Starting phenix.real_space_refine on Sat Jul 4 20:14:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d4q_30576/07_2026/7d4q_30576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d4q_30576/07_2026/7d4q_30576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d4q_30576/07_2026/7d4q_30576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d4q_30576/07_2026/7d4q_30576.map" model { file = "/net/cci-nas-00/data/ceres_data/7d4q_30576/07_2026/7d4q_30576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d4q_30576/07_2026/7d4q_30576.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7d4q_30576/07_2026/7d4q_30576.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d4q_30576/07_2026/7d4q_30576.cif" } resolution = 2.74 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= 0.162 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 Cl 8 4.86 5 C 14672 2.51 5 N 3596 2.21 5 O 3980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22388 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5443 Classifications: {'peptide': 668} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 643} Chain breaks: 5 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 154 Unusual residues: {' CA': 1, ' ZN': 1, 'GWR': 1, 'POV': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1155 SG CYS A 176 48.460 106.807 73.631 1.00159.66 S ATOM 1169 SG CYS A 178 49.650 109.652 75.896 1.00177.58 S ATOM 1191 SG CYS A 181 51.607 106.379 75.791 1.00186.60 S Restraints were copied for chains: B, C, D Time building chain proxies: 6.21, per 1000 atoms: 0.28 Number of scatterers: 22388 At special positions: 0 Unit cell: (133.823, 133.823, 135.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 Cl 8 17.00 S 116 16.00 P 8 15.00 O 3980 8.00 N 3596 7.00 C 14672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " Number of angles added : 12 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 77.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.514A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.833A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.992A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.665A pdb=" N ASP A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.693A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.965A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.760A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.566A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.644A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 734 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.514A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.833A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.992A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.665A pdb=" N ASP B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.693A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.964A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.760A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.566A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 634 through 650 removed outlier: 3.644A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 734 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.514A pdb=" N GLU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.833A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.992A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 433 removed outlier: 3.665A pdb=" N ASP C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.693A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 3.964A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 580 removed outlier: 3.760A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.566A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 632 Processing helix chain 'C' and resid 634 through 650 removed outlier: 3.644A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 734 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.514A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.833A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.992A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.665A pdb=" N ASP D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.693A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.964A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 580 removed outlier: 3.760A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.565A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 615 Processing helix chain 'D' and resid 615 through 632 Processing helix chain 'D' and resid 634 through 650 removed outlier: 3.644A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 734 Processing helix chain 'D' and resid 740 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.618A pdb=" N VAL B 166 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.617A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.618A pdb=" N VAL C 166 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.618A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3520 1.31 - 1.44: 6148 1.44 - 1.56: 13024 1.56 - 1.69: 16 1.69 - 1.82: 196 Bond restraints: 22904 Sorted by residual: bond pdb=" C31 GWR A 806 " pdb=" C32 GWR A 806 " ideal model delta sigma weight residual 1.387 1.534 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C31 GWR B 806 " pdb=" C32 GWR B 806 " ideal model delta sigma weight residual 1.387 1.534 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C31 GWR C 806 " pdb=" C32 GWR C 806 " ideal model delta sigma weight residual 1.387 1.534 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C31 GWR D 806 " pdb=" C32 GWR D 806 " ideal model delta sigma weight residual 1.387 1.534 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C29 GWR B 806 " pdb=" C31 GWR B 806 " ideal model delta sigma weight residual 1.388 1.534 -0.146 2.00e-02 2.50e+03 5.35e+01 ... (remaining 22899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 30339 2.24 - 4.48: 501 4.48 - 6.72: 88 6.72 - 8.97: 56 8.97 - 11.21: 24 Bond angle restraints: 31008 Sorted by residual: angle pdb=" C ILE A 18 " pdb=" CA ILE A 18 " pdb=" CB ILE A 18 " ideal model delta sigma weight residual 110.52 106.28 4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" C ILE B 18 " pdb=" CA ILE B 18 " pdb=" CB ILE B 18 " ideal model delta sigma weight residual 110.52 106.28 4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" C ILE C 18 " pdb=" CA ILE C 18 " pdb=" CB ILE C 18 " ideal model delta sigma weight residual 110.52 106.28 4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" C ILE D 18 " pdb=" CA ILE D 18 " pdb=" CB ILE D 18 " ideal model delta sigma weight residual 110.52 106.28 4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" CAM Y01 D 803 " pdb=" CAY Y01 D 803 " pdb=" OAW Y01 D 803 " ideal model delta sigma weight residual 111.19 122.40 -11.21 3.00e+00 1.11e-01 1.40e+01 ... (remaining 31003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 12836 17.89 - 35.78: 584 35.78 - 53.68: 124 53.68 - 71.57: 48 71.57 - 89.46: 24 Dihedral angle restraints: 13616 sinusoidal: 5704 harmonic: 7912 Sorted by residual: dihedral pdb=" CB GLU A 56 " pdb=" CG GLU A 56 " pdb=" CD GLU A 56 " pdb=" OE1 GLU A 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.46 -89.46 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 56 " pdb=" CG GLU C 56 " pdb=" CD GLU C 56 " pdb=" OE1 GLU C 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 56 " pdb=" CG GLU D 56 " pdb=" CD GLU D 56 " pdb=" OE1 GLU D 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 13613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3095 0.062 - 0.123: 324 0.123 - 0.185: 29 0.185 - 0.247: 8 0.247 - 0.308: 8 Chirality restraints: 3464 Sorted by residual: chirality pdb=" CA ILE C 18 " pdb=" N ILE C 18 " pdb=" C ILE C 18 " pdb=" CB ILE C 18 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ILE D 18 " pdb=" N ILE D 18 " pdb=" C ILE D 18 " pdb=" CB ILE D 18 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 3461 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 611 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE A 611 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE A 611 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 612 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 611 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C ILE B 611 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE B 611 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 612 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 611 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C ILE D 611 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE D 611 " 0.015 2.00e-02 2.50e+03 pdb=" N SER D 612 " 0.013 2.00e-02 2.50e+03 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4689 2.78 - 3.31: 22015 3.31 - 3.84: 37866 3.84 - 4.37: 44746 4.37 - 4.90: 76469 Nonbonded interactions: 185785 Sorted by model distance: nonbonded pdb=" OG1 THR D 140 " pdb=" OD1 ASP D 142 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 140 " pdb=" OD1 ASP A 142 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR C 140 " pdb=" OD1 ASP C 142 " model vdw 2.254 3.040 nonbonded pdb=" NE2 GLN C 573 " pdb=" O06 GWR C 806 " model vdw 2.288 3.120 ... (remaining 185780 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.220 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 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 : 0.009 0.147 22924 Z= 0.459 Angle : 0.781 11.207 31028 Z= 0.365 Chirality : 0.042 0.308 3464 Planarity : 0.003 0.032 3804 Dihedral : 12.126 89.462 8452 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.67 % Allowed : 4.19 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.16), residues: 2624 helix: 2.32 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.28 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 24 TYR 0.015 0.001 TYR C 118 PHE 0.015 0.001 PHE A 341 TRP 0.012 0.001 TRP A 315 HIS 0.002 0.001 HIS C 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00889 / 0.46 (22904) covalent geometry : angle 0.78094 / 0.37 (31008) SS BOND : bond 0.00363 / 0.18 ( 4) SS BOND : angle 0.46993 / 0.29 ( 8) hydrogen bonds : bond 0.11758 / 8.17 ( 1464) hydrogen bonds : angle 4.65360 / 3.42 ( 4284) metal coordination : bond 0.00997 / 0.89 ( 16) metal coordination : angle 1.00452 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 444 time to evaluate : 0.837 Fit side-chains REVERT: A 38 ASN cc_start: 0.6211 (t0) cc_final: 0.5982 (t0) REVERT: A 41 GLU cc_start: 0.6093 (mt-10) cc_final: 0.5870 (mt-10) REVERT: A 170 ARG cc_start: 0.6309 (mtp180) cc_final: 0.5647 (ptp-170) REVERT: A 186 GLU cc_start: 0.6093 (mt-10) cc_final: 0.5702 (mp0) REVERT: A 222 ARG cc_start: 0.6577 (ptp-170) cc_final: 0.5779 (mtm-85) REVERT: A 253 LYS cc_start: 0.5817 (tttt) cc_final: 0.5474 (ttpp) REVERT: A 257 ASP cc_start: 0.6826 (m-30) cc_final: 0.6275 (m-30) REVERT: A 272 ARG cc_start: 0.5758 (mtt180) cc_final: 0.4923 (mtt-85) REVERT: A 422 MET cc_start: 0.5880 (tpt) cc_final: 0.5508 (tpt) REVERT: A 442 MET cc_start: 0.4908 (mtp) cc_final: 0.4647 (mtp) REVERT: A 516 ASP cc_start: 0.5929 (m-30) cc_final: 0.5702 (t70) REVERT: A 551 ASN cc_start: 0.7500 (t0) cc_final: 0.7258 (t0) REVERT: A 617 LEU cc_start: 0.6508 (tp) cc_final: 0.6209 (mm) REVERT: A 636 ASP cc_start: 0.6520 (m-30) cc_final: 0.6304 (t70) REVERT: A 728 MET cc_start: 0.6136 (mmt) cc_final: 0.5772 (mmt) REVERT: A 745 GLU cc_start: 0.5297 (mt-10) cc_final: 0.5082 (mt-10) REVERT: A 760 LEU cc_start: 0.6479 (mm) cc_final: 0.6278 (mm) REVERT: B 38 ASN cc_start: 0.6209 (t0) cc_final: 0.5980 (t0) REVERT: B 41 GLU cc_start: 0.6092 (mt-10) cc_final: 0.5870 (mt-10) REVERT: B 170 ARG cc_start: 0.6308 (mtp180) cc_final: 0.5645 (ptp-170) REVERT: B 186 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5732 (mp0) REVERT: B 222 ARG cc_start: 0.6577 (ptp-170) cc_final: 0.5781 (mtm-85) REVERT: B 253 LYS cc_start: 0.5818 (tttt) cc_final: 0.5473 (ttpp) REVERT: B 257 ASP cc_start: 0.6824 (m-30) cc_final: 0.6272 (m-30) REVERT: B 272 ARG cc_start: 0.5725 (mtt180) cc_final: 0.4888 (mtt-85) REVERT: B 422 MET cc_start: 0.5879 (tpt) cc_final: 0.5506 (tpt) REVERT: B 442 MET cc_start: 0.4908 (mtp) cc_final: 0.4647 (mtp) REVERT: B 516 ASP cc_start: 0.5928 (m-30) cc_final: 0.5703 (t70) REVERT: B 551 ASN cc_start: 0.7500 (t0) cc_final: 0.7256 (t0) REVERT: B 617 LEU cc_start: 0.6509 (tp) cc_final: 0.6208 (mm) REVERT: B 636 ASP cc_start: 0.6538 (m-30) cc_final: 0.6301 (t70) REVERT: B 728 MET cc_start: 0.6149 (mmt) cc_final: 0.5787 (mmt) REVERT: B 745 GLU cc_start: 0.5296 (mt-10) cc_final: 0.5081 (mt-10) REVERT: B 760 LEU cc_start: 0.6478 (mm) cc_final: 0.6278 (mm) REVERT: C 38 ASN cc_start: 0.6210 (t0) cc_final: 0.5981 (t0) REVERT: C 41 GLU cc_start: 0.6076 (mt-10) cc_final: 0.5858 (mt-10) REVERT: C 170 ARG cc_start: 0.6311 (mtp180) cc_final: 0.5647 (ptp-170) REVERT: C 186 GLU cc_start: 0.6038 (mt-10) cc_final: 0.5644 (mp0) REVERT: C 222 ARG cc_start: 0.6578 (ptp-170) cc_final: 0.5781 (mtm-85) REVERT: C 253 LYS cc_start: 0.5815 (tttt) cc_final: 0.5467 (ttpp) REVERT: C 257 ASP cc_start: 0.6825 (m-30) cc_final: 0.6270 (m-30) REVERT: C 272 ARG cc_start: 0.5725 (mtt180) cc_final: 0.4888 (mtt-85) REVERT: C 422 MET cc_start: 0.5882 (tpt) cc_final: 0.5509 (tpt) REVERT: C 442 MET cc_start: 0.4910 (mtp) cc_final: 0.4649 (mtp) REVERT: C 516 ASP cc_start: 0.5928 (m-30) cc_final: 0.5704 (t70) REVERT: C 551 ASN cc_start: 0.7499 (t0) cc_final: 0.7256 (t0) REVERT: C 617 LEU cc_start: 0.6505 (tp) cc_final: 0.6203 (mm) REVERT: C 636 ASP cc_start: 0.6540 (m-30) cc_final: 0.6301 (t70) REVERT: C 728 MET cc_start: 0.6136 (mmt) cc_final: 0.5772 (mmt) REVERT: C 745 GLU cc_start: 0.5297 (mt-10) cc_final: 0.5082 (mt-10) REVERT: C 760 LEU cc_start: 0.6477 (mm) cc_final: 0.6276 (mm) REVERT: D 38 ASN cc_start: 0.6210 (t0) cc_final: 0.5980 (t0) REVERT: D 41 GLU cc_start: 0.6094 (mt-10) cc_final: 0.5872 (mt-10) REVERT: D 170 ARG cc_start: 0.6311 (mtp180) cc_final: 0.5647 (ptp-170) REVERT: D 186 GLU cc_start: 0.6038 (mt-10) cc_final: 0.5642 (mp0) REVERT: D 222 ARG cc_start: 0.6579 (ptp-170) cc_final: 0.5781 (mtm-85) REVERT: D 253 LYS cc_start: 0.5817 (tttt) cc_final: 0.5474 (ttpp) REVERT: D 257 ASP cc_start: 0.6830 (m-30) cc_final: 0.6280 (m-30) REVERT: D 272 ARG cc_start: 0.5762 (mtt180) cc_final: 0.4925 (mtt-85) REVERT: D 422 MET cc_start: 0.5881 (tpt) cc_final: 0.5509 (tpt) REVERT: D 442 MET cc_start: 0.4907 (mtp) cc_final: 0.4647 (mtp) REVERT: D 516 ASP cc_start: 0.5933 (m-30) cc_final: 0.5703 (t70) REVERT: D 551 ASN cc_start: 0.7508 (t0) cc_final: 0.7258 (t0) REVERT: D 617 LEU cc_start: 0.6503 (tp) cc_final: 0.6202 (mm) REVERT: D 636 ASP cc_start: 0.6537 (m-30) cc_final: 0.6296 (t70) REVERT: D 728 MET cc_start: 0.6135 (mmt) cc_final: 0.5772 (mmt) REVERT: D 745 GLU cc_start: 0.5299 (mt-10) cc_final: 0.5085 (mt-10) REVERT: D 760 LEU cc_start: 0.6476 (mm) cc_final: 0.6276 (mm) outliers start: 16 outliers final: 0 residues processed: 460 average time/residue: 0.6881 time to fit residues: 358.2984 Evaluate side-chains 320 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 629 GLN B 163 GLN B 629 GLN C 163 GLN C 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130266 restraints weight = 20351.618| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.57 r_work: 0.3240 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22924 Z= 0.166 Angle : 0.511 6.802 31028 Z= 0.261 Chirality : 0.038 0.190 3464 Planarity : 0.004 0.049 3804 Dihedral : 7.661 54.289 3192 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.01 % Allowed : 9.88 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.16), residues: 2624 helix: 2.33 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.29 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 71 TYR 0.010 0.001 TYR C 524 PHE 0.017 0.002 PHE C 341 TRP 0.015 0.001 TRP D 315 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (22904) covalent geometry : angle 0.50993 / 0.26 (31008) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 0.74331 / 0.45 ( 8) hydrogen bonds : bond 0.04714 / 3.12 ( 1464) hydrogen bonds : angle 3.93955 / 2.93 ( 4284) metal coordination : bond 0.00619 / 0.52 ( 16) metal coordination : angle 1.31356 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 337 time to evaluate : 0.843 Fit side-chains REVERT: A 38 ASN cc_start: 0.8161 (t0) cc_final: 0.7926 (t160) REVERT: A 41 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 170 ARG cc_start: 0.7334 (mtp180) cc_final: 0.6894 (ptt180) REVERT: A 222 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.7880 (mtm-85) REVERT: A 257 ASP cc_start: 0.8186 (m-30) cc_final: 0.7814 (m-30) REVERT: A 272 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7295 (mtt-85) REVERT: A 393 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6799 (pt) REVERT: A 422 MET cc_start: 0.6652 (tpt) cc_final: 0.6245 (tpt) REVERT: B 38 ASN cc_start: 0.8156 (t0) cc_final: 0.7923 (t160) REVERT: B 41 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7329 (mt-10) REVERT: B 170 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6920 (ptt180) REVERT: B 222 ARG cc_start: 0.8329 (ptp-170) cc_final: 0.7871 (mtm-85) REVERT: B 257 ASP cc_start: 0.8203 (m-30) cc_final: 0.7831 (m-30) REVERT: B 272 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7280 (mtt-85) REVERT: B 393 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6808 (pt) REVERT: B 422 MET cc_start: 0.6658 (tpt) cc_final: 0.6256 (tpt) REVERT: C 38 ASN cc_start: 0.8163 (t0) cc_final: 0.7932 (t160) REVERT: C 41 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 170 ARG cc_start: 0.7335 (mtp180) cc_final: 0.6914 (ptt180) REVERT: C 222 ARG cc_start: 0.8334 (ptp-170) cc_final: 0.7871 (mtm-85) REVERT: C 257 ASP cc_start: 0.8212 (m-30) cc_final: 0.7845 (m-30) REVERT: C 272 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7290 (mtt-85) REVERT: C 393 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6804 (pt) REVERT: C 422 MET cc_start: 0.6650 (tpt) cc_final: 0.6245 (tpt) REVERT: D 38 ASN cc_start: 0.8144 (t0) cc_final: 0.7899 (t0) REVERT: D 41 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7327 (mt-10) REVERT: D 170 ARG cc_start: 0.7331 (mtp180) cc_final: 0.6916 (ptt180) REVERT: D 222 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.7879 (mtm-85) REVERT: D 257 ASP cc_start: 0.8208 (m-30) cc_final: 0.7839 (m-30) REVERT: D 272 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7290 (mtt-85) REVERT: D 393 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6812 (pt) REVERT: D 422 MET cc_start: 0.6656 (tpt) cc_final: 0.6246 (tpt) outliers start: 24 outliers final: 8 residues processed: 345 average time/residue: 0.6766 time to fit residues: 264.6972 Evaluate side-chains 323 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 311 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 161 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 241 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 629 GLN A 748 GLN B 163 GLN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN B 629 GLN B 748 GLN C 163 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN C 629 GLN C 711 GLN C 748 GLN D 163 GLN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN D 629 GLN D 711 GLN D 748 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.170444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131233 restraints weight = 20343.442| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.50 r_work: 0.3260 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22924 Z= 0.116 Angle : 0.452 6.161 31028 Z= 0.234 Chirality : 0.035 0.153 3464 Planarity : 0.004 0.039 3804 Dihedral : 7.449 55.654 3192 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.01 % Allowed : 11.56 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.16), residues: 2624 helix: 2.47 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.15 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 71 TYR 0.011 0.001 TYR C 524 PHE 0.017 0.001 PHE B 341 TRP 0.014 0.001 TRP D 315 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (22904) covalent geometry : angle 0.45190 / 0.23 (31008) SS BOND : bond 0.00133 / 0.07 ( 4) SS BOND : angle 0.94100 / 0.54 ( 8) hydrogen bonds : bond 0.04297 / 2.82 ( 1464) hydrogen bonds : angle 3.81183 / 2.84 ( 4284) metal coordination : bond 0.00266 / 0.21 ( 16) metal coordination : angle 0.87163 / 0.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 315 time to evaluate : 0.857 Fit side-chains REVERT: A 38 ASN cc_start: 0.8062 (t0) cc_final: 0.7839 (t160) REVERT: A 41 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7265 (mm-30) REVERT: A 170 ARG cc_start: 0.7319 (mtp180) cc_final: 0.6901 (ptt180) REVERT: A 222 ARG cc_start: 0.8308 (ptp-170) cc_final: 0.7831 (mtm-85) REVERT: A 272 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7172 (mtt-85) REVERT: A 335 MET cc_start: 0.7221 (mmm) cc_final: 0.6517 (mpp) REVERT: A 393 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6675 (pp) REVERT: A 422 MET cc_start: 0.6666 (tpt) cc_final: 0.6263 (tpt) REVERT: A 467 GLU cc_start: 0.8275 (mp0) cc_final: 0.7884 (pm20) REVERT: A 512 ARG cc_start: 0.7997 (mtm110) cc_final: 0.7770 (mtm110) REVERT: B 38 ASN cc_start: 0.8065 (t0) cc_final: 0.7842 (t160) REVERT: B 41 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7268 (mm-30) REVERT: B 170 ARG cc_start: 0.7316 (mtp180) cc_final: 0.6898 (ptt180) REVERT: B 222 ARG cc_start: 0.8306 (ptp-170) cc_final: 0.7833 (mtm-85) REVERT: B 272 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7167 (mtt-85) REVERT: B 335 MET cc_start: 0.7230 (mmm) cc_final: 0.6526 (mpp) REVERT: B 393 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6682 (pp) REVERT: B 422 MET cc_start: 0.6664 (tpt) cc_final: 0.6259 (tpt) REVERT: B 467 GLU cc_start: 0.8268 (mp0) cc_final: 0.7876 (pm20) REVERT: B 512 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7789 (mtm110) REVERT: B 551 ASN cc_start: 0.8002 (t0) cc_final: 0.7801 (t0) REVERT: C 38 ASN cc_start: 0.8068 (t0) cc_final: 0.7850 (t160) REVERT: C 41 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7274 (mm-30) REVERT: C 170 ARG cc_start: 0.7317 (mtp180) cc_final: 0.6893 (ptt180) REVERT: C 222 ARG cc_start: 0.8310 (ptp-170) cc_final: 0.7835 (mtm-85) REVERT: C 272 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7168 (mtt-85) REVERT: C 335 MET cc_start: 0.7225 (mmm) cc_final: 0.6509 (mpp) REVERT: C 393 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6672 (pp) REVERT: C 422 MET cc_start: 0.6663 (tpt) cc_final: 0.6261 (tpt) REVERT: C 467 GLU cc_start: 0.8266 (mp0) cc_final: 0.7879 (pm20) REVERT: C 512 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7807 (mtm110) REVERT: D 38 ASN cc_start: 0.8057 (t0) cc_final: 0.7835 (t160) REVERT: D 41 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7267 (mm-30) REVERT: D 170 ARG cc_start: 0.7329 (mtp180) cc_final: 0.6898 (ptt180) REVERT: D 222 ARG cc_start: 0.8312 (ptp-170) cc_final: 0.7834 (mtm-85) REVERT: D 272 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7166 (mtt-85) REVERT: D 335 MET cc_start: 0.7242 (mmm) cc_final: 0.6540 (mpp) REVERT: D 393 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6680 (pp) REVERT: D 422 MET cc_start: 0.6667 (tpt) cc_final: 0.6263 (tpt) REVERT: D 467 GLU cc_start: 0.8275 (mp0) cc_final: 0.7888 (pm20) REVERT: D 512 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7763 (mtm110) REVERT: D 551 ASN cc_start: 0.7996 (t0) cc_final: 0.7795 (t0) outliers start: 24 outliers final: 4 residues processed: 327 average time/residue: 0.6185 time to fit residues: 231.5783 Evaluate side-chains 300 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 292 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 260 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 258 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 236 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 163 GLN A 537 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 537 GLN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 537 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 163 GLN D 537 GLN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130967 restraints weight = 20426.342| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.54 r_work: 0.3259 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22924 Z= 0.118 Angle : 0.447 6.742 31028 Z= 0.229 Chirality : 0.035 0.152 3464 Planarity : 0.003 0.037 3804 Dihedral : 7.334 54.354 3192 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.68 % Allowed : 11.73 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.16), residues: 2624 helix: 2.50 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 71 TYR 0.011 0.001 TYR A 524 PHE 0.017 0.001 PHE B 341 TRP 0.013 0.001 TRP D 315 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (22904) covalent geometry : angle 0.44659 / 0.23 (31008) SS BOND : bond 0.00099 / 0.05 ( 4) SS BOND : angle 0.56350 / 0.33 ( 8) hydrogen bonds : bond 0.04246 / 2.79 ( 1464) hydrogen bonds : angle 3.75087 / 2.80 ( 4284) metal coordination : bond 0.00237 / 0.19 ( 16) metal coordination : angle 0.64605 / 0.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 305 time to evaluate : 0.857 Fit side-chains REVERT: A 38 ASN cc_start: 0.8074 (t0) cc_final: 0.7859 (t160) REVERT: A 41 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7249 (mm-30) REVERT: A 170 ARG cc_start: 0.7356 (mtp180) cc_final: 0.6891 (ptt180) REVERT: A 222 ARG cc_start: 0.8316 (ptp-170) cc_final: 0.7825 (mtm-85) REVERT: A 240 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: A 272 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7205 (mtt-85) REVERT: A 393 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6631 (pp) REVERT: A 422 MET cc_start: 0.6626 (tpt) cc_final: 0.6224 (tpt) REVERT: A 467 GLU cc_start: 0.8286 (mp0) cc_final: 0.7920 (pm20) REVERT: A 551 ASN cc_start: 0.7902 (t0) cc_final: 0.7666 (t0) REVERT: B 38 ASN cc_start: 0.8074 (t0) cc_final: 0.7859 (t160) REVERT: B 41 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7249 (mm-30) REVERT: B 170 ARG cc_start: 0.7347 (mtp180) cc_final: 0.6889 (ptt180) REVERT: B 222 ARG cc_start: 0.8324 (ptp-170) cc_final: 0.7834 (mtm-85) REVERT: B 240 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: B 272 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7192 (mtt-85) REVERT: B 393 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6619 (pp) REVERT: B 422 MET cc_start: 0.6630 (tpt) cc_final: 0.6222 (tpt) REVERT: B 467 GLU cc_start: 0.8295 (mp0) cc_final: 0.7928 (pm20) REVERT: B 551 ASN cc_start: 0.8038 (t0) cc_final: 0.7834 (t0) REVERT: C 38 ASN cc_start: 0.8077 (t0) cc_final: 0.7864 (t160) REVERT: C 41 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7254 (mm-30) REVERT: C 170 ARG cc_start: 0.7344 (mtp180) cc_final: 0.6880 (ptt180) REVERT: C 222 ARG cc_start: 0.8318 (ptp-170) cc_final: 0.7827 (mtm-85) REVERT: C 240 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: C 272 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7225 (mtt-85) REVERT: C 393 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6629 (pp) REVERT: C 422 MET cc_start: 0.6628 (tpt) cc_final: 0.6330 (tpt) REVERT: C 467 GLU cc_start: 0.8279 (mp0) cc_final: 0.7917 (pm20) REVERT: C 551 ASN cc_start: 0.7903 (t0) cc_final: 0.7671 (t0) REVERT: D 38 ASN cc_start: 0.8064 (t0) cc_final: 0.7851 (t160) REVERT: D 41 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7248 (mm-30) REVERT: D 170 ARG cc_start: 0.7356 (mtp180) cc_final: 0.6884 (ptt180) REVERT: D 222 ARG cc_start: 0.8304 (ptp-170) cc_final: 0.7814 (mtm-85) REVERT: D 240 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: D 272 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7225 (mtt-85) REVERT: D 393 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6638 (pp) REVERT: D 422 MET cc_start: 0.6627 (tpt) cc_final: 0.6222 (tpt) REVERT: D 467 GLU cc_start: 0.8287 (mp0) cc_final: 0.7924 (pm20) outliers start: 40 outliers final: 12 residues processed: 333 average time/residue: 0.6597 time to fit residues: 249.9292 Evaluate side-chains 312 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 739 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 16 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 175 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 163 GLN A 711 GLN B 92 HIS B 163 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 92 HIS C 163 GLN C 711 GLN D 92 HIS D 163 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128555 restraints weight = 20169.430| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.57 r_work: 0.3222 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22924 Z= 0.204 Angle : 0.523 8.626 31028 Z= 0.267 Chirality : 0.038 0.152 3464 Planarity : 0.004 0.036 3804 Dihedral : 7.642 56.526 3192 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.34 % Allowed : 12.48 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.16), residues: 2624 helix: 2.20 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 71 TYR 0.014 0.001 TYR B 524 PHE 0.018 0.002 PHE B 341 TRP 0.015 0.001 TRP C 315 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 (22904) covalent geometry : angle 0.52342 / 0.27 (31008) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 0.73124 / 0.49 ( 8) hydrogen bonds : bond 0.05012 / 3.30 ( 1464) hydrogen bonds : angle 3.85275 / 2.87 ( 4284) metal coordination : bond 0.00402 / 0.33 ( 16) metal coordination : angle 0.36397 / 0.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 299 time to evaluate : 0.910 Fit side-chains REVERT: A 170 ARG cc_start: 0.7465 (mtp180) cc_final: 0.7053 (ptt180) REVERT: A 222 ARG cc_start: 0.8429 (ptp-170) cc_final: 0.7857 (mtm-85) REVERT: A 240 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: A 272 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7301 (mtt-85) REVERT: A 393 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6585 (pp) REVERT: A 467 GLU cc_start: 0.8350 (mp0) cc_final: 0.7997 (pm20) REVERT: A 528 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8418 (tp) REVERT: A 551 ASN cc_start: 0.8063 (t0) cc_final: 0.7829 (t0) REVERT: B 170 ARG cc_start: 0.7448 (mtp180) cc_final: 0.7044 (ptt180) REVERT: B 222 ARG cc_start: 0.8419 (ptp-170) cc_final: 0.7855 (mtm-85) REVERT: B 240 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: B 272 ARG cc_start: 0.7958 (mtt180) cc_final: 0.7297 (mtt-85) REVERT: B 393 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6618 (pp) REVERT: B 467 GLU cc_start: 0.8348 (mp0) cc_final: 0.7989 (pm20) REVERT: B 528 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8417 (tp) REVERT: B 551 ASN cc_start: 0.8030 (t0) cc_final: 0.7780 (t0) REVERT: C 170 ARG cc_start: 0.7456 (mtp180) cc_final: 0.7035 (ptt180) REVERT: C 222 ARG cc_start: 0.8417 (ptp-170) cc_final: 0.7849 (mtm-85) REVERT: C 240 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: C 272 ARG cc_start: 0.7964 (mtt180) cc_final: 0.7300 (mtt-85) REVERT: C 393 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6588 (pp) REVERT: C 467 GLU cc_start: 0.8347 (mp0) cc_final: 0.8012 (pm20) REVERT: C 551 ASN cc_start: 0.8057 (t0) cc_final: 0.7823 (t0) REVERT: D 170 ARG cc_start: 0.7464 (mtp180) cc_final: 0.7039 (ptt180) REVERT: D 222 ARG cc_start: 0.8424 (ptp-170) cc_final: 0.7850 (mtm-85) REVERT: D 240 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: D 272 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7296 (mtt-85) REVERT: D 393 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6589 (pp) REVERT: D 467 GLU cc_start: 0.8358 (mp0) cc_final: 0.8019 (pm20) REVERT: D 551 ASN cc_start: 0.8025 (t0) cc_final: 0.7814 (t0) outliers start: 32 outliers final: 2 residues processed: 319 average time/residue: 0.6446 time to fit residues: 234.9320 Evaluate side-chains 296 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 57 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 92 HIS A 711 GLN B 38 ASN B 92 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 38 ASN C 92 HIS C 711 GLN D 38 ASN D 92 HIS ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128430 restraints weight = 20367.367| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.55 r_work: 0.3214 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22924 Z= 0.198 Angle : 0.525 7.654 31028 Z= 0.268 Chirality : 0.038 0.154 3464 Planarity : 0.004 0.034 3804 Dihedral : 7.771 57.573 3192 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.51 % Allowed : 13.61 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.16), residues: 2624 helix: 2.04 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.02 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 71 TYR 0.014 0.001 TYR B 524 PHE 0.018 0.002 PHE A 520 TRP 0.016 0.001 TRP D 315 HIS 0.004 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (22904) covalent geometry : angle 0.52504 / 0.27 (31008) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.55526 / 0.35 ( 8) hydrogen bonds : bond 0.05102 / 3.36 ( 1464) hydrogen bonds : angle 3.89806 / 2.90 ( 4284) metal coordination : bond 0.00387 / 0.32 ( 16) metal coordination : angle 0.43798 / 0.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 0.898 Fit side-chains REVERT: A 170 ARG cc_start: 0.7494 (mtp180) cc_final: 0.7055 (ptt180) REVERT: A 240 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: A 272 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7308 (mtt-85) REVERT: A 393 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6493 (pp) REVERT: A 467 GLU cc_start: 0.8395 (mp0) cc_final: 0.8035 (pm20) REVERT: A 528 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8422 (tp) REVERT: A 551 ASN cc_start: 0.8102 (t0) cc_final: 0.7874 (t0) REVERT: B 170 ARG cc_start: 0.7481 (mtp180) cc_final: 0.7047 (ptt180) REVERT: B 240 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: B 272 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7332 (mtt-85) REVERT: B 393 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6533 (pp) REVERT: B 467 GLU cc_start: 0.8394 (mp0) cc_final: 0.8031 (pm20) REVERT: B 528 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8421 (tp) REVERT: B 551 ASN cc_start: 0.8038 (t0) cc_final: 0.7761 (t0) REVERT: C 170 ARG cc_start: 0.7489 (mtp180) cc_final: 0.7043 (ptt180) REVERT: C 240 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: C 272 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7340 (mtt-85) REVERT: C 393 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6485 (pp) REVERT: C 467 GLU cc_start: 0.8395 (mp0) cc_final: 0.8038 (pm20) REVERT: C 528 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8437 (tp) REVERT: C 551 ASN cc_start: 0.8105 (t0) cc_final: 0.7877 (t0) REVERT: D 170 ARG cc_start: 0.7481 (mtp180) cc_final: 0.7033 (ptt180) REVERT: D 240 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: D 272 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7309 (mtt-85) REVERT: D 393 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6490 (pp) REVERT: D 467 GLU cc_start: 0.8396 (mp0) cc_final: 0.8038 (pm20) REVERT: D 528 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8438 (tp) REVERT: D 551 ASN cc_start: 0.8078 (t0) cc_final: 0.7841 (t0) outliers start: 36 outliers final: 6 residues processed: 332 average time/residue: 0.6677 time to fit residues: 251.5663 Evaluate side-chains 310 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 617 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 261 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS B 92 HIS C 92 HIS D 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126704 restraints weight = 20395.590| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.65 r_work: 0.3197 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22924 Z= 0.229 Angle : 0.558 9.492 31028 Z= 0.283 Chirality : 0.040 0.185 3464 Planarity : 0.004 0.037 3804 Dihedral : 7.948 58.057 3192 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.68 % Allowed : 14.28 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.16), residues: 2624 helix: 1.89 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : -0.03 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.015 0.002 TYR A 524 PHE 0.018 0.002 PHE D 341 TRP 0.017 0.002 TRP C 315 HIS 0.005 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (22904) covalent geometry : angle 0.55814 / 0.28 (31008) SS BOND : bond 0.00105 / 0.05 ( 4) SS BOND : angle 0.58615 / 0.36 ( 8) hydrogen bonds : bond 0.05336 / 3.51 ( 1464) hydrogen bonds : angle 3.96534 / 2.95 ( 4284) metal coordination : bond 0.00468 / 0.39 ( 16) metal coordination : angle 0.35350 / 0.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 0.922 Fit side-chains REVERT: A 41 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: A 170 ARG cc_start: 0.7484 (mtp180) cc_final: 0.7056 (ptt180) REVERT: A 240 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: A 272 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7255 (mtt-85) REVERT: A 393 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6445 (pp) REVERT: A 467 GLU cc_start: 0.8413 (mp0) cc_final: 0.8090 (pm20) REVERT: A 528 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8431 (tp) REVERT: A 551 ASN cc_start: 0.8137 (t0) cc_final: 0.7863 (t0) REVERT: B 41 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: B 170 ARG cc_start: 0.7480 (mtp180) cc_final: 0.7049 (ptt180) REVERT: B 240 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7190 (mt-10) REVERT: B 272 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7246 (mtt-85) REVERT: B 393 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6408 (pp) REVERT: B 467 GLU cc_start: 0.8405 (mp0) cc_final: 0.8080 (pm20) REVERT: B 528 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8440 (tp) REVERT: B 551 ASN cc_start: 0.8065 (t0) cc_final: 0.7781 (t0) REVERT: C 41 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: C 170 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7049 (ptt180) REVERT: C 240 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: C 272 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7240 (mtt-85) REVERT: C 393 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6444 (pp) REVERT: C 467 GLU cc_start: 0.8415 (mp0) cc_final: 0.8092 (pm20) REVERT: C 528 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8406 (tp) REVERT: C 551 ASN cc_start: 0.8136 (t0) cc_final: 0.7848 (t0) REVERT: D 41 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: D 170 ARG cc_start: 0.7477 (mtp180) cc_final: 0.7044 (ptt180) REVERT: D 240 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: D 272 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7246 (mtt-85) REVERT: D 393 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6454 (pp) REVERT: D 467 GLU cc_start: 0.8416 (mp0) cc_final: 0.8096 (pm20) REVERT: D 528 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8405 (tp) REVERT: D 551 ASN cc_start: 0.8163 (t0) cc_final: 0.7898 (t0) outliers start: 40 outliers final: 4 residues processed: 335 average time/residue: 0.6172 time to fit residues: 237.0184 Evaluate side-chains 320 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 239 optimal weight: 0.0770 chunk 249 optimal weight: 0.0670 chunk 223 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 711 GLN B 92 HIS B 711 GLN C 92 HIS C 711 GLN D 92 HIS D 711 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130788 restraints weight = 20057.522| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.47 r_work: 0.3282 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22924 Z= 0.106 Angle : 0.463 8.728 31028 Z= 0.236 Chirality : 0.036 0.186 3464 Planarity : 0.003 0.036 3804 Dihedral : 7.460 54.542 3192 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.68 % Allowed : 14.74 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.16), residues: 2624 helix: 2.25 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.010 0.001 TYR D 200 PHE 0.015 0.001 PHE A 341 TRP 0.016 0.001 TRP C 315 HIS 0.004 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (22904) covalent geometry : angle 0.46257 / 0.24 (31008) SS BOND : bond 0.00003 / 0.00 ( 4) SS BOND : angle 0.45789 / 0.33 ( 8) hydrogen bonds : bond 0.04158 / 2.72 ( 1464) hydrogen bonds : angle 3.83485 / 2.86 ( 4284) metal coordination : bond 0.00128 / 0.09 ( 16) metal coordination : angle 0.80522 / 0.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7444 (mtp180) cc_final: 0.6935 (ptt-90) REVERT: A 228 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7804 (tmtm) REVERT: A 272 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7196 (mtt-85) REVERT: A 335 MET cc_start: 0.7516 (mpp) cc_final: 0.6933 (mpp) REVERT: A 393 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6411 (pp) REVERT: A 422 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5911 (tpt) REVERT: A 467 GLU cc_start: 0.8328 (mp0) cc_final: 0.8005 (pm20) REVERT: A 551 ASN cc_start: 0.7887 (t0) cc_final: 0.7615 (t0) REVERT: B 170 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6932 (ptt-90) REVERT: B 228 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7801 (tmtm) REVERT: B 272 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7215 (mtt-85) REVERT: B 422 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.5919 (tpt) REVERT: B 467 GLU cc_start: 0.8311 (mp0) cc_final: 0.7984 (pm20) REVERT: B 528 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8343 (tp) REVERT: B 551 ASN cc_start: 0.7891 (t0) cc_final: 0.7615 (t0) REVERT: C 170 ARG cc_start: 0.7443 (mtp180) cc_final: 0.6934 (ptt-90) REVERT: C 228 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7806 (tmtm) REVERT: C 272 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7190 (mtt-85) REVERT: C 335 MET cc_start: 0.7520 (mpp) cc_final: 0.6932 (mpp) REVERT: C 393 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6399 (pp) REVERT: C 422 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.5917 (tpt) REVERT: C 467 GLU cc_start: 0.8318 (mp0) cc_final: 0.7984 (pm20) REVERT: C 551 ASN cc_start: 0.7866 (t0) cc_final: 0.7594 (t0) REVERT: D 170 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6929 (ptt-90) REVERT: D 228 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7796 (tmtm) REVERT: D 272 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7192 (mtt-85) REVERT: D 335 MET cc_start: 0.7534 (mpp) cc_final: 0.6936 (mpp) REVERT: D 393 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6381 (pp) REVERT: D 422 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5914 (tpt) REVERT: D 467 GLU cc_start: 0.8323 (mp0) cc_final: 0.7987 (pm20) REVERT: D 551 ASN cc_start: 0.7875 (t0) cc_final: 0.7619 (t0) outliers start: 40 outliers final: 0 residues processed: 340 average time/residue: 0.5936 time to fit residues: 230.0749 Evaluate side-chains 307 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 295 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 422 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 209 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 711 GLN B 92 HIS B 711 GLN C 92 HIS C 711 GLN D 92 HIS D 711 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132019 restraints weight = 20171.103| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.60 r_work: 0.3269 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22924 Z= 0.120 Angle : 0.476 9.508 31028 Z= 0.244 Chirality : 0.036 0.214 3464 Planarity : 0.004 0.039 3804 Dihedral : 7.370 54.065 3192 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.38 % Allowed : 14.99 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.16), residues: 2624 helix: 2.26 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.11 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 71 TYR 0.009 0.001 TYR B 524 PHE 0.017 0.001 PHE D 341 TRP 0.014 0.001 TRP C 315 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (22904) covalent geometry : angle 0.47561 / 0.24 (31008) SS BOND : bond 0.00051 / 0.03 ( 4) SS BOND : angle 0.44952 / 0.31 ( 8) hydrogen bonds : bond 0.04327 / 2.83 ( 1464) hydrogen bonds : angle 3.83996 / 2.86 ( 4284) metal coordination : bond 0.00156 / 0.12 ( 16) metal coordination : angle 0.57729 / 0.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 312 time to evaluate : 0.858 Fit side-chains REVERT: A 38 ASN cc_start: 0.8177 (t0) cc_final: 0.7642 (t0) REVERT: A 170 ARG cc_start: 0.7448 (mtp180) cc_final: 0.6930 (ptt-90) REVERT: A 272 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7153 (mtt-85) REVERT: A 393 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6396 (pp) REVERT: A 422 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.5887 (tpt) REVERT: A 467 GLU cc_start: 0.8336 (mp0) cc_final: 0.8013 (pm20) REVERT: A 551 ASN cc_start: 0.7934 (t0) cc_final: 0.7650 (t0) REVERT: B 38 ASN cc_start: 0.8160 (t0) cc_final: 0.7673 (t0) REVERT: B 170 ARG cc_start: 0.7449 (mtp180) cc_final: 0.6919 (ptt-90) REVERT: B 272 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7153 (mtt-85) REVERT: B 393 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6352 (pp) REVERT: B 422 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5898 (tpt) REVERT: B 467 GLU cc_start: 0.8330 (mp0) cc_final: 0.7991 (pm20) REVERT: B 528 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8363 (tp) REVERT: B 551 ASN cc_start: 0.7948 (t0) cc_final: 0.7669 (t0) REVERT: C 38 ASN cc_start: 0.8164 (t0) cc_final: 0.7674 (t0) REVERT: C 170 ARG cc_start: 0.7444 (mtp180) cc_final: 0.6928 (ptt-90) REVERT: C 272 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7152 (mtt-85) REVERT: C 393 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6396 (pp) REVERT: C 422 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5896 (tpt) REVERT: C 467 GLU cc_start: 0.8330 (mp0) cc_final: 0.8004 (pm20) REVERT: C 551 ASN cc_start: 0.7927 (t0) cc_final: 0.7646 (t0) REVERT: D 38 ASN cc_start: 0.8156 (t0) cc_final: 0.7672 (t0) REVERT: D 170 ARG cc_start: 0.7432 (mtp180) cc_final: 0.6919 (ptt-90) REVERT: D 272 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7154 (mtt-85) REVERT: D 393 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6404 (pp) REVERT: D 422 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.5894 (tpt) REVERT: D 467 GLU cc_start: 0.8334 (mp0) cc_final: 0.8010 (pm20) REVERT: D 551 ASN cc_start: 0.7933 (t0) cc_final: 0.7675 (t0) outliers start: 33 outliers final: 0 residues processed: 327 average time/residue: 0.5685 time to fit residues: 213.2495 Evaluate side-chains 313 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 304 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 422 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 220 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 189 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 626 ASN A 711 GLN B 92 HIS B 626 ASN B 711 GLN C 92 HIS C 626 ASN C 711 GLN D 92 HIS D 626 ASN D 711 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.169350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130612 restraints weight = 20324.976| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.61 r_work: 0.3241 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22924 Z= 0.135 Angle : 0.499 9.449 31028 Z= 0.257 Chirality : 0.037 0.216 3464 Planarity : 0.004 0.039 3804 Dihedral : 7.408 54.054 3192 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.63 % Allowed : 15.87 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.16), residues: 2624 helix: 2.16 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.10 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.011 0.001 TYR B 524 PHE 0.012 0.001 PHE B 341 TRP 0.013 0.001 TRP B 315 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (22904) covalent geometry : angle 0.49896 / 0.26 (31008) SS BOND : bond 0.00047 / 0.02 ( 4) SS BOND : angle 0.41787 / 0.29 ( 8) hydrogen bonds : bond 0.04472 / 2.93 ( 1464) hydrogen bonds : angle 3.86934 / 2.89 ( 4284) metal coordination : bond 0.00202 / 0.17 ( 16) metal coordination : angle 0.53183 / 0.33 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 309 time to evaluate : 0.888 Fit side-chains REVERT: A 38 ASN cc_start: 0.8161 (t0) cc_final: 0.7699 (t0) REVERT: A 170 ARG cc_start: 0.7441 (mtp180) cc_final: 0.6966 (ptt-90) REVERT: A 272 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7212 (mtt-85) REVERT: A 393 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6401 (pp) REVERT: A 422 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.5867 (tpt) REVERT: A 467 GLU cc_start: 0.8344 (mp0) cc_final: 0.7997 (pm20) REVERT: A 551 ASN cc_start: 0.7969 (t0) cc_final: 0.7697 (t0) REVERT: B 170 ARG cc_start: 0.7444 (mtp180) cc_final: 0.6958 (ptt-90) REVERT: B 272 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7198 (mtt-85) REVERT: B 335 MET cc_start: 0.7305 (mmm) cc_final: 0.6785 (mpp) REVERT: B 393 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6355 (pp) REVERT: B 422 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.5877 (tpt) REVERT: B 467 GLU cc_start: 0.8348 (mp0) cc_final: 0.8007 (pm20) REVERT: B 528 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8383 (tp) REVERT: B 551 ASN cc_start: 0.7984 (t0) cc_final: 0.7709 (t0) REVERT: C 38 ASN cc_start: 0.8200 (t0) cc_final: 0.7679 (t0) REVERT: C 170 ARG cc_start: 0.7442 (mtp180) cc_final: 0.6957 (ptt-90) REVERT: C 272 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7206 (mtt-85) REVERT: C 393 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6400 (pp) REVERT: C 422 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.5880 (tpt) REVERT: C 467 GLU cc_start: 0.8344 (mp0) cc_final: 0.7996 (pm20) REVERT: C 551 ASN cc_start: 0.7961 (t0) cc_final: 0.7693 (t0) REVERT: D 170 ARG cc_start: 0.7443 (mtp180) cc_final: 0.6952 (ptt-90) REVERT: D 272 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7205 (mtt-85) REVERT: D 393 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6396 (pp) REVERT: D 422 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.5877 (tpt) REVERT: D 467 GLU cc_start: 0.8341 (mp0) cc_final: 0.7995 (pm20) REVERT: D 551 ASN cc_start: 0.7952 (t0) cc_final: 0.7688 (t0) outliers start: 15 outliers final: 0 residues processed: 320 average time/residue: 0.5829 time to fit residues: 214.5416 Evaluate side-chains 309 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 300 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 422 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 158 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 202 optimal weight: 0.0370 chunk 40 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 711 GLN B 92 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 92 HIS C 711 GLN D 92 HIS ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130735 restraints weight = 20346.195| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.67 r_work: 0.3239 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22924 Z= 0.146 Angle : 0.530 10.122 31028 Z= 0.270 Chirality : 0.037 0.164 3464 Planarity : 0.004 0.039 3804 Dihedral : 7.459 54.001 3192 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.80 % Allowed : 16.25 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.16), residues: 2624 helix: 2.10 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.10 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.012 0.001 TYR B 524 PHE 0.019 0.001 PHE D 341 TRP 0.013 0.001 TRP C 315 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (22904) covalent geometry : angle 0.52963 / 0.27 (31008) SS BOND : bond 0.00063 / 0.03 ( 4) SS BOND : angle 0.41769 / 0.28 ( 8) hydrogen bonds : bond 0.04610 / 3.02 ( 1464) hydrogen bonds : angle 3.92713 / 2.93 ( 4284) metal coordination : bond 0.00234 / 0.20 ( 16) metal coordination : angle 0.50593 / 0.31 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8154.32 seconds wall clock time: 139 minutes 45.70 seconds (8385.70 seconds total)