Starting phenix.real_space_refine on Wed Mar 4 04:06:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x24_32957/03_2026/7x24_32957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x24_32957/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7x24_32957/03_2026/7x24_32957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x24_32957/03_2026/7x24_32957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x24_32957/03_2026/7x24_32957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x24_32957/03_2026/7x24_32957.map" } 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-5986/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.50, per 1000 atoms: 0.24 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: 0.83 Conformation dependent library (CDL) restraints added in 429.2 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: 1.69 Time building geometry restraints manager: 1.06 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: 6325 32.79 - 65.57: 183 65.57 - 98.36: 17 98.36 - 131.15: 3 131.15 - 163.93: 4 Dihedral angle restraints: 6532 sinusoidal: 2874 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 6529 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 15.936 163.933 4173 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 covalent geometry : bond 0.00596 (10489) covalent geometry : angle 1.21242 (14191) SS BOND : bond 0.00132 ( 3) SS BOND : angle 1.04853 ( 6) hydrogen bonds : bond 0.15766 ( 470) hydrogen bonds : angle 6.43657 ( 1377) Misc. bond : bond 0.00179 ( 3) link_NAG-ASN : bond 0.01628 ( 1) link_NAG-ASN : angle 7.65119 ( 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 : 0.256 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: 0.1124 time to fit residues: 23.6486 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 : 0.375 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3683 r_free = 0.3683 target = 0.154189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117682 restraints weight = 12663.384| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.80 r_work: 0.2961 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0813 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 : 0.603 13.059 14200 Z= 0.306 Chirality : 0.045 0.163 1606 Planarity : 0.004 0.050 1769 Dihedral : 12.673 149.069 1790 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.64 % Allowed : 8.17 % Favored : 91.18 % 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 covalent geometry : bond 0.00401 (10489) covalent geometry : angle 0.59006 (14191) SS BOND : bond 0.00051 ( 3) SS BOND : angle 1.71704 ( 6) hydrogen bonds : bond 0.04768 ( 470) hydrogen bonds : angle 5.12389 ( 1377) Misc. bond : bond 0.00194 ( 3) link_NAG-ASN : bond 0.01374 ( 1) link_NAG-ASN : angle 8.13386 ( 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 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6133 (ttt-90) cc_final: 0.5549 (ptm160) REVERT: A 365 LYS cc_start: 0.7945 (tttp) cc_final: 0.7643 (mtpp) REVERT: A 860 GLN cc_start: 0.7987 (mp10) cc_final: 0.7651 (mm110) outliers start: 7 outliers final: 5 residues processed: 142 average time/residue: 0.1152 time to fit residues: 22.2987 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 : 0.324 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS B 104 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.155080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119119 restraints weight = 12762.306| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.84 r_work: 0.2963 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10496 Z= 0.130 Angle : 0.559 13.463 14200 Z= 0.283 Chirality : 0.043 0.162 1606 Planarity : 0.004 0.049 1769 Dihedral : 12.272 151.149 1790 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.01 % Allowed : 10.65 % Favored : 88.34 % 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: 0.33 (0.24), residues: 1259 helix: 1.42 (0.23), residues: 537 sheet: -0.40 (0.39), residues: 162 loop : -0.73 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 TYR 0.017 0.001 TYR A 881 PHE 0.012 0.001 PHE A 935 TRP 0.010 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00306 (10489) covalent geometry : angle 0.54270 (14191) SS BOND : bond 0.00059 ( 3) SS BOND : angle 1.53838 ( 6) hydrogen bonds : bond 0.04116 ( 470) hydrogen bonds : angle 4.66585 ( 1377) Misc. bond : bond 0.00166 ( 3) link_NAG-ASN : bond 0.00700 ( 1) link_NAG-ASN : angle 8.91764 ( 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 155 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6682 (mt) REVERT: A 87 ARG cc_start: 0.6145 (ttt-90) cc_final: 0.5633 (ptm160) REVERT: A 180 GLN cc_start: 0.7692 (pm20) cc_final: 0.7430 (pm20) REVERT: A 365 LYS cc_start: 0.7949 (tttp) cc_final: 0.7657 (mtpp) REVERT: A 473 GLU cc_start: 0.7767 (tp30) cc_final: 0.7452 (tp30) REVERT: B 103 LEU cc_start: 0.8257 (mt) cc_final: 0.7969 (mm) outliers start: 11 outliers final: 6 residues processed: 151 average time/residue: 0.1046 time to fit residues: 21.8374 Evaluate side-chains 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3742 r_free = 0.3742 target = 0.159799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124973 restraints weight = 12578.810| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.68 r_work: 0.3049 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10496 Z= 0.110 Angle : 0.531 13.048 14200 Z= 0.270 Chirality : 0.042 0.167 1606 Planarity : 0.004 0.047 1769 Dihedral : 11.923 150.430 1790 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.64 % Allowed : 12.95 % Favored : 86.41 % 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: 1.56 (0.23), residues: 538 sheet: -0.31 (0.39), residues: 161 loop : -0.69 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.016 0.001 TYR A 881 PHE 0.012 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 covalent geometry : bond 0.00250 (10489) covalent geometry : angle 0.51625 (14191) SS BOND : bond 0.00062 ( 3) SS BOND : angle 1.15358 ( 6) hydrogen bonds : bond 0.03730 ( 470) hydrogen bonds : angle 4.47291 ( 1377) Misc. bond : bond 0.00157 ( 3) link_NAG-ASN : bond 0.01225 ( 1) link_NAG-ASN : angle 8.48745 ( 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 149 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6629 (mt) REVERT: A 87 ARG cc_start: 0.6231 (ttt-90) cc_final: 0.5686 (ptm160) REVERT: A 180 GLN cc_start: 0.7707 (pm20) cc_final: 0.7437 (pm20) REVERT: A 365 LYS cc_start: 0.7961 (tttp) cc_final: 0.7662 (mtpp) REVERT: A 457 ARG cc_start: 0.7256 (mtt180) cc_final: 0.6731 (mtt180) REVERT: A 860 GLN cc_start: 0.7982 (mp10) cc_final: 0.7676 (mm110) REVERT: B 103 LEU cc_start: 0.8279 (mt) cc_final: 0.8050 (mm) outliers start: 7 outliers final: 6 residues processed: 146 average time/residue: 0.1144 time to fit residues: 22.7016 Evaluate side-chains 145 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 806 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 551 HIS A 569 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 = 0.3716 r_free = 0.3716 target = 0.157576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122583 restraints weight = 12530.025| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.67 r_work: 0.2982 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10496 Z= 0.159 Angle : 0.572 12.593 14200 Z= 0.289 Chirality : 0.044 0.240 1606 Planarity : 0.004 0.048 1769 Dihedral : 12.224 152.710 1790 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.65 % Allowed : 13.31 % Favored : 85.03 % 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: 0.36 (0.24), residues: 1259 helix: 1.38 (0.23), residues: 537 sheet: -0.15 (0.40), residues: 150 loop : -0.73 (0.26), residues: 572 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 0.009 0.001 TRP A1001 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00386 (10489) covalent geometry : angle 0.55896 (14191) SS BOND : bond 0.00074 ( 3) SS BOND : angle 1.31635 ( 6) hydrogen bonds : bond 0.04224 ( 470) hydrogen bonds : angle 4.52076 ( 1377) Misc. bond : bond 0.00178 ( 3) link_NAG-ASN : bond 0.01751 ( 1) link_NAG-ASN : angle 8.20336 ( 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 158 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6545 (mt) REVERT: A 87 ARG cc_start: 0.6282 (ttt-90) cc_final: 0.5714 (ptm160) REVERT: A 125 TRP cc_start: 0.7347 (t60) cc_final: 0.7095 (t60) REVERT: A 180 GLN cc_start: 0.7690 (pm20) cc_final: 0.7387 (pm20) REVERT: A 233 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 365 LYS cc_start: 0.7999 (tttp) cc_final: 0.7655 (mtpp) REVERT: A 457 ARG cc_start: 0.7290 (mtt180) cc_final: 0.6741 (mtt180) REVERT: A 501 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7065 (pp30) REVERT: B 229 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7618 (mm-30) outliers start: 18 outliers final: 15 residues processed: 150 average time/residue: 0.1153 time to fit residues: 23.6780 Evaluate side-chains 150 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN 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 28 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN A 551 HIS A 689 GLN ** 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 = 0.3674 r_free = 0.3674 target = 0.153505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117482 restraints weight = 12846.934| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.63 r_work: 0.2972 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10496 Z= 0.171 Angle : 0.597 13.510 14200 Z= 0.301 Chirality : 0.045 0.308 1606 Planarity : 0.004 0.051 1769 Dihedral : 12.496 155.343 1790 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.93 % Allowed : 14.14 % Favored : 83.93 % 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: 0.26 (0.23), residues: 1259 helix: 1.25 (0.22), residues: 535 sheet: -0.19 (0.40), residues: 147 loop : -0.72 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.019 0.001 TYR A 881 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 covalent geometry : bond 0.00417 (10489) covalent geometry : angle 0.58268 (14191) SS BOND : bond 0.00111 ( 3) SS BOND : angle 1.41991 ( 6) hydrogen bonds : bond 0.04357 ( 470) hydrogen bonds : angle 4.57643 ( 1377) Misc. bond : bond 0.00191 ( 3) link_NAG-ASN : bond 0.02012 ( 1) link_NAG-ASN : angle 8.71759 ( 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 159 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.373 Fit side-chains REVERT: A 84 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6489 (mt) REVERT: A 87 ARG cc_start: 0.6253 (ttt-90) cc_final: 0.5635 (ptm160) REVERT: A 125 TRP cc_start: 0.7354 (t60) cc_final: 0.7127 (t60) REVERT: A 180 GLN cc_start: 0.7606 (pm20) cc_final: 0.7302 (pm20) REVERT: A 233 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 365 LYS cc_start: 0.7970 (tttp) cc_final: 0.7643 (mtpp) REVERT: A 442 ARG cc_start: 0.7218 (ttp-170) cc_final: 0.6917 (tpp80) REVERT: A 501 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7011 (pp30) REVERT: A 875 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 220 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: B 229 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7662 (mm-30) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 0.1200 time to fit residues: 24.3311 Evaluate side-chains 156 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN 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 875 LEU 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 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 LEU 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: 4.9990 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A 569 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 = 0.3711 r_free = 0.3711 target = 0.156922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121020 restraints weight = 12667.654| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.73 r_work: 0.3002 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10496 Z= 0.110 Angle : 0.535 13.093 14200 Z= 0.270 Chirality : 0.043 0.317 1606 Planarity : 0.004 0.051 1769 Dihedral : 11.965 153.858 1790 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.56 % Allowed : 15.15 % Favored : 83.29 % 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: 0.46 (0.24), residues: 1259 helix: 1.48 (0.23), residues: 539 sheet: -0.06 (0.40), residues: 149 loop : -0.71 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 80 TYR 0.016 0.001 TYR A 881 PHE 0.012 0.001 PHE A 935 TRP 0.012 0.001 TRP A1001 HIS 0.001 0.000 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00253 (10489) covalent geometry : angle 0.51978 (14191) SS BOND : bond 0.00031 ( 3) SS BOND : angle 1.05953 ( 6) hydrogen bonds : bond 0.03666 ( 470) hydrogen bonds : angle 4.36546 ( 1377) Misc. bond : bond 0.00163 ( 3) link_NAG-ASN : bond 0.01784 ( 1) link_NAG-ASN : angle 8.49634 ( 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 159 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6386 (mt) REVERT: A 87 ARG cc_start: 0.6229 (ttt-90) cc_final: 0.5638 (ptm160) REVERT: A 125 TRP cc_start: 0.7237 (t60) cc_final: 0.7020 (t60) REVERT: A 180 GLN cc_start: 0.7491 (pm20) cc_final: 0.7190 (pm20) REVERT: A 233 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 240 SER cc_start: 0.7993 (t) cc_final: 0.7722 (p) REVERT: A 281 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7178 (mtp85) REVERT: A 365 LYS cc_start: 0.7947 (tttp) cc_final: 0.7625 (mtpp) REVERT: A 442 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.6932 (tpp80) REVERT: A 501 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7060 (pp30) REVERT: B 220 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: B 229 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7316 (mm-30) outliers start: 17 outliers final: 13 residues processed: 154 average time/residue: 0.1210 time to fit residues: 25.1650 Evaluate side-chains 151 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN 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 28 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 20 optimal weight: 7.9990 chunk 8 optimal weight: 0.0060 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A 569 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 = 0.3713 r_free = 0.3713 target = 0.156975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121120 restraints weight = 12587.633| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.76 r_work: 0.3011 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10496 Z= 0.102 Angle : 0.527 12.709 14200 Z= 0.265 Chirality : 0.042 0.270 1606 Planarity : 0.004 0.050 1769 Dihedral : 11.557 153.913 1790 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.47 % Allowed : 15.89 % Favored : 82.64 % 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: 0.57 (0.24), residues: 1259 helix: 1.62 (0.23), residues: 540 sheet: -0.17 (0.40), residues: 161 loop : -0.66 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 80 TYR 0.015 0.001 TYR A 881 PHE 0.013 0.001 PHE A 935 TRP 0.012 0.001 TRP A1001 HIS 0.001 0.000 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00230 (10489) covalent geometry : angle 0.51291 (14191) SS BOND : bond 0.00023 ( 3) SS BOND : angle 1.06354 ( 6) hydrogen bonds : bond 0.03449 ( 470) hydrogen bonds : angle 4.28719 ( 1377) Misc. bond : bond 0.00154 ( 3) link_NAG-ASN : bond 0.01554 ( 1) link_NAG-ASN : angle 8.28508 ( 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 155 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6497 (mt) REVERT: A 87 ARG cc_start: 0.6291 (ttt-90) cc_final: 0.5701 (ptm160) REVERT: A 125 TRP cc_start: 0.7224 (t60) cc_final: 0.7005 (t60) REVERT: A 180 GLN cc_start: 0.7478 (pm20) cc_final: 0.7182 (pm20) REVERT: A 240 SER cc_start: 0.8048 (t) cc_final: 0.7779 (p) REVERT: A 281 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7204 (mtp85) REVERT: A 365 LYS cc_start: 0.7936 (tttp) cc_final: 0.7614 (mtpp) REVERT: A 442 ARG cc_start: 0.7278 (ttp-170) cc_final: 0.6956 (tpp80) REVERT: A 501 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7134 (pp30) REVERT: A 540 GLN cc_start: 0.6549 (mp10) cc_final: 0.6302 (mp10) REVERT: B 229 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7306 (mm-30) outliers start: 16 outliers final: 10 residues processed: 150 average time/residue: 0.1276 time to fit residues: 25.6502 Evaluate side-chains 146 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 184 ILE 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 906 ASP Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 83 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 2 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 97 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS B 193 ASN B 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.156955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121607 restraints weight = 12694.081| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.77 r_work: 0.3026 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10496 Z= 0.102 Angle : 0.518 12.092 14200 Z= 0.261 Chirality : 0.042 0.213 1606 Planarity : 0.004 0.050 1769 Dihedral : 11.265 154.831 1790 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.47 % Allowed : 15.61 % Favored : 82.92 % 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: 0.65 (0.24), residues: 1259 helix: 1.72 (0.23), residues: 539 sheet: -0.10 (0.40), residues: 161 loop : -0.67 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 80 TYR 0.015 0.001 TYR A 881 PHE 0.014 0.001 PHE A 935 TRP 0.010 0.001 TRP A1001 HIS 0.001 0.000 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00234 (10489) covalent geometry : angle 0.50503 (14191) SS BOND : bond 0.00020 ( 3) SS BOND : angle 0.95063 ( 6) hydrogen bonds : bond 0.03399 ( 470) hydrogen bonds : angle 4.20653 ( 1377) Misc. bond : bond 0.00147 ( 3) link_NAG-ASN : bond 0.01428 ( 1) link_NAG-ASN : angle 7.84234 ( 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: 16 poor density : 140 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6457 (mt) REVERT: A 87 ARG cc_start: 0.6295 (ttt-90) cc_final: 0.5718 (ptm160) REVERT: A 125 TRP cc_start: 0.7207 (t60) cc_final: 0.6994 (t60) REVERT: A 180 GLN cc_start: 0.7466 (pm20) cc_final: 0.7153 (pm20) REVERT: A 240 SER cc_start: 0.8055 (t) cc_final: 0.7788 (p) REVERT: A 365 LYS cc_start: 0.7923 (tttp) cc_final: 0.7574 (mtpp) REVERT: A 442 ARG cc_start: 0.7253 (ttp-170) cc_final: 0.6953 (tpp80) REVERT: A 501 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7137 (pp30) REVERT: A 540 GLN cc_start: 0.6570 (mp10) cc_final: 0.6346 (mp10) REVERT: B 229 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7269 (mt-10) outliers start: 16 outliers final: 11 residues processed: 151 average time/residue: 0.1167 time to fit residues: 23.7865 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 : 0.391 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 843 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 88 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.157912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121552 restraints weight = 12581.742| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.77 r_work: 0.3032 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10496 Z= 0.098 Angle : 0.514 11.519 14200 Z= 0.259 Chirality : 0.042 0.269 1606 Planarity : 0.004 0.050 1769 Dihedral : 11.038 155.095 1790 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.38 % Allowed : 16.07 % Favored : 82.55 % 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: 0.72 (0.24), residues: 1259 helix: 1.77 (0.23), residues: 540 sheet: -0.06 (0.40), residues: 161 loop : -0.62 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.015 0.001 TYR A 881 PHE 0.014 0.001 PHE A 935 TRP 0.011 0.001 TRP A 430 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00222 (10489) covalent geometry : angle 0.50182 (14191) SS BOND : bond 0.00031 ( 3) SS BOND : angle 0.94562 ( 6) hydrogen bonds : bond 0.03308 ( 470) hydrogen bonds : angle 4.17580 ( 1377) Misc. bond : bond 0.00141 ( 3) link_NAG-ASN : bond 0.01362 ( 1) link_NAG-ASN : angle 7.52185 ( 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 156 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6287 (ttt-90) cc_final: 0.5716 (ptm160) REVERT: A 125 TRP cc_start: 0.7234 (t60) cc_final: 0.7025 (t60) REVERT: A 180 GLN cc_start: 0.7450 (pm20) cc_final: 0.7138 (pm20) REVERT: A 240 SER cc_start: 0.7987 (t) cc_final: 0.7719 (p) REVERT: A 365 LYS cc_start: 0.7882 (tttp) cc_final: 0.7589 (mtpp) REVERT: A 442 ARG cc_start: 0.7219 (ttp-170) cc_final: 0.6962 (tpp80) REVERT: A 501 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7166 (pp30) REVERT: A 540 GLN cc_start: 0.6610 (mp10) cc_final: 0.6395 (mp10) REVERT: B 229 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7254 (mt-10) outliers start: 15 outliers final: 10 residues processed: 150 average time/residue: 0.1199 time to fit residues: 24.4735 Evaluate side-chains 145 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN 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: 9.9990 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118215 restraints weight = 12770.477| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.77 r_work: 0.2985 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1699 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= 0.150 Angle : 0.571 11.265 14200 Z= 0.287 Chirality : 0.045 0.397 1606 Planarity : 0.004 0.050 1769 Dihedral : 11.508 158.620 1790 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.47 % Allowed : 16.07 % Favored : 82.46 % 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: 0.55 (0.24), residues: 1259 helix: 1.55 (0.23), residues: 538 sheet: 0.05 (0.41), residues: 150 loop : -0.67 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.019 0.001 TYR A 805 PHE 0.014 0.001 PHE A 935 TRP 0.011 0.001 TRP A 430 HIS 0.002 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00369 (10489) covalent geometry : angle 0.56083 (14191) SS BOND : bond 0.00072 ( 3) SS BOND : angle 1.24011 ( 6) hydrogen bonds : bond 0.04003 ( 470) hydrogen bonds : angle 4.32846 ( 1377) Misc. bond : bond 0.00164 ( 3) link_NAG-ASN : bond 0.01397 ( 1) link_NAG-ASN : angle 7.31238 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2475.21 seconds wall clock time: 43 minutes 2.84 seconds (2582.84 seconds total)