Starting phenix.real_space_refine on Thu Sep 18 10:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u6p_8512/09_2025/5u6p_8512.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u6p_8512/09_2025/5u6p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2025/5u6p_8512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2025/5u6p_8512.map" model { file = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2025/5u6p_8512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u6p_8512/09_2025/5u6p_8512.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: {'RNA': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 3.02, per 1000 atoms: 0.19 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: 1.45 Conformation dependent library (CDL) restraints added in 640.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.61 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: 3.08 Time building geometry restraints manager: 1.83 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: 17624 1.97 - 3.94: 4006 3.94 - 5.91: 154 5.91 - 7.88: 12 7.88 - 9.85: 4 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: 9304 31.61 - 63.21: 64 63.21 - 94.82: 0 94.82 - 126.43: 0 126.43 - 158.03: 12 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: 1587 0.057 - 0.114: 591 0.114 - 0.171: 229 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: 0.04 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: 0.920 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 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= 0.518 Angle : 1.410 9.850 21800 Z= 1.084 Chirality : 0.073 0.285 2484 Planarity : 0.006 0.112 2748 Dihedral : 12.411 158.034 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 aren 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 covalent geometry : bond 0.00730 (16016) covalent geometry : angle 1.40951 (21800) hydrogen bonds : bond 0.19194 ( 1160) hydrogen bonds : angle 5.71463 ( 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 : 0.581 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: 0.1216 time to fit residues: 93.3188 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 : 0.433 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3546 r_free = 0.3546 target = 0.119474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.094456 restraints weight = 30576.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097290 restraints weight = 14542.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099046 restraints weight = 9332.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099968 restraints weight = 7287.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100288 restraints weight = 6437.391| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16016 Z= 0.162 Angle : 0.595 8.220 21800 Z= 0.317 Chirality : 0.041 0.150 2484 Planarity : 0.005 0.067 2748 Dihedral : 11.825 166.562 2304 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.41 % Allowed : 10.23 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.19), residues: 1992 helix: 3.09 (0.13), residues: 1420 sheet: -0.08 (0.44), residues: 96 loop : -1.81 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 112 TYR 0.023 0.001 TYR B 411 PHE 0.031 0.002 PHE D 186 TRP 0.050 0.003 TRP B 281 HIS 0.007 0.002 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00347 (16016) covalent geometry : angle 0.59453 (21800) hydrogen bonds : bond 0.05295 ( 1160) hydrogen bonds : angle 4.38771 ( 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 423 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 389 time to evaluate : 0.588 Fit side-chains REVERT: A 189 ASP cc_start: 0.8664 (t0) cc_final: 0.8463 (t0) REVERT: A 234 TYR cc_start: 0.7656 (m-80) cc_final: 0.6145 (t80) REVERT: A 236 PHE cc_start: 0.8511 (t80) cc_final: 0.8240 (t80) REVERT: A 386 TYR cc_start: 0.8885 (t80) cc_final: 0.8621 (t80) REVERT: A 388 MET cc_start: 0.8125 (mmm) cc_final: 0.7848 (mmm) REVERT: A 419 SER cc_start: 0.9323 (t) cc_final: 0.9111 (p) REVERT: A 439 TYR cc_start: 0.9037 (m-80) cc_final: 0.8722 (m-80) REVERT: B 140 ASP cc_start: 0.7776 (m-30) cc_final: 0.7484 (t0) REVERT: B 149 MET cc_start: 0.8592 (tpp) cc_final: 0.8369 (tpp) REVERT: B 234 TYR cc_start: 0.7575 (m-80) cc_final: 0.5974 (t80) REVERT: B 281 TRP cc_start: 0.8030 (m100) cc_final: 0.7717 (m100) REVERT: C 234 TYR cc_start: 0.7498 (m-80) cc_final: 0.6076 (t80) REVERT: C 281 TRP cc_start: 0.8032 (m100) cc_final: 0.7724 (m100) REVERT: D 234 TYR cc_start: 0.7503 (m-80) cc_final: 0.6008 (t80) outliers start: 34 outliers final: 16 residues processed: 397 average time/residue: 0.0988 time to fit residues: 62.9673 Evaluate side-chains 344 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 328 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL 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 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: 0.3980 chunk 200 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 179 ASN D 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.119318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094536 restraints weight = 31125.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097357 restraints weight = 14796.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099128 restraints weight = 9457.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100015 restraints weight = 7322.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100616 restraints weight = 6446.457| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16016 Z= 0.133 Angle : 0.557 12.702 21800 Z= 0.283 Chirality : 0.039 0.137 2484 Planarity : 0.004 0.052 2748 Dihedral : 11.752 171.990 2304 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.70 % Allowed : 12.86 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.19), residues: 1992 helix: 2.88 (0.13), residues: 1432 sheet: 0.23 (0.48), residues: 96 loop : -1.67 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.026 0.001 TYR A 217 PHE 0.018 0.001 PHE B 569 TRP 0.052 0.002 TRP D 281 HIS 0.014 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00285 (16016) covalent geometry : angle 0.55696 (21800) hydrogen bonds : bond 0.04242 ( 1160) hydrogen bonds : angle 4.18046 ( 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 384 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 360 time to evaluate : 0.597 Fit side-chains REVERT: A 234 TYR cc_start: 0.7841 (m-80) cc_final: 0.6178 (t80) REVERT: A 236 PHE cc_start: 0.8464 (t80) cc_final: 0.8207 (t80) REVERT: A 353 MET cc_start: 0.8186 (ttm) cc_final: 0.7884 (mtp) REVERT: A 388 MET cc_start: 0.8268 (mmm) cc_final: 0.7990 (mmm) REVERT: A 419 SER cc_start: 0.9306 (t) cc_final: 0.9021 (p) REVERT: A 517 HIS cc_start: 0.7766 (m-70) cc_final: 0.7466 (m90) REVERT: B 112 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7609 (ttm-80) REVERT: B 234 TYR cc_start: 0.7522 (m-80) cc_final: 0.6056 (t80) REVERT: B 281 TRP cc_start: 0.8059 (m100) cc_final: 0.7735 (m100) REVERT: B 287 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: B 300 ASN cc_start: 0.8197 (m-40) cc_final: 0.7942 (m-40) REVERT: B 353 MET cc_start: 0.8306 (ttm) cc_final: 0.7931 (mtp) REVERT: C 189 ASP cc_start: 0.8707 (t0) cc_final: 0.8324 (t0) REVERT: C 225 ASP cc_start: 0.8058 (m-30) cc_final: 0.7820 (m-30) REVERT: C 234 TYR cc_start: 0.7610 (m-80) cc_final: 0.6143 (t80) REVERT: C 281 TRP cc_start: 0.7919 (m100) cc_final: 0.7662 (m100) REVERT: C 300 ASN cc_start: 0.8256 (m-40) cc_final: 0.8043 (m-40) REVERT: C 353 MET cc_start: 0.8253 (ttm) cc_final: 0.7884 (mtp) REVERT: C 517 HIS cc_start: 0.7666 (m-70) cc_final: 0.7415 (m90) REVERT: D 189 ASP cc_start: 0.8893 (t0) cc_final: 0.8629 (t0) REVERT: D 234 TYR cc_start: 0.7492 (m-80) cc_final: 0.6021 (t80) REVERT: D 380 ILE cc_start: 0.9546 (mm) cc_final: 0.9180 (tt) outliers start: 24 outliers final: 12 residues processed: 368 average time/residue: 0.0967 time to fit residues: 57.7171 Evaluate side-chains 350 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 337 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 40.0000 chunk 31 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.092808 restraints weight = 30968.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.095639 restraints weight = 15024.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.097378 restraints weight = 9687.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098362 restraints weight = 7556.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098728 restraints weight = 6620.916| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16016 Z= 0.155 Angle : 0.536 8.460 21800 Z= 0.276 Chirality : 0.039 0.153 2484 Planarity : 0.004 0.059 2748 Dihedral : 11.597 170.249 2304 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.12 % Allowed : 13.57 % 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 aren not related in a simple way. whole: 2.71 (0.19), residues: 1992 helix: 2.86 (0.13), residues: 1420 sheet: 0.52 (0.52), residues: 96 loop : -1.45 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 560 TYR 0.022 0.001 TYR A 217 PHE 0.022 0.001 PHE A 143 TRP 0.062 0.002 TRP A 281 HIS 0.008 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00349 (16016) covalent geometry : angle 0.53574 (21800) hydrogen bonds : bond 0.04119 ( 1160) hydrogen bonds : angle 4.12260 ( 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 397 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 353 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 225 ASP cc_start: 0.8170 (m-30) cc_final: 0.7946 (m-30) REVERT: A 234 TYR cc_start: 0.7757 (m-80) cc_final: 0.6164 (t80) REVERT: A 236 PHE cc_start: 0.8474 (t80) cc_final: 0.8223 (t80) REVERT: A 278 ILE cc_start: 0.9213 (tp) cc_final: 0.9011 (tp) REVERT: A 282 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 300 ASN cc_start: 0.8420 (m-40) cc_final: 0.8082 (m110) REVERT: A 353 MET cc_start: 0.8226 (ttm) cc_final: 0.7871 (mtp) REVERT: A 419 SER cc_start: 0.9299 (t) cc_final: 0.9048 (p) REVERT: A 436 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7279 (tt0) REVERT: A 494 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 517 HIS cc_start: 0.7780 (m-70) cc_final: 0.7491 (m90) REVERT: B 234 TYR cc_start: 0.7723 (m-80) cc_final: 0.6107 (t80) REVERT: B 281 TRP cc_start: 0.8033 (m100) cc_final: 0.7716 (m100) REVERT: B 300 ASN cc_start: 0.8415 (m-40) cc_final: 0.8114 (m-40) REVERT: B 353 MET cc_start: 0.8280 (ttm) cc_final: 0.7922 (mtp) REVERT: B 380 ILE cc_start: 0.9565 (mm) cc_final: 0.9222 (tt) REVERT: B 388 MET cc_start: 0.8416 (mmm) cc_final: 0.8182 (mmm) REVERT: B 418 MET cc_start: 0.8055 (mtt) cc_final: 0.7670 (mtt) REVERT: C 140 ASP cc_start: 0.7788 (m-30) cc_final: 0.7567 (t0) REVERT: C 225 ASP cc_start: 0.8190 (m-30) cc_final: 0.7984 (m-30) REVERT: C 234 TYR cc_start: 0.7785 (m-80) cc_final: 0.6176 (t80) REVERT: C 281 TRP cc_start: 0.7993 (m100) cc_final: 0.7709 (m100) REVERT: C 353 MET cc_start: 0.8263 (ttm) cc_final: 0.7910 (mtp) REVERT: C 380 ILE cc_start: 0.9557 (mm) cc_final: 0.9242 (tt) REVERT: C 419 SER cc_start: 0.9299 (t) cc_final: 0.9082 (t) REVERT: C 517 HIS cc_start: 0.7702 (m-70) cc_final: 0.7456 (m90) REVERT: D 225 ASP cc_start: 0.8545 (m-30) cc_final: 0.8099 (m-30) REVERT: D 234 TYR cc_start: 0.7723 (m-80) cc_final: 0.6138 (t80) REVERT: D 380 ILE cc_start: 0.9561 (mm) cc_final: 0.9218 (tt) REVERT: D 388 MET cc_start: 0.8414 (mmm) cc_final: 0.8205 (mmm) REVERT: D 418 MET cc_start: 0.8075 (mtt) cc_final: 0.7687 (mtt) outliers start: 44 outliers final: 36 residues processed: 369 average time/residue: 0.0951 time to fit residues: 56.8000 Evaluate side-chains 368 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 150 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 269 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 188 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 164 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 152 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096325 restraints weight = 30834.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.097453 restraints weight = 16077.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098392 restraints weight = 10954.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098664 restraints weight = 8905.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098774 restraints weight = 8358.827| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16016 Z= 0.119 Angle : 0.517 11.147 21800 Z= 0.262 Chirality : 0.038 0.150 2484 Planarity : 0.004 0.048 2748 Dihedral : 11.641 172.322 2304 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.13 % Allowed : 14.99 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.19), residues: 1992 helix: 2.83 (0.13), residues: 1424 sheet: 0.61 (0.53), residues: 96 loop : -1.23 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 112 TYR 0.018 0.001 TYR D 411 PHE 0.022 0.001 PHE A 143 TRP 0.060 0.002 TRP A 281 HIS 0.007 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00261 (16016) covalent geometry : angle 0.51718 (21800) hydrogen bonds : bond 0.03714 ( 1160) hydrogen bonds : angle 4.03204 ( 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 394 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 364 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7951 (p0) cc_final: 0.7345 (p0) REVERT: A 234 TYR cc_start: 0.7903 (m-80) cc_final: 0.6040 (t80) REVERT: A 236 PHE cc_start: 0.8651 (t80) cc_final: 0.8370 (t80) REVERT: A 282 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7642 (mt-10) REVERT: A 300 ASN cc_start: 0.8599 (m-40) cc_final: 0.8224 (m110) REVERT: A 353 MET cc_start: 0.8041 (ttm) cc_final: 0.7670 (mtp) REVERT: A 419 SER cc_start: 0.9260 (t) cc_final: 0.9004 (p) REVERT: A 436 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7455 (tt0) REVERT: A 494 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 517 HIS cc_start: 0.7769 (m-70) cc_final: 0.7492 (m90) REVERT: B 234 TYR cc_start: 0.7921 (m-80) cc_final: 0.6156 (t80) REVERT: B 281 TRP cc_start: 0.8230 (m100) cc_final: 0.7797 (m100) REVERT: B 300 ASN cc_start: 0.8528 (m-40) cc_final: 0.8317 (m110) REVERT: B 353 MET cc_start: 0.8225 (ttm) cc_final: 0.7881 (mtp) REVERT: B 380 ILE cc_start: 0.9561 (mm) cc_final: 0.9213 (tt) REVERT: B 388 MET cc_start: 0.8290 (mmm) cc_final: 0.8079 (mmm) REVERT: B 418 MET cc_start: 0.8102 (mtt) cc_final: 0.7803 (mtt) REVERT: B 419 SER cc_start: 0.9275 (t) cc_final: 0.9048 (t) REVERT: B 512 MET cc_start: 0.8130 (ptp) cc_final: 0.7843 (ptp) REVERT: B 569 PHE cc_start: 0.8657 (t80) cc_final: 0.8167 (t80) REVERT: C 234 TYR cc_start: 0.7932 (m-80) cc_final: 0.6135 (t80) REVERT: C 281 TRP cc_start: 0.8030 (m100) cc_final: 0.7722 (m100) REVERT: C 353 MET cc_start: 0.8201 (ttm) cc_final: 0.7844 (mtp) REVERT: C 380 ILE cc_start: 0.9548 (mm) cc_final: 0.9252 (tt) REVERT: C 388 MET cc_start: 0.8357 (mmm) cc_final: 0.8141 (mmm) REVERT: C 419 SER cc_start: 0.9273 (t) cc_final: 0.9050 (t) REVERT: C 517 HIS cc_start: 0.7731 (m-70) cc_final: 0.7453 (m90) REVERT: D 225 ASP cc_start: 0.8657 (m-30) cc_final: 0.8313 (m-30) REVERT: D 234 TYR cc_start: 0.7911 (m-80) cc_final: 0.6132 (t80) REVERT: D 281 TRP cc_start: 0.7989 (m100) cc_final: 0.7580 (m100) REVERT: D 282 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8107 (mt-10) REVERT: D 380 ILE cc_start: 0.9554 (mm) cc_final: 0.9248 (tt) REVERT: D 418 MET cc_start: 0.8086 (mtt) cc_final: 0.7800 (mtt) REVERT: D 436 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7539 (mt-10) outliers start: 30 outliers final: 24 residues processed: 378 average time/residue: 0.0992 time to fit residues: 59.5999 Evaluate side-chains 363 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 339 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 MET 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 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 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 188 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 166 optimal weight: 0.0980 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN C 408 GLN D 300 ASN D 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093708 restraints weight = 30868.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.095342 restraints weight = 15397.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096312 restraints weight = 10316.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.096360 restraints weight = 9299.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096460 restraints weight = 8510.801| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16016 Z= 0.164 Angle : 0.532 8.011 21800 Z= 0.273 Chirality : 0.038 0.134 2484 Planarity : 0.004 0.043 2748 Dihedral : 11.575 170.006 2304 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.56 % Allowed : 14.99 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.19), residues: 1992 helix: 2.81 (0.13), residues: 1424 sheet: 0.67 (0.54), residues: 96 loop : -1.18 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 560 TYR 0.019 0.001 TYR D 411 PHE 0.021 0.001 PHE A 143 TRP 0.065 0.002 TRP A 281 HIS 0.007 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00373 (16016) covalent geometry : angle 0.53203 (21800) hydrogen bonds : bond 0.03970 ( 1160) hydrogen bonds : angle 4.04617 ( 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 380 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 344 time to evaluate : 0.612 Fit side-chains REVERT: A 189 ASP cc_start: 0.8706 (t0) cc_final: 0.8380 (t0) REVERT: A 234 TYR cc_start: 0.7972 (m-80) cc_final: 0.6165 (t80) REVERT: A 236 PHE cc_start: 0.8683 (t80) cc_final: 0.8413 (t80) REVERT: A 282 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7568 (mt-10) REVERT: A 300 ASN cc_start: 0.8666 (m-40) cc_final: 0.8324 (m110) REVERT: A 353 MET cc_start: 0.8157 (ttm) cc_final: 0.7815 (mtp) REVERT: A 418 MET cc_start: 0.8580 (mmm) cc_final: 0.8304 (mtm) REVERT: A 419 SER cc_start: 0.9417 (t) cc_final: 0.9167 (p) REVERT: A 436 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7392 (tt0) REVERT: A 517 HIS cc_start: 0.7791 (m-70) cc_final: 0.7534 (m90) REVERT: B 189 ASP cc_start: 0.8715 (t0) cc_final: 0.8513 (t0) REVERT: B 234 TYR cc_start: 0.7931 (m-80) cc_final: 0.6185 (t80) REVERT: B 281 TRP cc_start: 0.8106 (m100) cc_final: 0.7728 (m100) REVERT: B 300 ASN cc_start: 0.8474 (m-40) cc_final: 0.8174 (m-40) REVERT: B 353 MET cc_start: 0.8256 (ttm) cc_final: 0.7874 (mtp) REVERT: B 380 ILE cc_start: 0.9571 (mm) cc_final: 0.9249 (tt) REVERT: B 388 MET cc_start: 0.8370 (mmm) cc_final: 0.8156 (mmm) REVERT: B 436 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7302 (tt0) REVERT: C 234 TYR cc_start: 0.7911 (m-80) cc_final: 0.6167 (t80) REVERT: C 281 TRP cc_start: 0.8107 (m100) cc_final: 0.7786 (m100) REVERT: C 353 MET cc_start: 0.8203 (ttm) cc_final: 0.7853 (mtp) REVERT: C 380 ILE cc_start: 0.9560 (mm) cc_final: 0.9270 (tt) REVERT: C 388 MET cc_start: 0.8343 (mmm) cc_final: 0.8138 (mmm) REVERT: C 419 SER cc_start: 0.9277 (t) cc_final: 0.9019 (p) REVERT: C 517 HIS cc_start: 0.7707 (m-70) cc_final: 0.7467 (m90) REVERT: D 234 TYR cc_start: 0.7916 (m-80) cc_final: 0.6160 (t80) REVERT: D 281 TRP cc_start: 0.7886 (m100) cc_final: 0.7583 (m100) REVERT: D 380 ILE cc_start: 0.9575 (mm) cc_final: 0.9265 (tt) REVERT: D 436 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7514 (mt-10) outliers start: 36 outliers final: 27 residues processed: 361 average time/residue: 0.0948 time to fit residues: 55.6323 Evaluate side-chains 360 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 333 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 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 238 ILE 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 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: 0.9980 chunk 110 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.094469 restraints weight = 30807.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095573 restraints weight = 15858.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096354 restraints weight = 11202.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097058 restraints weight = 8915.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097039 restraints weight = 8436.081| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16016 Z= 0.151 Angle : 0.531 9.711 21800 Z= 0.269 Chirality : 0.038 0.150 2484 Planarity : 0.003 0.041 2748 Dihedral : 11.606 171.566 2304 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.34 % Allowed : 16.26 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.19), residues: 1992 helix: 2.76 (0.13), residues: 1424 sheet: 0.58 (0.53), residues: 96 loop : -1.10 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 560 TYR 0.021 0.001 TYR B 411 PHE 0.019 0.001 PHE A 143 TRP 0.071 0.002 TRP A 281 HIS 0.006 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00339 (16016) covalent geometry : angle 0.53059 (21800) hydrogen bonds : bond 0.03811 ( 1160) hydrogen bonds : angle 4.00274 ( 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 378 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 345 time to evaluate : 0.649 Fit side-chains REVERT: A 144 TYR cc_start: 0.8475 (m-80) cc_final: 0.8106 (m-80) REVERT: A 234 TYR cc_start: 0.8003 (m-80) cc_final: 0.6269 (t80) REVERT: A 236 PHE cc_start: 0.8687 (t80) cc_final: 0.8418 (t80) REVERT: A 281 TRP cc_start: 0.7651 (m100) cc_final: 0.7273 (m100) REVERT: A 282 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 300 ASN cc_start: 0.8707 (m-40) cc_final: 0.8348 (m110) REVERT: A 353 MET cc_start: 0.8015 (ttm) cc_final: 0.7643 (mtp) REVERT: A 418 MET cc_start: 0.8606 (mmm) cc_final: 0.8351 (mtm) REVERT: A 419 SER cc_start: 0.9352 (t) cc_final: 0.9107 (p) REVERT: A 436 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7475 (tt0) REVERT: A 517 HIS cc_start: 0.7794 (m-70) cc_final: 0.7525 (m90) REVERT: B 189 ASP cc_start: 0.8552 (t0) cc_final: 0.8333 (t0) REVERT: B 234 TYR cc_start: 0.7950 (m-80) cc_final: 0.6193 (t80) REVERT: B 281 TRP cc_start: 0.8232 (m100) cc_final: 0.7781 (m100) REVERT: B 282 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 300 ASN cc_start: 0.8675 (m-40) cc_final: 0.8421 (m-40) REVERT: B 353 MET cc_start: 0.8234 (ttm) cc_final: 0.7857 (mtp) REVERT: B 380 ILE cc_start: 0.9564 (mm) cc_final: 0.9238 (tt) REVERT: B 388 MET cc_start: 0.8308 (mmm) cc_final: 0.8101 (mmm) REVERT: B 436 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7379 (tt0) REVERT: C 234 TYR cc_start: 0.7991 (m-80) cc_final: 0.6165 (t80) REVERT: C 281 TRP cc_start: 0.8070 (m100) cc_final: 0.7766 (m100) REVERT: C 353 MET cc_start: 0.8198 (ttm) cc_final: 0.7850 (mtp) REVERT: C 380 ILE cc_start: 0.9553 (mm) cc_final: 0.9263 (tt) REVERT: C 388 MET cc_start: 0.8342 (mmm) cc_final: 0.8125 (mmm) REVERT: C 517 HIS cc_start: 0.7776 (m-70) cc_final: 0.7500 (m90) REVERT: D 234 TYR cc_start: 0.7992 (m-80) cc_final: 0.6172 (t80) REVERT: D 380 ILE cc_start: 0.9570 (mm) cc_final: 0.9256 (tt) REVERT: D 419 SER cc_start: 0.9439 (m) cc_final: 0.9130 (t) outliers start: 33 outliers final: 29 residues processed: 358 average time/residue: 0.0965 time to fit residues: 56.0960 Evaluate side-chains 361 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 332 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 307 LEU 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 187 LEU Chi-restraints excluded: chain B residue 225 ASP 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 150 LEU Chi-restraints excluded: chain C residue 184 THR 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 184 THR 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 385 CYS Chi-restraints excluded: chain D residue 459 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 175 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.093838 restraints weight = 31002.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096701 restraints weight = 14951.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098499 restraints weight = 9563.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099328 restraints weight = 7441.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100058 restraints weight = 6555.763| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3891 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= 0.115 Angle : 0.519 12.695 21800 Z= 0.261 Chirality : 0.037 0.146 2484 Planarity : 0.003 0.038 2748 Dihedral : 11.725 176.623 2304 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.85 % Allowed : 16.83 % 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 aren not related in a simple way. whole: 2.72 (0.19), residues: 1992 helix: 2.71 (0.13), residues: 1436 sheet: 0.57 (0.54), residues: 96 loop : -1.02 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 560 TYR 0.018 0.001 TYR B 411 PHE 0.016 0.001 PHE D 226 TRP 0.061 0.002 TRP A 281 HIS 0.005 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00247 (16016) covalent geometry : angle 0.51853 (21800) hydrogen bonds : bond 0.03551 ( 1160) hydrogen bonds : angle 3.91378 ( 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 379 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 353 time to evaluate : 0.619 Fit side-chains REVERT: A 234 TYR cc_start: 0.7819 (m-80) cc_final: 0.6199 (t80) REVERT: A 236 PHE cc_start: 0.8471 (t80) cc_final: 0.8231 (t80) REVERT: A 282 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 283 GLU cc_start: 0.7278 (mp0) cc_final: 0.6980 (mp0) REVERT: A 300 ASN cc_start: 0.8681 (m-40) cc_final: 0.8456 (m-40) REVERT: A 353 MET cc_start: 0.8055 (ttm) cc_final: 0.7706 (mtp) REVERT: A 418 MET cc_start: 0.8493 (mmm) cc_final: 0.8239 (mtm) REVERT: A 419 SER cc_start: 0.9335 (t) cc_final: 0.9068 (p) REVERT: A 436 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7469 (tt0) REVERT: A 517 HIS cc_start: 0.7736 (m-70) cc_final: 0.7487 (m90) REVERT: B 234 TYR cc_start: 0.7772 (m-80) cc_final: 0.6172 (t80) REVERT: B 281 TRP cc_start: 0.8086 (m100) cc_final: 0.7724 (m100) REVERT: B 282 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7899 (mt-10) REVERT: B 300 ASN cc_start: 0.8514 (m-40) cc_final: 0.8287 (m-40) REVERT: B 353 MET cc_start: 0.8094 (ttm) cc_final: 0.7739 (mtp) REVERT: B 380 ILE cc_start: 0.9544 (mm) cc_final: 0.9212 (tt) REVERT: B 388 MET cc_start: 0.8327 (mmm) cc_final: 0.8121 (mmm) REVERT: B 419 SER cc_start: 0.9248 (t) cc_final: 0.8983 (p) REVERT: B 436 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7350 (tt0) REVERT: B 512 MET cc_start: 0.8160 (ptp) cc_final: 0.7812 (ptp) REVERT: B 569 PHE cc_start: 0.8691 (t80) cc_final: 0.8107 (t80) REVERT: C 189 ASP cc_start: 0.8713 (t0) cc_final: 0.8493 (t0) REVERT: C 234 TYR cc_start: 0.7798 (m-80) cc_final: 0.6148 (t80) REVERT: C 281 TRP cc_start: 0.8047 (m100) cc_final: 0.7745 (m100) REVERT: C 287 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7394 (tpt) REVERT: C 353 MET cc_start: 0.8157 (ttm) cc_final: 0.7816 (mtp) REVERT: C 380 ILE cc_start: 0.9535 (mm) cc_final: 0.9255 (tt) REVERT: C 388 MET cc_start: 0.8285 (mmm) cc_final: 0.8079 (mmm) REVERT: C 517 HIS cc_start: 0.7741 (m-70) cc_final: 0.7460 (m90) REVERT: D 234 TYR cc_start: 0.7808 (m-80) cc_final: 0.6162 (t80) REVERT: D 281 TRP cc_start: 0.7717 (m100) cc_final: 0.7429 (m100) REVERT: D 380 ILE cc_start: 0.9536 (mm) cc_final: 0.9232 (tt) REVERT: D 569 PHE cc_start: 0.8802 (t80) cc_final: 0.8376 (t80) outliers start: 26 outliers final: 19 residues processed: 366 average time/residue: 0.0936 time to fit residues: 55.9967 Evaluate side-chains 359 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 339 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 225 ASP 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 287 MET Chi-restraints excluded: chain C residue 291 LEU 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 153 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 385 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 105 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.094413 restraints weight = 30846.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097287 restraints weight = 14953.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099026 restraints weight = 9635.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099846 restraints weight = 7510.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100365 restraints weight = 6634.930| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16016 Z= 0.114 Angle : 0.539 13.126 21800 Z= 0.266 Chirality : 0.037 0.164 2484 Planarity : 0.003 0.034 2748 Dihedral : 11.757 178.961 2304 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.78 % Allowed : 17.68 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.19), residues: 1992 helix: 2.71 (0.13), residues: 1432 sheet: 0.57 (0.54), residues: 96 loop : -1.03 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 560 TYR 0.018 0.001 TYR B 411 PHE 0.013 0.001 PHE A 226 TRP 0.051 0.002 TRP A 281 HIS 0.003 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00246 (16016) covalent geometry : angle 0.53858 (21800) hydrogen bonds : bond 0.03446 ( 1160) hydrogen bonds : angle 3.86470 ( 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 380 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 355 time to evaluate : 0.618 Fit side-chains REVERT: A 234 TYR cc_start: 0.7842 (m-80) cc_final: 0.6186 (t80) REVERT: A 282 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 300 ASN cc_start: 0.8636 (m-40) cc_final: 0.8383 (m-40) REVERT: A 353 MET cc_start: 0.8033 (ttm) cc_final: 0.7702 (mtp) REVERT: A 418 MET cc_start: 0.8437 (mmm) cc_final: 0.8164 (mtm) REVERT: A 419 SER cc_start: 0.9287 (t) cc_final: 0.9044 (p) REVERT: A 436 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7446 (tt0) REVERT: A 517 HIS cc_start: 0.7738 (m-70) cc_final: 0.7478 (m90) REVERT: A 569 PHE cc_start: 0.8909 (t80) cc_final: 0.8565 (t80) REVERT: B 189 ASP cc_start: 0.8401 (t0) cc_final: 0.7973 (t0) REVERT: B 234 TYR cc_start: 0.7861 (m-80) cc_final: 0.6157 (t80) REVERT: B 281 TRP cc_start: 0.8108 (m100) cc_final: 0.7766 (m100) REVERT: B 287 MET cc_start: 0.7574 (tpt) cc_final: 0.7332 (tpt) REVERT: B 300 ASN cc_start: 0.8437 (m-40) cc_final: 0.8122 (m-40) REVERT: B 353 MET cc_start: 0.8093 (ttm) cc_final: 0.7716 (mtp) REVERT: B 380 ILE cc_start: 0.9541 (mm) cc_final: 0.9209 (tt) REVERT: B 388 MET cc_start: 0.8304 (mmm) cc_final: 0.8096 (mmm) REVERT: B 419 SER cc_start: 0.9127 (t) cc_final: 0.8881 (p) REVERT: B 436 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7341 (tt0) REVERT: C 234 TYR cc_start: 0.7833 (m-80) cc_final: 0.6154 (t80) REVERT: C 236 PHE cc_start: 0.8452 (t80) cc_final: 0.8189 (t80) REVERT: C 281 TRP cc_start: 0.7985 (m100) cc_final: 0.7710 (m100) REVERT: C 287 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7420 (tpt) REVERT: C 353 MET cc_start: 0.8104 (ttm) cc_final: 0.7782 (mtp) REVERT: C 380 ILE cc_start: 0.9535 (mm) cc_final: 0.9236 (tt) REVERT: C 388 MET cc_start: 0.8277 (mmm) cc_final: 0.8077 (mmm) REVERT: C 418 MET cc_start: 0.8406 (mmm) cc_final: 0.8179 (mtm) REVERT: C 517 HIS cc_start: 0.7697 (m-70) cc_final: 0.7436 (m90) REVERT: D 234 TYR cc_start: 0.7880 (m-80) cc_final: 0.6147 (t80) REVERT: D 281 TRP cc_start: 0.7623 (m100) cc_final: 0.7342 (m100) REVERT: D 380 ILE cc_start: 0.9541 (mm) cc_final: 0.9210 (tt) REVERT: D 569 PHE cc_start: 0.8759 (t80) cc_final: 0.8200 (t80) outliers start: 25 outliers final: 18 residues processed: 367 average time/residue: 0.0969 time to fit residues: 57.9066 Evaluate side-chains 363 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 344 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 B residue 106 VAL Chi-restraints excluded: chain B residue 225 ASP 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 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 459 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 25 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 149 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 189 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094683 restraints weight = 30220.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097464 restraints weight = 14926.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099187 restraints weight = 9794.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100196 restraints weight = 7743.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100659 restraints weight = 6826.486| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16016 Z= 0.116 Angle : 0.543 12.233 21800 Z= 0.268 Chirality : 0.037 0.149 2484 Planarity : 0.003 0.039 2748 Dihedral : 11.730 178.925 2304 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.56 % Allowed : 18.18 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.19), residues: 1992 helix: 2.65 (0.13), residues: 1436 sheet: 0.59 (0.54), residues: 96 loop : -0.94 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 560 TYR 0.016 0.001 TYR B 411 PHE 0.029 0.001 PHE C 569 TRP 0.047 0.002 TRP A 281 HIS 0.002 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00254 (16016) covalent geometry : angle 0.54274 (21800) hydrogen bonds : bond 0.03427 ( 1160) hydrogen bonds : angle 3.85823 ( 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 365 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 343 time to evaluate : 0.616 Fit side-chains REVERT: A 234 TYR cc_start: 0.7759 (m-80) cc_final: 0.6248 (t80) REVERT: A 282 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 300 ASN cc_start: 0.8555 (m-40) cc_final: 0.8312 (m-40) REVERT: A 353 MET cc_start: 0.8047 (ttm) cc_final: 0.7711 (mtp) REVERT: A 418 MET cc_start: 0.8439 (mmm) cc_final: 0.8159 (mtm) REVERT: A 419 SER cc_start: 0.9288 (t) cc_final: 0.9031 (p) REVERT: A 436 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7467 (tt0) REVERT: A 517 HIS cc_start: 0.7731 (m-70) cc_final: 0.7474 (m90) REVERT: A 569 PHE cc_start: 0.8909 (t80) cc_final: 0.8530 (t80) REVERT: B 189 ASP cc_start: 0.8307 (t0) cc_final: 0.8008 (t0) REVERT: B 234 TYR cc_start: 0.7851 (m-80) cc_final: 0.6160 (t80) REVERT: B 281 TRP cc_start: 0.8104 (m100) cc_final: 0.7768 (m100) REVERT: B 287 MET cc_start: 0.7589 (tpt) cc_final: 0.7355 (tpt) REVERT: B 300 ASN cc_start: 0.8423 (m-40) cc_final: 0.8124 (m-40) REVERT: B 353 MET cc_start: 0.7994 (ttm) cc_final: 0.7608 (mtp) REVERT: B 380 ILE cc_start: 0.9545 (mm) cc_final: 0.9206 (tt) REVERT: B 418 MET cc_start: 0.8577 (mmt) cc_final: 0.8355 (mmt) REVERT: B 419 SER cc_start: 0.9082 (t) cc_final: 0.8839 (p) REVERT: B 436 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7350 (tt0) REVERT: C 234 TYR cc_start: 0.7880 (m-80) cc_final: 0.6218 (t80) REVERT: C 236 PHE cc_start: 0.8437 (t80) cc_final: 0.8182 (t80) REVERT: C 281 TRP cc_start: 0.7997 (m100) cc_final: 0.7777 (m100) REVERT: C 287 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7431 (tpt) REVERT: C 353 MET cc_start: 0.8090 (ttm) cc_final: 0.7773 (mtp) REVERT: C 380 ILE cc_start: 0.9525 (mm) cc_final: 0.9226 (tt) REVERT: C 517 HIS cc_start: 0.7668 (m-70) cc_final: 0.7365 (m90) REVERT: D 189 ASP cc_start: 0.8555 (t0) cc_final: 0.8332 (t0) REVERT: D 234 TYR cc_start: 0.7868 (m-80) cc_final: 0.6179 (t80) REVERT: D 281 TRP cc_start: 0.7475 (m100) cc_final: 0.7169 (m100) REVERT: D 380 ILE cc_start: 0.9523 (mm) cc_final: 0.9206 (tt) REVERT: D 418 MET cc_start: 0.8581 (mmt) cc_final: 0.8305 (mmt) REVERT: D 512 MET cc_start: 0.8197 (ptp) cc_final: 0.7893 (ptp) REVERT: D 569 PHE cc_start: 0.8750 (t80) cc_final: 0.8197 (t80) outliers start: 22 outliers final: 20 residues processed: 354 average time/residue: 0.0905 time to fit residues: 51.5279 Evaluate side-chains 354 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 333 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 225 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 459 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 125 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 157 optimal weight: 0.0870 chunk 155 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 39 optimal weight: 0.0000 overall best weight: 1.3766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.093039 restraints weight = 30707.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095844 restraints weight = 15220.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097610 restraints weight = 9873.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098617 restraints weight = 7669.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098951 restraints weight = 6708.038| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16016 Z= 0.147 Angle : 0.576 11.922 21800 Z= 0.285 Chirality : 0.038 0.167 2484 Planarity : 0.003 0.034 2748 Dihedral : 11.655 176.941 2304 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.78 % Allowed : 18.39 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.19), residues: 1992 helix: 2.64 (0.14), residues: 1432 sheet: 0.58 (0.54), residues: 96 loop : -1.03 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.023 0.001 TYR C 217 PHE 0.024 0.001 PHE C 569 TRP 0.054 0.002 TRP A 281 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00333 (16016) covalent geometry : angle 0.57556 (21800) hydrogen bonds : bond 0.03636 ( 1160) hydrogen bonds : angle 3.92676 ( 3468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.11 seconds wall clock time: 46 minutes 30.70 seconds (2790.70 seconds total)