Starting phenix.real_space_refine on Mon Jul 28 21:47:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x24_32957/07_2025/7x24_32957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x24_32957/07_2025/7x24_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2025/7x24_32957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2025/7x24_32957.map" model { file = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2025/7x24_32957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x24_32957/07_2025/7x24_32957.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.96, per 1000 atoms: 0.68 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: 3.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.36 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: 4.72 Time building geometry restraints manager: 3.17 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: 1.410 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: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.580 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A 968 HIS 0.003 0.001 HIS A 868 PHE 0.025 0.002 PHE A 128 TYR 0.015 0.001 TYR A 805 ARG 0.007 0.000 ARG A 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01628 ( 1) link_NAG-ASN : angle 7.65119 ( 3) hydrogen bonds : bond 0.15766 ( 470) hydrogen bonds : angle 6.43657 ( 1377) SS BOND : bond 0.00132 ( 3) SS BOND : angle 1.04853 ( 6) covalent geometry : bond 0.00596 (10489) covalent geometry : angle 1.21242 (14191) Misc. bond : bond 0.00179 ( 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 : 1.375 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: 0.3229 time to fit residues: 69.0777 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 : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.160418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124877 restraints weight = 12416.724| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.71 r_work: 0.3025 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10496 Z= 0.122 Angle : 0.558 12.607 14200 Z= 0.284 Chirality : 0.043 0.161 1606 Planarity : 0.004 0.048 1769 Dihedral : 12.347 149.103 1790 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.37 % Allowed : 8.08 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1259 helix: 1.59 (0.23), residues: 531 sheet: 0.12 (0.40), residues: 149 loop : -0.70 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 902 HIS 0.002 0.001 HIS A 505 PHE 0.011 0.001 PHE A 318 TYR 0.018 0.001 TYR A 805 ARG 0.003 0.000 ARG A 87 Details of bonding type rmsd link_NAG-ASN : bond 0.01365 ( 1) link_NAG-ASN : angle 7.87558 ( 3) hydrogen bonds : bond 0.04275 ( 470) hydrogen bonds : angle 5.02479 ( 1377) SS BOND : bond 0.00079 ( 3) SS BOND : angle 1.53718 ( 6) covalent geometry : bond 0.00277 (10489) covalent geometry : angle 0.54580 (14191) Misc. bond : bond 0.00180 ( 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 146 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6157 (ttt-90) cc_final: 0.5603 (ptm160) REVERT: A 180 GLN cc_start: 0.7699 (pm20) cc_final: 0.7463 (pm20) REVERT: A 365 LYS cc_start: 0.7923 (tttp) cc_final: 0.7652 (mtpp) REVERT: A 457 ARG cc_start: 0.7369 (mtt180) cc_final: 0.7144 (mtt180) REVERT: A 860 GLN cc_start: 0.8049 (mp10) cc_final: 0.7739 (mm110) outliers start: 4 outliers final: 3 residues processed: 143 average time/residue: 0.2773 time to fit residues: 54.0434 Evaluate side-chains 136 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 806 ILE 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 111 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3719 r_free = 0.3719 target = 0.157859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122092 restraints weight = 12619.461| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.62 r_work: 0.3043 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1074 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= 0.165 Angle : 0.595 13.062 14200 Z= 0.300 Chirality : 0.044 0.165 1606 Planarity : 0.004 0.049 1769 Dihedral : 12.392 150.376 1790 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.29 % Allowed : 9.83 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1259 helix: 1.45 (0.23), residues: 529 sheet: -0.12 (0.40), residues: 152 loop : -0.72 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1001 HIS 0.003 0.001 HIS A 868 PHE 0.012 0.002 PHE A 935 TYR 0.019 0.001 TYR A 881 ARG 0.002 0.000 ARG A 920 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 1) link_NAG-ASN : angle 8.66224 ( 3) hydrogen bonds : bond 0.04473 ( 470) hydrogen bonds : angle 4.73696 ( 1377) SS BOND : bond 0.00033 ( 3) SS BOND : angle 1.55169 ( 6) covalent geometry : bond 0.00399 (10489) covalent geometry : angle 0.58048 (14191) Misc. bond : bond 0.00180 ( 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 149 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6869 (mt) REVERT: A 87 ARG cc_start: 0.6173 (ttt-90) cc_final: 0.5658 (ptm160) REVERT: A 180 GLN cc_start: 0.7683 (pm20) cc_final: 0.7439 (pm20) REVERT: A 365 LYS cc_start: 0.7966 (tttp) cc_final: 0.7670 (mtpp) REVERT: A 473 GLU cc_start: 0.7765 (tp30) cc_final: 0.7474 (tp30) REVERT: B 103 LEU cc_start: 0.8266 (mt) cc_final: 0.7958 (mm) outliers start: 14 outliers final: 8 residues processed: 142 average time/residue: 0.2640 time to fit residues: 51.5499 Evaluate side-chains 139 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 502 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** 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 = 0.3714 r_free = 0.3714 target = 0.157333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121743 restraints weight = 12473.315| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.58 r_work: 0.3031 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10496 Z= 0.148 Angle : 0.567 13.030 14200 Z= 0.289 Chirality : 0.044 0.159 1606 Planarity : 0.004 0.048 1769 Dihedral : 12.305 151.398 1790 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.19 % Allowed : 12.67 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1259 helix: 1.42 (0.23), residues: 529 sheet: -0.10 (0.41), residues: 150 loop : -0.71 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 PHE 0.013 0.001 PHE A 935 TYR 0.018 0.001 TYR A 881 ARG 0.004 0.000 ARG A 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01709 ( 1) link_NAG-ASN : angle 8.44637 ( 3) hydrogen bonds : bond 0.04164 ( 470) hydrogen bonds : angle 4.58453 ( 1377) SS BOND : bond 0.00027 ( 3) SS BOND : angle 1.32331 ( 6) covalent geometry : bond 0.00354 (10489) covalent geometry : angle 0.55295 (14191) Misc. bond : bond 0.00184 ( 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 148 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6266 (ttt-90) cc_final: 0.5705 (ptm160) REVERT: A 125 TRP cc_start: 0.7322 (t60) cc_final: 0.7070 (t60) REVERT: A 180 GLN cc_start: 0.7675 (pm20) cc_final: 0.7404 (pm20) REVERT: A 233 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 365 LYS cc_start: 0.7999 (tttp) cc_final: 0.7670 (mtpp) REVERT: B 103 LEU cc_start: 0.8231 (mt) cc_final: 0.7958 (mm) REVERT: B 229 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7569 (mm-30) outliers start: 13 outliers final: 13 residues processed: 141 average time/residue: 0.2735 time to fit residues: 52.5827 Evaluate side-chains 143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 271 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 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 108 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** 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 = 0.3690 r_free = 0.3690 target = 0.154940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119827 restraints weight = 12683.101| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.81 r_work: 0.2935 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10496 Z= 0.133 Angle : 0.549 13.154 14200 Z= 0.278 Chirality : 0.043 0.158 1606 Planarity : 0.004 0.048 1769 Dihedral : 12.250 152.268 1790 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.38 % Allowed : 13.41 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1259 helix: 1.39 (0.23), residues: 537 sheet: -0.06 (0.41), residues: 150 loop : -0.69 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 PHE 0.013 0.001 PHE A 935 TYR 0.017 0.001 TYR A 881 ARG 0.002 0.000 ARG A 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01871 ( 1) link_NAG-ASN : angle 8.55052 ( 3) hydrogen bonds : bond 0.03990 ( 470) hydrogen bonds : angle 4.50054 ( 1377) SS BOND : bond 0.00020 ( 3) SS BOND : angle 1.25795 ( 6) covalent geometry : bond 0.00316 (10489) covalent geometry : angle 0.53471 (14191) Misc. bond : bond 0.00181 ( 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 149 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6865 (mt) REVERT: A 87 ARG cc_start: 0.6201 (ttt-90) cc_final: 0.5668 (ptm160) REVERT: A 125 TRP cc_start: 0.7260 (t60) cc_final: 0.7019 (t60) REVERT: A 180 GLN cc_start: 0.7622 (pm20) cc_final: 0.7317 (pm20) REVERT: A 233 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 365 LYS cc_start: 0.7977 (tttp) cc_final: 0.7643 (mtpp) REVERT: A 501 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7084 (pp30) REVERT: B 229 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7442 (mm-30) outliers start: 15 outliers final: 12 residues processed: 143 average time/residue: 0.3048 time to fit residues: 59.9828 Evaluate side-chains 145 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 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 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 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 17 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 chunk 45 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 569 HIS A 689 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3703 r_free = 0.3703 target = 0.156410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121271 restraints weight = 12544.580| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.71 r_work: 0.2979 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1469 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= 0.160 Angle : 0.583 12.987 14200 Z= 0.295 Chirality : 0.044 0.158 1606 Planarity : 0.004 0.051 1769 Dihedral : 12.415 155.129 1790 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.93 % Allowed : 13.77 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1259 helix: 1.30 (0.23), residues: 534 sheet: -0.09 (0.41), residues: 147 loop : -0.68 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1001 HIS 0.003 0.001 HIS A 868 PHE 0.014 0.002 PHE A 935 TYR 0.018 0.001 TYR A 881 ARG 0.004 0.000 ARG A 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01579 ( 1) link_NAG-ASN : angle 8.51048 ( 3) hydrogen bonds : bond 0.04279 ( 470) hydrogen bonds : angle 4.56661 ( 1377) SS BOND : bond 0.00080 ( 3) SS BOND : angle 1.48804 ( 6) covalent geometry : bond 0.00391 (10489) covalent geometry : angle 0.56861 (14191) Misc. bond : bond 0.00196 ( 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 161 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6900 (mt) REVERT: A 87 ARG cc_start: 0.6268 (ttt-90) cc_final: 0.5710 (ptm160) REVERT: A 125 TRP cc_start: 0.7382 (t60) cc_final: 0.7154 (t60) REVERT: A 180 GLN cc_start: 0.7604 (pm20) cc_final: 0.7298 (pm20) REVERT: A 233 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 365 LYS cc_start: 0.7973 (tttp) cc_final: 0.7645 (mtpp) REVERT: A 442 ARG cc_start: 0.7245 (ttp-170) cc_final: 0.6887 (tpp80) REVERT: A 501 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7013 (pp30) REVERT: A 875 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8489 (mp) REVERT: B 220 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7428 (pm20) REVERT: B 229 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7645 (mm-30) outliers start: 21 outliers final: 16 residues processed: 153 average time/residue: 0.2943 time to fit residues: 61.6681 Evaluate side-chains 157 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** 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 = 0.3700 r_free = 0.3700 target = 0.155968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120540 restraints weight = 12750.569| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.74 r_work: 0.3016 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10496 Z= 0.124 Angle : 0.544 12.621 14200 Z= 0.276 Chirality : 0.043 0.152 1606 Planarity : 0.004 0.051 1769 Dihedral : 12.154 154.713 1790 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.65 % Allowed : 14.97 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1259 helix: 1.41 (0.23), residues: 537 sheet: -0.02 (0.41), residues: 149 loop : -0.68 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1001 HIS 0.001 0.000 HIS A 868 PHE 0.013 0.001 PHE A 935 TYR 0.017 0.001 TYR A 881 ARG 0.004 0.000 ARG A 485 Details of bonding type rmsd link_NAG-ASN : bond 0.01327 ( 1) link_NAG-ASN : angle 8.27227 ( 3) hydrogen bonds : bond 0.03884 ( 470) hydrogen bonds : angle 4.43427 ( 1377) SS BOND : bond 0.00021 ( 3) SS BOND : angle 1.22705 ( 6) covalent geometry : bond 0.00293 (10489) covalent geometry : angle 0.52980 (14191) Misc. bond : bond 0.00175 ( 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 156 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6228 (ttt-90) cc_final: 0.5678 (ptm160) REVERT: A 125 TRP cc_start: 0.7371 (t60) cc_final: 0.7151 (t60) REVERT: A 180 GLN cc_start: 0.7596 (pm20) cc_final: 0.7292 (pm20) REVERT: A 233 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 240 SER cc_start: 0.8173 (t) cc_final: 0.7877 (p) REVERT: A 281 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7364 (mtp85) REVERT: A 365 LYS cc_start: 0.7987 (tttp) cc_final: 0.7662 (mtpp) REVERT: A 442 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.6898 (tpp80) REVERT: A 501 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7052 (pp30) REVERT: B 220 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: B 229 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7638 (mm-30) outliers start: 18 outliers final: 13 residues processed: 152 average time/residue: 0.2635 time to fit residues: 54.7559 Evaluate side-chains 150 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 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 947 ILE 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 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 53 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 117 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** 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 = 0.3715 r_free = 0.3715 target = 0.157212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122123 restraints weight = 12646.359| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.81 r_work: 0.2981 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10496 Z= 0.114 Angle : 0.542 12.276 14200 Z= 0.275 Chirality : 0.042 0.206 1606 Planarity : 0.004 0.051 1769 Dihedral : 11.881 154.739 1790 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.56 % Allowed : 15.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1259 helix: 1.50 (0.23), residues: 537 sheet: -0.26 (0.40), residues: 161 loop : -0.67 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1001 HIS 0.001 0.000 HIS A 868 PHE 0.013 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG A 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01416 ( 1) link_NAG-ASN : angle 7.78279 ( 3) hydrogen bonds : bond 0.03670 ( 470) hydrogen bonds : angle 4.36269 ( 1377) SS BOND : bond 0.00010 ( 3) SS BOND : angle 1.21061 ( 6) covalent geometry : bond 0.00266 (10489) covalent geometry : angle 0.52944 (14191) Misc. bond : bond 0.00165 ( 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 160 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6200 (ttt-90) cc_final: 0.5663 (ptm160) REVERT: A 125 TRP cc_start: 0.7236 (t60) cc_final: 0.7030 (t60) REVERT: A 180 GLN cc_start: 0.7501 (pm20) cc_final: 0.7187 (pm20) REVERT: A 240 SER cc_start: 0.8025 (t) cc_final: 0.7752 (p) REVERT: A 281 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7218 (mtp85) REVERT: A 365 LYS cc_start: 0.7939 (tttp) cc_final: 0.7612 (mtpp) REVERT: A 442 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6929 (tpp80) REVERT: A 501 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6971 (pp30) REVERT: B 220 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: B 229 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7347 (mm-30) outliers start: 17 outliers final: 12 residues processed: 156 average time/residue: 0.3619 time to fit residues: 77.7214 Evaluate side-chains 148 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 362 ARG 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 843 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 219 ASP Chi-restraints excluded: chain B residue 220 GLU 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 109 optimal weight: 0.0570 chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 118 optimal weight: 0.0970 chunk 112 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.158821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122860 restraints weight = 12730.678| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.68 r_work: 0.3055 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10496 Z= 0.097 Angle : 0.518 12.157 14200 Z= 0.263 Chirality : 0.042 0.307 1606 Planarity : 0.004 0.051 1769 Dihedral : 11.324 153.712 1790 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1259 helix: 1.70 (0.23), residues: 539 sheet: -0.07 (0.40), residues: 161 loop : -0.63 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1001 HIS 0.001 0.000 HIS A 551 PHE 0.013 0.001 PHE A 935 TYR 0.014 0.001 TYR A 881 ARG 0.004 0.000 ARG A 80 Details of bonding type rmsd link_NAG-ASN : bond 0.02089 ( 1) link_NAG-ASN : angle 7.93994 ( 3) hydrogen bonds : bond 0.03249 ( 470) hydrogen bonds : angle 4.20566 ( 1377) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.80503 ( 6) covalent geometry : bond 0.00212 (10489) covalent geometry : angle 0.50537 (14191) Misc. bond : bond 0.00148 ( 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 159 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6354 (ttt-90) cc_final: 0.5815 (ptm160) REVERT: A 125 TRP cc_start: 0.7361 (t60) cc_final: 0.7139 (t60) REVERT: A 180 GLN cc_start: 0.7535 (pm20) cc_final: 0.7232 (pm20) REVERT: A 240 SER cc_start: 0.8054 (t) cc_final: 0.7792 (p) REVERT: A 281 ARG cc_start: 0.7764 (mmm160) cc_final: 0.7368 (mtp85) REVERT: A 365 LYS cc_start: 0.7963 (tttp) cc_final: 0.7654 (mtpp) REVERT: A 442 ARG cc_start: 0.7270 (ttp-170) cc_final: 0.6967 (tpp80) REVERT: A 501 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7078 (pp30) REVERT: B 229 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7479 (mm-30) outliers start: 16 outliers final: 8 residues processed: 156 average time/residue: 0.2680 time to fit residues: 57.5392 Evaluate side-chains 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 966 VAL 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 219 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 52 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3729 r_free = 0.3729 target = 0.158522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123008 restraints weight = 12695.036| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.75 r_work: 0.3001 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10496 Z= 0.109 Angle : 0.540 12.094 14200 Z= 0.270 Chirality : 0.043 0.342 1606 Planarity : 0.004 0.050 1769 Dihedral : 11.281 154.995 1790 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.10 % Allowed : 16.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1259 helix: 1.69 (0.23), residues: 538 sheet: -0.05 (0.40), residues: 161 loop : -0.65 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 430 HIS 0.002 0.000 HIS A 505 PHE 0.028 0.001 PHE A 128 TYR 0.018 0.001 TYR A 805 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd link_NAG-ASN : bond 0.01878 ( 1) link_NAG-ASN : angle 7.84227 ( 3) hydrogen bonds : bond 0.03490 ( 470) hydrogen bonds : angle 4.26091 ( 1377) SS BOND : bond 0.00034 ( 3) SS BOND : angle 0.90797 ( 6) covalent geometry : bond 0.00252 (10489) covalent geometry : angle 0.52779 (14191) Misc. bond : bond 0.00147 ( 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 153 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6362 (ttt-90) cc_final: 0.5824 (ptm160) REVERT: A 125 TRP cc_start: 0.7267 (t60) cc_final: 0.7054 (t60) REVERT: A 180 GLN cc_start: 0.7517 (pm20) cc_final: 0.7207 (pm20) REVERT: A 240 SER cc_start: 0.8084 (t) cc_final: 0.7817 (p) REVERT: A 365 LYS cc_start: 0.7952 (tttp) cc_final: 0.7605 (mtpp) REVERT: A 442 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.6993 (tpp80) REVERT: A 457 ARG cc_start: 0.7264 (mtt180) cc_final: 0.6771 (ttt180) REVERT: A 501 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7177 (pp30) REVERT: B 229 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7321 (mm-30) outliers start: 12 outliers final: 9 residues processed: 150 average time/residue: 0.2698 time to fit residues: 55.1020 Evaluate side-chains 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 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 966 VAL 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 219 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 109 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 27 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS ** B 193 ASN ** 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 = 0.3764 r_free = 0.3764 target = 0.161869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127303 restraints weight = 12445.991| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.70 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: 0.8067 moved from start: 0.1826 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= 0.094 Angle : 0.520 11.895 14200 Z= 0.261 Chirality : 0.042 0.345 1606 Planarity : 0.004 0.051 1769 Dihedral : 10.942 154.604 1790 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.10 % Allowed : 16.53 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1259 helix: 1.79 (0.23), residues: 539 sheet: 0.01 (0.40), residues: 161 loop : -0.58 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1001 HIS 0.002 0.000 HIS A 505 PHE 0.026 0.001 PHE A 128 TYR 0.014 0.001 TYR A 881 ARG 0.004 0.000 ARG A 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01748 ( 1) link_NAG-ASN : angle 7.73427 ( 3) hydrogen bonds : bond 0.03173 ( 470) hydrogen bonds : angle 4.15903 ( 1377) SS BOND : bond 0.00091 ( 3) SS BOND : angle 0.75064 ( 6) covalent geometry : bond 0.00208 (10489) covalent geometry : angle 0.50791 (14191) Misc. bond : bond 0.00137 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6505.27 seconds wall clock time: 116 minutes 41.16 seconds (7001.16 seconds total)