Starting phenix.real_space_refine on Thu Jul 2 22:49:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x24_32957/07_2026/7x24_32957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x24_32957/07_2026/7x24_32957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2026/7x24_32957.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2026/7x24_32957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2026/7x24_32957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2026/7x24_32957.map" model { file = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2026/7x24_32957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2026/7x24_32957.cif" } resolution = 3.4 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= 0.004 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: 9 Type Number sf(0) Gaussians K 3 8.98 5 Al 1 5.89 5 P 5 5.49 5 Mg 1 5.21 5 S 50 5.16 5 C 6673 2.51 5 N 1651 2.21 5 O 1898 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s 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: 10286 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7666 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 36, 'TRANS': 949} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 323 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 2, 'PCW': 5} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.23 Number of scatterers: 10286 At special positions: 0 Unit cell: (122.01, 103.75, 171.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 3 19.00 S 50 16.00 P 5 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1898 8.00 N 1651 7.00 C 6673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " 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=3, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 381.7 milliseconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 49.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 108 through 111 removed outlier: 3.532A pdb=" N GLY A 111 " --> pdb=" O GLN A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 111' Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 163 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.685A pdb=" N PHE A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.652A pdb=" N THR A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 294 through 324 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 347 through 365 removed outlier: 3.543A pdb=" N THR A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.187A pdb=" N THR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 429 through 440 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 543 through 560 Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.730A pdb=" N ASP A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 758 Processing helix chain 'A' and resid 768 through 793 removed outlier: 3.857A pdb=" N THR A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.673A pdb=" N GLU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 815 through 825 Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.504A pdb=" N ARG A 846 " --> pdb=" O ILE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'A' and resid 870 through 887 Processing helix chain 'A' and resid 891 through 896 removed outlier: 3.785A pdb=" N ILE A 896 " --> pdb=" O THR A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 950 Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 984 removed outlier: 3.915A pdb=" N TRP A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1004 through 1025 Processing helix chain 'A' and resid 1030 through 1035 Processing helix chain 'B' and resid 29 through 59 Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.120A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.162A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.985A pdb=" N TYR B 167 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 168 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 218 through 226 removed outlier: 3.591A pdb=" N LYS B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.617A pdb=" N PHE B 236 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 185 Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 removed outlier: 6.662A pdb=" N CYS A 261 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 225 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU A 263 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS A 223 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 271 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE A 215 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 205 removed outlier: 6.662A pdb=" N CYS A 261 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 225 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU A 263 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS A 223 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 271 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE A 215 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 6.225A pdb=" N GLY A 743 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A 762 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA A 745 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 384 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR A 727 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS A 386 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE A 385 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 628 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N SER A 387 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.658A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N PHE A 595 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR A 571 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE A 597 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS A 569 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 599 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 515 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 487 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.658A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS A 530 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE A 597 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR A 532 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLY A 599 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N MET A 534 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 12.531A pdb=" N LEU A 601 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA8, first strand: chain 'A' and resid 910 through 911 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.175A pdb=" N ILE B 88 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 485 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3192 1.34 - 1.46: 1544 1.46 - 1.58: 5660 1.58 - 1.69: 10 1.69 - 1.81: 83 Bond restraints: 10489 Sorted by residual: bond pdb=" C11 PCW A1104 " pdb=" O3 PCW A1104 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C11 PCW A1106 " pdb=" O3 PCW A1106 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C11 PCW A1109 " pdb=" O3 PCW A1109 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C11 PCW A1108 " pdb=" O3 PCW A1108 " ideal model delta sigma weight residual 1.326 1.452 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C31 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sigma weight residual 1.333 1.458 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 10484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.13: 14185 14.13 - 28.25: 4 28.25 - 42.38: 0 42.38 - 56.50: 0 56.50 - 70.63: 2 Bond angle restraints: 14191 Sorted by residual: angle pdb=" F1 ALF A1111 " pdb="AL ALF A1111 " pdb=" F2 ALF A1111 " ideal model delta sigma weight residual 108.68 179.31 -70.63 3.00e+00 1.11e-01 5.54e+02 angle pdb=" F3 ALF A1111 " pdb="AL ALF A1111 " pdb=" F4 ALF A1111 " ideal model delta sigma weight residual 109.63 179.61 -69.98 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1111 " pdb="AL ALF A1111 " pdb=" F4 ALF A1111 " ideal model delta sigma weight residual 110.21 89.78 20.43 3.00e+00 1.11e-01 4.64e+01 angle pdb=" F1 ALF A1111 " pdb="AL ALF A1111 " pdb=" F3 ALF A1111 " ideal model delta sigma weight residual 109.69 89.72 19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F2 ALF A1111 " pdb="AL ALF A1111 " pdb=" F3 ALF A1111 " ideal model delta sigma weight residual 109.59 90.14 19.45 3.00e+00 1.11e-01 4.20e+01 ... (remaining 14186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.79: 6109 32.79 - 65.57: 162 65.57 - 98.36: 15 98.36 - 131.15: 3 131.15 - 163.93: 4 Dihedral angle restraints: 6293 sinusoidal: 2635 harmonic: 3658 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual -86.00 -137.28 51.28 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" N PCW A1106 " pdb=" C4 PCW A1106 " pdb=" C5 PCW A1106 " pdb=" O4P PCW A1106 " ideal model delta sinusoidal sigma weight residual -66.66 97.27 -163.93 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" N PCW A1108 " pdb=" C4 PCW A1108 " pdb=" C5 PCW A1108 " pdb=" O4P PCW A1108 " ideal model delta sinusoidal sigma weight residual 293.34 143.48 149.86 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 6290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1405 0.067 - 0.134: 187 0.134 - 0.201: 9 0.201 - 0.269: 3 0.269 - 0.336: 2 Chirality restraints: 1606 Sorted by residual: chirality pdb=" C2 PCW A1104 " pdb=" C1 PCW A1104 " pdb=" C3 PCW A1104 " pdb=" O2 PCW A1104 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C13 CLR A1107 " pdb=" C12 CLR A1107 " pdb=" C14 CLR A1107 " pdb=" C17 CLR A1107 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C13 CLR B 402 " pdb=" C12 CLR B 402 " pdb=" C14 CLR B 402 " pdb=" C17 CLR B 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1603 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.301 2.00e-02 2.50e+03 2.53e-01 8.01e+02 pdb=" C7 NAG B 401 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 686 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 687 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 687 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 687 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 128 " 0.007 2.00e-02 2.50e+03 1.13e-02 2.23e+00 pdb=" CG PHE A 128 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 128 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 128 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 128 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 128 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 128 " 0.000 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 185 2.69 - 3.30: 11618 3.30 - 3.92: 19682 3.92 - 4.53: 27006 4.53 - 5.14: 42531 Nonbonded interactions: 101022 Sorted by model distance: nonbonded pdb=" F1 ALF A1111 " pdb="MG MG A1112 " model vdw 2.080 2.120 nonbonded pdb=" OD2 ASP A 388 " pdb="MG MG A1112 " model vdw 2.090 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1112 " model vdw 2.105 2.170 nonbonded pdb=" O ILE A 907 " pdb=" NH2 ARG A 923 " model vdw 2.252 3.120 nonbonded pdb=" OD2 ASP A 388 " pdb=" F1 ALF A1111 " model vdw 2.272 2.990 ... (remaining 101017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.006 0.128 10496 Z= 0.287 Angle : 1.217 70.627 14200 Z= 0.467 Chirality : 0.047 0.336 1606 Planarity : 0.007 0.253 1769 Dihedral : 15.744 163.933 3934 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.37 (0.24), residues: 1259 helix: 1.45 (0.23), residues: 525 sheet: -0.33 (0.39), residues: 164 loop : -0.67 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 80 TYR 0.015 0.001 TYR A 805 PHE 0.025 0.002 PHE A 128 TRP 0.007 0.001 TRP A 968 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.29 (10489) covalent geometry : angle 1.21242 / 0.47 (14191) SS BOND : bond 0.00132 / 0.07 ( 3) SS BOND : angle 1.04853 / 0.50 ( 6) hydrogen bonds : bond 0.15766 / 10.31 ( 470) hydrogen bonds : angle 6.43657 / 4.67 ( 1377) Misc. bond : bond 0.00179 / 0.10 ( 3) link_NAG-ASN : bond 0.01628 / 1.02 ( 1) link_NAG-ASN : angle 7.65119 / 3.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7743 (tttp) cc_final: 0.7481 (mtpp) REVERT: A 421 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6735 (mm-40) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1161 time to fit residues: 24.4193 Evaluate side-chains 125 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 343 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.154275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117088 restraints weight = 12655.807| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.58 r_work: 0.3001 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10496 Z= 0.167 Angle : 0.604 13.160 14200 Z= 0.307 Chirality : 0.045 0.163 1606 Planarity : 0.004 0.050 1769 Dihedral : 11.788 150.008 1551 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.64 % Allowed : 8.26 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.37 (0.24), residues: 1259 helix: 1.41 (0.23), residues: 529 sheet: -0.08 (0.40), residues: 150 loop : -0.73 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.020 0.001 TYR A 805 PHE 0.011 0.002 PHE A 935 TRP 0.008 0.001 TRP A 902 HIS 0.002 0.001 HIS A 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (10489) covalent geometry : angle 0.59139 / 0.30 (14191) SS BOND : bond 0.00048 / 0.03 ( 3) SS BOND : angle 1.75480 / 0.88 ( 6) hydrogen bonds : bond 0.04701 / 3.15 ( 470) hydrogen bonds : angle 5.11935 / 3.74 ( 1377) Misc. bond : bond 0.00196 / 0.11 ( 3) link_NAG-ASN : bond 0.01684 / 1.05 ( 1) link_NAG-ASN : angle 8.12904 / 3.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6176 (ttt-90) cc_final: 0.5588 (ptm160) REVERT: A 365 LYS cc_start: 0.7958 (tttp) cc_final: 0.7655 (mtpp) REVERT: A 860 GLN cc_start: 0.8065 (mp10) cc_final: 0.7752 (mm110) outliers start: 7 outliers final: 5 residues processed: 145 average time/residue: 0.1079 time to fit residues: 21.5710 Evaluate side-chains 139 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN A 501 GLN A 551 HIS B 104 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.158070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123377 restraints weight = 12647.349| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.69 r_work: 0.2996 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10496 Z= 0.107 Angle : 0.536 13.189 14200 Z= 0.272 Chirality : 0.042 0.160 1606 Planarity : 0.004 0.048 1769 Dihedral : 11.188 152.591 1551 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.83 % Allowed : 10.65 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.48 (0.24), residues: 1259 helix: 1.58 (0.23), residues: 536 sheet: -0.35 (0.39), residues: 163 loop : -0.68 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.016 0.001 TYR A 881 PHE 0.011 0.001 PHE A 935 TRP 0.009 0.001 TRP A1001 HIS 0.002 0.000 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (10489) covalent geometry : angle 0.51986 / 0.27 (14191) SS BOND : bond 0.00115 / 0.06 ( 3) SS BOND : angle 1.29344 / 0.67 ( 6) hydrogen bonds : bond 0.03829 / 2.58 ( 470) hydrogen bonds : angle 4.59419 / 3.37 ( 1377) Misc. bond : bond 0.00151 / 0.08 ( 3) link_NAG-ASN : bond 0.00870 / 0.54 ( 1) link_NAG-ASN : angle 8.71957 / 3.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6823 (mt) REVERT: A 87 ARG cc_start: 0.6151 (ttt-90) cc_final: 0.5659 (ptm160) REVERT: A 180 GLN cc_start: 0.7662 (pm20) cc_final: 0.7411 (pm20) REVERT: A 365 LYS cc_start: 0.7923 (tttp) cc_final: 0.7642 (mtpp) REVERT: A 473 GLU cc_start: 0.7746 (tp30) cc_final: 0.7460 (tp30) REVERT: A 860 GLN cc_start: 0.7923 (mp10) cc_final: 0.7586 (mm110) REVERT: B 103 LEU cc_start: 0.8244 (mt) cc_final: 0.7935 (mm) outliers start: 9 outliers final: 6 residues processed: 145 average time/residue: 0.1088 time to fit residues: 21.8749 Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN A 501 GLN A 551 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.157165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122037 restraints weight = 12620.321| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.64 r_work: 0.2986 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10496 Z= 0.167 Angle : 0.587 12.740 14200 Z= 0.298 Chirality : 0.044 0.171 1606 Planarity : 0.004 0.048 1769 Dihedral : 11.360 158.955 1551 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.29 % Allowed : 12.40 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.38 (0.24), residues: 1259 helix: 1.41 (0.23), residues: 531 sheet: -0.18 (0.40), residues: 150 loop : -0.70 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.023 0.001 TYR A 805 PHE 0.014 0.002 PHE A 935 TRP 0.010 0.001 TRP A1001 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (10489) covalent geometry : angle 0.57377 / 0.29 (14191) SS BOND : bond 0.00033 / 0.02 ( 3) SS BOND : angle 1.48357 / 0.73 ( 6) hydrogen bonds : bond 0.04370 / 2.96 ( 470) hydrogen bonds : angle 4.61280 / 3.38 ( 1377) Misc. bond : bond 0.00190 / 0.11 ( 3) link_NAG-ASN : bond 0.01152 / 0.72 ( 1) link_NAG-ASN : angle 8.41825 / 3.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6253 (ttt-90) cc_final: 0.5701 (ptm160) REVERT: A 180 GLN cc_start: 0.7717 (pm20) cc_final: 0.7430 (pm20) REVERT: A 365 LYS cc_start: 0.8000 (tttp) cc_final: 0.7652 (mtpp) REVERT: B 103 LEU cc_start: 0.8287 (mt) cc_final: 0.8033 (mm) REVERT: B 229 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7638 (mm-30) outliers start: 14 outliers final: 12 residues processed: 144 average time/residue: 0.1073 time to fit residues: 21.2480 Evaluate side-chains 141 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN A 551 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.157206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122244 restraints weight = 12640.854| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.74 r_work: 0.2987 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10496 Z= 0.118 Angle : 0.538 12.750 14200 Z= 0.273 Chirality : 0.043 0.200 1606 Planarity : 0.004 0.047 1769 Dihedral : 11.012 161.332 1551 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.10 % Allowed : 13.77 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.43 (0.24), residues: 1259 helix: 1.47 (0.23), residues: 537 sheet: -0.26 (0.39), residues: 157 loop : -0.68 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.016 0.001 TYR A 881 PHE 0.012 0.001 PHE A 935 TRP 0.011 0.001 TRP A 430 HIS 0.002 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10489) covalent geometry : angle 0.52448 / 0.27 (14191) SS BOND : bond 0.00044 / 0.02 ( 3) SS BOND : angle 1.12730 / 0.54 ( 6) hydrogen bonds : bond 0.03788 / 2.57 ( 470) hydrogen bonds : angle 4.43802 / 3.26 ( 1377) Misc. bond : bond 0.00166 / 0.09 ( 3) link_NAG-ASN : bond 0.01956 / 1.22 ( 1) link_NAG-ASN : angle 8.23069 / 3.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6177 (ttt-90) cc_final: 0.5630 (ptm160) REVERT: A 125 TRP cc_start: 0.7230 (t60) cc_final: 0.6987 (t60) REVERT: A 180 GLN cc_start: 0.7594 (pm20) cc_final: 0.7300 (pm20) REVERT: A 233 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 365 LYS cc_start: 0.7956 (tttp) cc_final: 0.7625 (mtpp) REVERT: A 442 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.6932 (tpp80) REVERT: A 457 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6587 (mtt180) REVERT: B 229 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7357 (mm-30) outliers start: 12 outliers final: 10 residues processed: 143 average time/residue: 0.1088 time to fit residues: 21.3670 Evaluate side-chains 141 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN A 551 HIS A 569 HIS A 689 GLN B 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.157631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122744 restraints weight = 12750.996| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.78 r_work: 0.2996 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10496 Z= 0.108 Angle : 0.523 12.773 14200 Z= 0.266 Chirality : 0.042 0.239 1606 Planarity : 0.004 0.050 1769 Dihedral : 10.635 161.094 1551 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.19 % Allowed : 14.05 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.50 (0.24), residues: 1259 helix: 1.57 (0.23), residues: 539 sheet: -0.28 (0.39), residues: 161 loop : -0.68 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 TYR 0.015 0.001 TYR A 881 PHE 0.013 0.001 PHE A 935 TRP 0.010 0.001 TRP A1001 HIS 0.002 0.000 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10489) covalent geometry : angle 0.50862 / 0.26 (14191) SS BOND : bond 0.00013 / 0.01 ( 3) SS BOND : angle 1.08564 / 0.53 ( 6) hydrogen bonds : bond 0.03562 / 2.42 ( 470) hydrogen bonds : angle 4.32127 / 3.18 ( 1377) Misc. bond : bond 0.00160 / 0.09 ( 3) link_NAG-ASN : bond 0.01758 / 1.10 ( 1) link_NAG-ASN : angle 8.40440 / 3.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6179 (ttt-90) cc_final: 0.5638 (ptm160) REVERT: A 125 TRP cc_start: 0.7268 (t60) cc_final: 0.7024 (t60) REVERT: A 180 GLN cc_start: 0.7620 (pm20) cc_final: 0.7315 (pm20) REVERT: A 233 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 240 SER cc_start: 0.8051 (t) cc_final: 0.7784 (p) REVERT: A 365 LYS cc_start: 0.7945 (tttp) cc_final: 0.7660 (mtpp) REVERT: A 457 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6650 (mtt180) REVERT: A 860 GLN cc_start: 0.7981 (mp10) cc_final: 0.7618 (mm110) REVERT: B 220 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: B 229 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7382 (mm-30) outliers start: 13 outliers final: 10 residues processed: 143 average time/residue: 0.1102 time to fit residues: 21.6972 Evaluate side-chains 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN A 551 HIS B 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.159211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125173 restraints weight = 12530.602| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.79 r_work: 0.2973 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10496 Z= 0.114 Angle : 0.528 12.816 14200 Z= 0.267 Chirality : 0.042 0.273 1606 Planarity : 0.004 0.050 1769 Dihedral : 10.501 162.772 1551 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.56 % Allowed : 14.69 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.50 (0.24), residues: 1259 helix: 1.57 (0.23), residues: 538 sheet: -0.24 (0.39), residues: 161 loop : -0.68 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.016 0.001 TYR A 881 PHE 0.013 0.001 PHE A 935 TRP 0.009 0.001 TRP A1001 HIS 0.001 0.000 HIS A 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (10489) covalent geometry : angle 0.51367 / 0.26 (14191) SS BOND : bond 0.00020 / 0.01 ( 3) SS BOND : angle 0.99552 / 0.48 ( 6) hydrogen bonds : bond 0.03613 / 2.45 ( 470) hydrogen bonds : angle 4.31206 / 3.18 ( 1377) Misc. bond : bond 0.00158 / 0.09 ( 3) link_NAG-ASN : bond 0.01845 / 1.15 ( 1) link_NAG-ASN : angle 8.41508 / 3.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6224 (ttt-90) cc_final: 0.5650 (ptm160) REVERT: A 125 TRP cc_start: 0.7257 (t60) cc_final: 0.7018 (t60) REVERT: A 180 GLN cc_start: 0.7540 (pm20) cc_final: 0.7220 (pm20) REVERT: A 197 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8103 (tt) REVERT: A 240 SER cc_start: 0.8052 (t) cc_final: 0.7772 (p) REVERT: A 365 LYS cc_start: 0.7937 (tttp) cc_final: 0.7651 (mtpp) REVERT: A 442 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.6958 (tpp80) REVERT: A 457 ARG cc_start: 0.7187 (mtt180) cc_final: 0.6628 (mtt180) REVERT: B 229 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7376 (mm-30) outliers start: 17 outliers final: 12 residues processed: 147 average time/residue: 0.1191 time to fit residues: 23.8803 Evaluate side-chains 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 0.0570 chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 0.0010 chunk 45 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN A 551 HIS A 860 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.158607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123947 restraints weight = 12524.588| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.79 r_work: 0.3022 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10496 Z= 0.096 Angle : 0.511 12.667 14200 Z= 0.257 Chirality : 0.042 0.273 1606 Planarity : 0.004 0.050 1769 Dihedral : 10.083 162.172 1551 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.01 % Allowed : 15.43 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.69 (0.24), residues: 1259 helix: 1.75 (0.23), residues: 539 sheet: -0.15 (0.40), residues: 161 loop : -0.62 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.014 0.001 TYR A 881 PHE 0.012 0.001 PHE A 935 TRP 0.010 0.001 TRP A1001 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (10489) covalent geometry : angle 0.49657 / 0.25 (14191) SS BOND : bond 0.00064 / 0.04 ( 3) SS BOND : angle 0.87126 / 0.43 ( 6) hydrogen bonds : bond 0.03259 / 2.21 ( 470) hydrogen bonds : angle 4.20910 / 3.09 ( 1377) Misc. bond : bond 0.00145 / 0.08 ( 3) link_NAG-ASN : bond 0.01502 / 0.94 ( 1) link_NAG-ASN : angle 8.32781 / 3.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6210 (ttt-90) cc_final: 0.5651 (ptm160) REVERT: A 125 TRP cc_start: 0.7186 (t60) cc_final: 0.6959 (t60) REVERT: A 180 GLN cc_start: 0.7466 (pm20) cc_final: 0.7150 (pm20) REVERT: A 197 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8025 (tt) REVERT: A 240 SER cc_start: 0.8034 (t) cc_final: 0.7793 (p) REVERT: A 365 LYS cc_start: 0.7909 (tttp) cc_final: 0.7627 (mtpp) REVERT: A 442 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.7033 (tpp80) REVERT: A 457 ARG cc_start: 0.7192 (mtt180) cc_final: 0.6684 (mtt180) REVERT: A 473 GLU cc_start: 0.7727 (tp30) cc_final: 0.7335 (tp30) REVERT: A 540 GLN cc_start: 0.6531 (mp10) cc_final: 0.6307 (mp10) REVERT: A 860 GLN cc_start: 0.7935 (mp-120) cc_final: 0.7555 (mm110) REVERT: B 129 MET cc_start: 0.6822 (mmp) cc_final: 0.6268 (mmp) REVERT: B 229 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7308 (mt-10) outliers start: 11 outliers final: 9 residues processed: 146 average time/residue: 0.1129 time to fit residues: 22.2552 Evaluate side-chains 145 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 0.0070 chunk 120 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN A 551 HIS A 569 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.161954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127062 restraints weight = 12472.896| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.62 r_work: 0.3064 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10496 Z= 0.094 Angle : 0.509 12.211 14200 Z= 0.255 Chirality : 0.042 0.352 1606 Planarity : 0.004 0.049 1769 Dihedral : 9.778 161.436 1551 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.19 % Allowed : 15.70 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.77 (0.24), residues: 1259 helix: 1.82 (0.23), residues: 539 sheet: -0.10 (0.39), residues: 163 loop : -0.57 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.015 0.001 TYR A 805 PHE 0.013 0.001 PHE A 935 TRP 0.010 0.001 TRP A 430 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (10489) covalent geometry : angle 0.49550 / 0.25 (14191) SS BOND : bond 0.00051 / 0.03 ( 3) SS BOND : angle 0.79928 / 0.38 ( 6) hydrogen bonds : bond 0.03204 / 2.16 ( 470) hydrogen bonds : angle 4.15712 / 3.06 ( 1377) Misc. bond : bond 0.00134 / 0.07 ( 3) link_NAG-ASN : bond 0.01448 / 0.91 ( 1) link_NAG-ASN : angle 8.00647 / 3.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.7471 (mm110) cc_final: 0.6788 (mm-40) REVERT: A 87 ARG cc_start: 0.6271 (ttt-90) cc_final: 0.5735 (ptm160) REVERT: A 125 TRP cc_start: 0.7180 (t60) cc_final: 0.6943 (t60) REVERT: A 180 GLN cc_start: 0.7428 (pm20) cc_final: 0.7115 (pm20) REVERT: A 197 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8061 (tt) REVERT: A 240 SER cc_start: 0.7967 (t) cc_final: 0.7707 (p) REVERT: A 365 LYS cc_start: 0.7882 (tttp) cc_final: 0.7610 (mtpp) REVERT: A 442 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.7014 (tpp80) REVERT: A 457 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6687 (mtt180) REVERT: A 473 GLU cc_start: 0.7647 (tp30) cc_final: 0.7259 (tp30) REVERT: A 540 GLN cc_start: 0.6566 (mp10) cc_final: 0.6349 (mp10) REVERT: A 860 GLN cc_start: 0.7886 (mp-120) cc_final: 0.7527 (mm110) REVERT: B 129 MET cc_start: 0.6842 (mmp) cc_final: 0.6290 (mmp) REVERT: B 229 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7245 (mt-10) outliers start: 13 outliers final: 10 residues processed: 151 average time/residue: 0.1142 time to fit residues: 23.3705 Evaluate side-chains 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 88 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.158064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122009 restraints weight = 12606.504| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.72 r_work: 0.3051 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10496 Z= 0.101 Angle : 0.514 11.798 14200 Z= 0.258 Chirality : 0.042 0.320 1606 Planarity : 0.004 0.049 1769 Dihedral : 9.715 162.664 1551 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.19 % Allowed : 15.61 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.78 (0.24), residues: 1259 helix: 1.82 (0.23), residues: 538 sheet: -0.07 (0.40), residues: 161 loop : -0.57 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.015 0.001 TYR A 881 PHE 0.028 0.001 PHE A 550 TRP 0.009 0.001 TRP A 430 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (10489) covalent geometry : angle 0.50166 / 0.26 (14191) SS BOND : bond 0.00018 / 0.01 ( 3) SS BOND : angle 0.91130 / 0.44 ( 6) hydrogen bonds : bond 0.03336 / 2.26 ( 470) hydrogen bonds : angle 4.16222 / 3.06 ( 1377) Misc. bond : bond 0.00136 / 0.07 ( 3) link_NAG-ASN : bond 0.01438 / 0.90 ( 1) link_NAG-ASN : angle 7.76149 / 3.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.7450 (mm110) cc_final: 0.6779 (mm-40) REVERT: A 87 ARG cc_start: 0.6307 (ttt-90) cc_final: 0.5784 (ptm160) REVERT: A 125 TRP cc_start: 0.7364 (t60) cc_final: 0.7128 (t60) REVERT: A 180 GLN cc_start: 0.7515 (pm20) cc_final: 0.7181 (pm20) REVERT: A 197 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 240 SER cc_start: 0.8095 (t) cc_final: 0.7812 (p) REVERT: A 365 LYS cc_start: 0.7894 (tttp) cc_final: 0.7601 (mtpp) REVERT: A 442 ARG cc_start: 0.7269 (ttp-170) cc_final: 0.7010 (tpp80) REVERT: A 457 ARG cc_start: 0.7293 (mtt180) cc_final: 0.6829 (mtt180) REVERT: A 473 GLU cc_start: 0.7863 (tp30) cc_final: 0.7480 (tp30) REVERT: A 540 GLN cc_start: 0.6596 (mp10) cc_final: 0.6391 (mp10) REVERT: B 129 MET cc_start: 0.6873 (mmp) cc_final: 0.6314 (mmp) REVERT: B 229 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7496 (mt-10) outliers start: 13 outliers final: 10 residues processed: 145 average time/residue: 0.1134 time to fit residues: 22.3714 Evaluate side-chains 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 2 optimal weight: 0.0470 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118294 restraints weight = 12827.102| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.94 r_work: 0.2904 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10496 Z= 0.169 Angle : 0.590 11.524 14200 Z= 0.297 Chirality : 0.045 0.332 1606 Planarity : 0.004 0.049 1769 Dihedral : 10.522 170.072 1551 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.10 % Allowed : 15.79 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.51 (0.24), residues: 1259 helix: 1.45 (0.23), residues: 536 sheet: 0.02 (0.41), residues: 150 loop : -0.60 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 485 TYR 0.020 0.001 TYR A 881 PHE 0.027 0.002 PHE A 128 TRP 0.013 0.002 TRP A 430 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (10489) covalent geometry : angle 0.57909 / 0.29 (14191) SS BOND : bond 0.00105 / 0.06 ( 3) SS BOND : angle 1.27427 / 0.63 ( 6) hydrogen bonds : bond 0.04314 / 2.93 ( 470) hydrogen bonds : angle 4.44968 / 3.27 ( 1377) Misc. bond : bond 0.00176 / 0.10 ( 3) link_NAG-ASN : bond 0.01482 / 0.93 ( 1) link_NAG-ASN : angle 7.53199 / 2.92 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2476.33 seconds wall clock time: 43 minutes 13.70 seconds (2593.70 seconds total)