037 0.161 2484 Planarity : 0.003 0.037 2748 Dihedral : 8.637 135.814 2304 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.35 % Allowed : 17.33 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.19), residues: 1992 helix: 2.82 (0.13), residues: 1428 sheet: 0.56 (0.53), residues: 96 loop : -1.01 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 560 TYR 0.015 0.001 TYR B 411 PHE 0.017 0.001 PHE D 226 TRP 0.053 0.002 TRP A 281 HIS 0.004 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (16016) covalent geometry : angle 0.56163 / 0.26 (21800) hydrogen bonds : bond 0.03510 / 2.42 ( 1160) hydrogen bonds : angle 3.86789 / 2.86 ( 3468) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 349 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7950 (p0) cc_final: 0.7530 (p0) REVERT: A 234 TYR cc_start: 0.7847 (m-80) cc_final: 0.6190 (t80) REVERT: A 236 PHE cc_start: 0.8476 (t80) cc_final: 0.8215 (t80) REVERT: A 281 TRP cc_start: 0.7169 (m100) cc_final: 0.6845 (m100) REVERT: A 353 MET cc_start: 0.7970 (ttm) cc_final: 0.7656 (mtp) REVERT: A 418 MET cc_start: 0.8380 (mmm) cc_final: 0.8177 (mtm) REVERT: A 419 SER cc_start: 0.9250 (t) cc_final: 0.9013 (p) REVERT: A 517 HIS cc_start: 0.7729 (m-70) cc_final: 0.7462 (m90) REVERT: B 189 ASP cc_start: 0.8774 (t0) cc_final: 0.8487 (t0) REVERT: B 225 ASP cc_start: 0.8272 (m-30) cc_final: 0.7976 (m-30) REVERT: B 234 TYR cc_start: 0.7771 (m-80) cc_final: 0.6176 (t80) REVERT: B 281 TRP cc_start: 0.7980 (m100) cc_final: 0.7765 (m100) REVERT: B 380 ILE cc_start: 0.9535 (mm) cc_final: 0.9239 (tt) REVERT: B 512 MET cc_start: 0.8126 (ptp) cc_final: 0.7844 (ptp) REVERT: B 569 PHE cc_start: 0.8593 (t80) cc_final: 0.7964 (t80) REVERT: C 189 ASP cc_start: 0.8883 (t0) cc_final: 0.8649 (t0) REVERT: C 234 TYR cc_start: 0.7865 (m-80) cc_final: 0.6139 (t80) REVERT: C 236 PHE cc_start: 0.8394 (t80) cc_final: 0.8131 (t80) REVERT: C 281 TRP cc_start: 0.7873 (m100) cc_final: 0.7644 (m100) REVERT: C 418 MET cc_start: 0.8578 (mmt) cc_final: 0.8298 (mmt) REVERT: C 512 MET cc_start: 0.8130 (ptp) cc_final: 0.7865 (ptp) REVERT: C 569 PHE cc_start: 0.8775 (t80) cc_final: 0.8267 (t80) REVERT: D 234 TYR cc_start: 0.7862 (m-80) cc_final: 0.6162 (t80) REVERT: D 281 TRP cc_start: 0.8028 (m100) cc_final: 0.7808 (m100) REVERT: D 436 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7302 (mt-10) REVERT: D 569 PHE cc_start: 0.8734 (t80) cc_final: 0.8278 (t80) outliers start: 19 outliers final: 15 residues processed: 359 average time/residue: 0.0894 time to fit residues: 52.5516 Evaluate side-chains 351 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 336 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 26 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN D 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097280 restraints weight = 30070.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100046 restraints weight = 14981.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101751 restraints weight = 9871.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102715 restraints weight = 7818.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103092 restraints weight = 6913.336| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16016 Z= 0.108 Angle : 0.571 10.973 21800 Z= 0.268 Chirality : 0.037 0.152 2484 Planarity : 0.004 0.076 2748 Dihedral : 8.613 135.658 2304 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.14 % Allowed : 18.39 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.19), residues: 1992 helix: 2.78 (0.13), residues: 1428 sheet: 0.57 (0.54), residues: 96 loop : -0.95 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 560 TYR 0.017 0.001 TYR C 411 PHE 0.015 0.001 PHE A 226 TRP 0.047 0.002 TRP A 281 HIS 0.005 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (16016) covalent geometry : angle 0.57131 / 0.27 (21800) hydrogen bonds : bond 0.03394 / 2.35 ( 1160) hydrogen bonds : angle 3.83674 / 2.83 ( 3468) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 337 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 189 ASP cc_start: 0.8324 (t0) cc_final: 0.8116 (t0) REVERT: A 233 ASP cc_start: 0.7995 (p0) cc_final: 0.7651 (p0) REVERT: A 234 TYR cc_start: 0.7692 (m-80) cc_final: 0.6146 (t80) REVERT: A 236 PHE cc_start: 0.8508 (t80) cc_final: 0.8255 (t80) REVERT: A 281 TRP cc_start: 0.7115 (m100) cc_final: 0.6759 (m100) REVERT: A 353 MET cc_start: 0.7998 (ttm) cc_final: 0.7670 (mtp) REVERT: A 418 MET cc_start: 0.8472 (mmm) cc_final: 0.8249 (mtm) REVERT: A 419 SER cc_start: 0.9228 (t) cc_final: 0.8999 (p) REVERT: A 517 HIS cc_start: 0.7695 (m-70) cc_final: 0.7449 (m90) REVERT: A 569 PHE cc_start: 0.8840 (t80) cc_final: 0.8450 (t80) REVERT: B 189 ASP cc_start: 0.8360 (t0) cc_final: 0.7472 (t0) REVERT: B 225 ASP cc_start: 0.8279 (m-30) cc_final: 0.8014 (m-30) REVERT: B 234 TYR cc_start: 0.7772 (m-80) cc_final: 0.6163 (t80) REVERT: B 281 TRP cc_start: 0.7987 (m100) cc_final: 0.7781 (m100) REVERT: B 353 MET cc_start: 0.8149 (ttm) cc_final: 0.7921 (ttm) REVERT: B 380 ILE cc_start: 0.9538 (mm) cc_final: 0.9237 (tt) REVERT: C 234 TYR cc_start: 0.7830 (m-80) cc_final: 0.6129 (t80) REVERT: C 236 PHE cc_start: 0.8348 (t80) cc_final: 0.8090 (t80) REVERT: C 281 TRP cc_start: 0.7801 (m100) cc_final: 0.7504 (m100) REVERT: C 418 MET cc_start: 0.8536 (mmt) cc_final: 0.8262 (mmt) REVERT: C 500 ASP cc_start: 0.7724 (m-30) cc_final: 0.7468 (m-30) REVERT: C 512 MET cc_start: 0.8143 (ptp) cc_final: 0.7896 (ptp) REVERT: C 569 PHE cc_start: 0.8683 (t80) cc_final: 0.8064 (t80) REVERT: D 234 TYR cc_start: 0.7857 (m-80) cc_final: 0.6143 (t80) REVERT: D 436 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7299 (mt-10) REVERT: D 569 PHE cc_start: 0.8783 (t80) cc_final: 0.8360 (t80) outliers start: 16 outliers final: 13 residues processed: 347 average time/residue: 0.0888 time to fit residues: 50.8891 Evaluate side-chains 339 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 326 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 25 optimal weight: 0.3980 chunk 193 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 189 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 0.0040 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096694 restraints weight = 30074.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099446 restraints weight = 14982.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101136 restraints weight = 9879.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102142 restraints weight = 7815.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102553 restraints weight = 6903.773| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16016 Z= 0.111 Angle : 0.568 9.626 21800 Z= 0.267 Chirality : 0.037 0.143 2484 Planarity : 0.004 0.081 2748 Dihedral : 8.612 135.633 2304 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.78 % Allowed : 18.75 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.19), residues: 1992 helix: 2.80 (0.13), residues: 1428 sheet: 0.59 (0.54), residues: 96 loop : -0.91 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 112 TYR 0.016 0.001 TYR C 411 PHE 0.015 0.001 PHE B 226 TRP 0.050 0.002 TRP D 281 HIS 0.005 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (16016) covalent geometry : angle 0.56789 / 0.27 (21800) hydrogen bonds : bond 0.03358 / 2.31 ( 1160) hydrogen bonds : angle 3.82281 / 2.83 ( 3468) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 337 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 234 TYR cc_start: 0.7676 (m-80) cc_final: 0.6117 (t80) REVERT: A 236 PHE cc_start: 0.8501 (t80) cc_final: 0.8246 (t80) REVERT: A 281 TRP cc_start: 0.7076 (m100) cc_final: 0.6718 (m100) REVERT: A 353 MET cc_start: 0.8038 (ttm) cc_final: 0.7778 (mtp) REVERT: A 419 SER cc_start: 0.9240 (t) cc_final: 0.9009 (p) REVERT: A 517 HIS cc_start: 0.7743 (m-70) cc_final: 0.7468 (m90) REVERT: A 569 PHE cc_start: 0.8825 (t80) cc_final: 0.8426 (t80) REVERT: B 225 ASP cc_start: 0.8291 (m-30) cc_final: 0.7976 (m-30) REVERT: B 234 TYR cc_start: 0.7842 (m-80) cc_final: 0.6161 (t80) REVERT: B 281 TRP cc_start: 0.8011 (m100) cc_final: 0.7797 (m100) REVERT: B 289 TYR cc_start: 0.6737 (m-80) cc_final: 0.6307 (m-10) REVERT: B 380 ILE cc_start: 0.9530 (mm) cc_final: 0.9222 (tt) REVERT: B 418 MET cc_start: 0.8562 (mmt) cc_final: 0.8330 (mmt) REVERT: C 234 TYR cc_start: 0.7892 (m-80) cc_final: 0.6183 (t80) REVERT: C 236 PHE cc_start: 0.8386 (t80) cc_final: 0.8115 (t80) REVERT: C 281 TRP cc_start: 0.7796 (m100) cc_final: 0.7493 (m100) REVERT: C 500 ASP cc_start: 0.7705 (m-30) cc_final: 0.7455 (m-30) REVERT: D 234 TYR cc_start: 0.7856 (m-80) cc_final: 0.6141 (t80) REVERT: D 281 TRP cc_start: 0.7768 (m100) cc_final: 0.7454 (m100) REVERT: D 283 GLU cc_start: 0.7404 (mp0) cc_final: 0.7202 (mp0) REVERT: D 436 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7267 (mt-10) REVERT: D 569 PHE cc_start: 0.8794 (t80) cc_final: 0.8274 (t80) outliers start: 11 outliers final: 9 residues processed: 343 average time/residue: 0.0897 time to fit residues: 50.9069 Evaluate side-chains 332 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 323 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 225 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 125 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.093028 restraints weight = 30800.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095830 restraints weight = 15194.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097548 restraints weight = 9854.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098360 restraints weight = 7689.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098756 restraints weight = 6792.363| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16016 Z= 0.158 Angle : 0.610 12.503 21800 Z= 0.287 Chirality : 0.039 0.168 2484 Planarity : 0.004 0.073 2748 Dihedral : 8.664 135.975 2304 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.99 % Allowed : 19.67 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.19), residues: 1992 helix: 2.71 (0.13), residues: 1436 sheet: 0.55 (0.54), residues: 96 loop : -0.94 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 112 TYR 0.018 0.001 TYR C 411 PHE 0.016 0.001 PHE D 226 TRP 0.051 0.002 TRP D 281 HIS 0.005 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (16016) covalent geometry : angle 0.60958 / 0.29 (21800) hydrogen bonds : bond 0.03630 / 2.51 ( 1160) hydrogen bonds : angle 3.91418 / 2.90 ( 3468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2610.07 seconds wall clock time: 45 minutes 51.86 seconds (2751.86 seconds total)