Starting phenix.real_space_refine on Fri Sep 11 19:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ylb_73079/09_2026/9ylb_73079.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ylb_73079/09_2026/9ylb_73079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ylb_73079/09_2026/9ylb_73079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ylb_73079/09_2026/9ylb_73079.map" model { file = "/net/cci-nas-00/data/ceres_data/9ylb_73079/09_2026/9ylb_73079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ylb_73079/09_2026/9ylb_73079.cif" } resolution = 3.24 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= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 57 5.16 5 C 6921 2.51 5 N 1828 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10855 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7786 Classifications: {'peptide': 983} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 930} Chain breaks: 1 Chain: "B" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1850 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 209} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1160 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.22 Number of scatterers: 10855 At special positions: 0 Unit cell: (88.561, 104.566, 129.107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 7 15.00 O 2042 8.00 N 1828 7.00 C 6921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS B 188 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 388.2 milliseconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 39.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.092A pdb=" N TYR A 49 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 50 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.799A pdb=" N LYS A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.621A pdb=" N GLY A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.892A pdb=" N VAL A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 114' Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.562A pdb=" N VAL A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 4.000A pdb=" N ASN A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.792A pdb=" N SER A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 320 through 340 Processing helix chain 'A' and resid 347 through 363 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 387 through 408 Processing helix chain 'A' and resid 421 through 427 removed outlier: 4.386A pdb=" N VAL A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.897A pdb=" N GLU A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 546 through 550 removed outlier: 3.661A pdb=" N GLU A 550 " --> pdb=" O PRO A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.704A pdb=" N THR A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 663 Processing helix chain 'A' and resid 669 through 675 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.131A pdb=" N VAL A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 686 " --> pdb=" O CYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 712 Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.904A pdb=" N LEU A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 769 Processing helix chain 'A' and resid 779 through 788 removed outlier: 3.525A pdb=" N ASN A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 894 through 914 removed outlier: 3.555A pdb=" N THR A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 914 " --> pdb=" O ILE A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 980 Processing helix chain 'A' and resid 1001 through 1005 removed outlier: 3.733A pdb=" N LEU A1005 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1014 removed outlier: 3.511A pdb=" N LYS A1014 " --> pdb=" O HIS A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.775A pdb=" N MET B 217 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 251 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 267 through 289 removed outlier: 3.517A pdb=" N LYS B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASP B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N PHE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.690A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLN B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.851A pdb=" N ILE C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.305A pdb=" N TYR C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 67' Processing helix chain 'C' and resid 111 through 121 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.683A pdb=" N GLN C 130 " --> pdb=" O PRO C 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.504A pdb=" N VAL A 88 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER A 138 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 90 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 64 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N HIS A 91 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N HIS A 63 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL A 158 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 65 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 160 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER A 67 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 157 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA A 186 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A 159 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N VAL A 188 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 183 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 262 removed outlier: 6.781A pdb=" N LEU A 245 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN A 290 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE A 247 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA A 288 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU A 249 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS A 284 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N HIS A 284 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ASN A 220 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY A 286 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.197A pdb=" N ILE A 493 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS A 541 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 495 " --> pdb=" O HIS A 541 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN A 462 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE A 565 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE A 464 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 591 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL A 602 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LYS A 922 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 944 through 946 Processing sheet with id=AA6, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.739A pdb=" N TRP A 958 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR A1046 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 960 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 985 " --> pdb=" O SER A1027 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.739A pdb=" N TRP A 958 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR A1046 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 960 " --> pdb=" O TYR A1046 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 134 through 136 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 107 removed outlier: 3.630A pdb=" N LEU C 104 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N LEU C 156 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C 91 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU C 158 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL C 93 " --> pdb=" O LEU C 158 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1107 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: 1.94 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2813 1.33 - 1.45: 1903 1.45 - 1.57: 6292 1.57 - 1.69: 10 1.69 - 1.81: 87 Bond restraints: 11105 Sorted by residual: bond pdb=" C1' AMP C1101 " pdb=" O4' AMP C1101 " ideal model delta sigma weight residual 1.415 1.661 -0.246 1.50e-02 4.44e+03 2.68e+02 bond pdb=" C1' AMP C1101 " pdb=" C2' AMP C1101 " ideal model delta sigma weight residual 1.526 1.330 0.196 1.50e-02 4.44e+03 1.72e+02 bond pdb=" C4' AMP C1101 " pdb=" O4' AMP C1101 " ideal model delta sigma weight residual 1.454 1.311 0.143 1.50e-02 4.44e+03 9.06e+01 bond pdb=" C ILE C 163 " pdb=" N GLY C 164 " ideal model delta sigma weight residual 1.331 1.216 0.115 1.53e-02 4.27e+03 5.69e+01 bond pdb=" C3' AMP C1101 " pdb=" O3' AMP C1101 " ideal model delta sigma weight residual 1.427 1.330 0.097 1.50e-02 4.44e+03 4.15e+01 ... (remaining 11100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 14870 2.75 - 5.50: 163 5.50 - 8.24: 16 8.24 - 10.99: 7 10.99 - 13.74: 2 Bond angle restraints: 15058 Sorted by residual: angle pdb=" N VAL C 37 " pdb=" CA VAL C 37 " pdb=" C VAL C 37 " ideal model delta sigma weight residual 113.71 107.66 6.05 9.50e-01 1.11e+00 4.05e+01 angle pdb=" N ILE B 160 " pdb=" CA ILE B 160 " pdb=" C ILE B 160 " ideal model delta sigma weight residual 113.20 107.87 5.33 9.60e-01 1.09e+00 3.08e+01 angle pdb=" CA PRO A 431 " pdb=" N PRO A 431 " pdb=" CD PRO A 431 " ideal model delta sigma weight residual 112.00 105.21 6.79 1.40e+00 5.10e-01 2.35e+01 angle pdb=" O2P AMP C1101 " pdb=" P AMP C1101 " pdb=" O3P AMP C1101 " ideal model delta sigma weight residual 119.90 106.63 13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" CA LEU A 688 " pdb=" CB LEU A 688 " pdb=" CG LEU A 688 " ideal model delta sigma weight residual 116.30 130.04 -13.74 3.50e+00 8.16e-02 1.54e+01 ... (remaining 15053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 6384 32.72 - 65.45: 352 65.45 - 98.17: 21 98.17 - 130.89: 9 130.89 - 163.61: 3 Dihedral angle restraints: 6769 sinusoidal: 2801 harmonic: 3968 Sorted by residual: dihedral pdb=" C5' AMP C1101 " pdb=" O5' AMP C1101 " pdb=" P AMP C1101 " pdb=" O3P AMP C1101 " ideal model delta sinusoidal sigma weight residual -60.00 -178.10 118.10 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" CB CYS A 625 " pdb=" SG CYS A 625 " pdb=" SG CYS B 188 " pdb=" CB CYS B 188 " ideal model delta sinusoidal sigma weight residual -86.00 -135.06 49.06 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" C6 IHP A1101 " pdb=" C1 IHP A1101 " pdb=" C2 IHP A1101 " pdb=" O12 IHP A1101 " ideal model delta sinusoidal sigma weight residual 61.05 -102.56 163.61 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 6766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.955: 1688 0.955 - 1.910: 0 1.910 - 2.865: 0 2.865 - 3.820: 0 3.820 - 4.774: 3 Chirality restraints: 1691 Sorted by residual: chirality pdb=" C2 IHP A1101 " pdb=" C1 IHP A1101 " pdb=" C3 IHP A1101 " pdb=" O12 IHP A1101 " both_signs ideal model delta sigma weight residual False -2.52 2.26 -4.77 2.00e-01 2.50e+01 5.70e+02 chirality pdb=" C4 IHP A1101 " pdb=" C3 IHP A1101 " pdb=" C5 IHP A1101 " pdb=" O14 IHP A1101 " both_signs ideal model delta sigma weight residual False 2.48 -2.23 4.71 2.00e-01 2.50e+01 5.54e+02 chirality pdb=" C1 IHP A1101 " pdb=" C2 IHP A1101 " pdb=" C6 IHP A1101 " pdb=" O11 IHP A1101 " both_signs ideal model delta sigma weight residual False 2.32 -1.99 4.31 2.00e-01 2.50e+01 4.64e+02 ... (remaining 1688 not shown) Planarity restraints: 1924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 513 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO A 514 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 735 " 0.019 2.00e-02 2.50e+03 1.39e-02 4.84e+00 pdb=" CG TRP A 735 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 735 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 735 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 735 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 735 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 735 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 735 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 735 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 735 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 178 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B 179 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.025 5.00e-02 4.00e+02 ... (remaining 1921 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 211 2.68 - 3.23: 10313 3.23 - 3.79: 16402 3.79 - 4.34: 21718 4.34 - 4.90: 36664 Nonbonded interactions: 85308 Sorted by model distance: nonbonded pdb=" O CYS B 188 " pdb=" OG1 THR B 194 " model vdw 2.121 3.040 nonbonded pdb=" O GLY B 145 " pdb=" OH TYR B 282 " model vdw 2.186 3.040 nonbonded pdb=" OG SER A 108 " pdb=" OD1 ASP A 110 " model vdw 2.186 3.040 nonbonded pdb=" OG SER A 779 " pdb=" OD1 ASP A 781 " model vdw 2.195 3.040 nonbonded pdb=" NH2 ARG A 947 " pdb=" O ALA A1029 " model vdw 2.228 3.120 ... (remaining 85303 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: 1.080 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 0.246 11107 Z= 0.351 Angle : 0.704 13.741 15060 Z= 0.352 Chirality : 0.199 4.774 1691 Planarity : 0.004 0.081 1924 Dihedral : 19.230 163.613 4194 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.05 % Favored : 91.58 % Rotamer: Outliers : 1.41 % Allowed : 28.52 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.42 (0.24), residues: 1354 helix: 1.02 (0.24), residues: 490 sheet: -0.18 (0.40), residues: 196 loop : -1.31 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 615 TYR 0.016 0.001 TYR A 994 PHE 0.019 0.001 PHE A 656 TRP 0.038 0.002 TRP A 735 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.34 (11105) covalent geometry : angle 0.70366 / 0.35 (15058) SS BOND : bond 0.00387 / 0.20 ( 1) SS BOND : angle 0.33907 / 0.17 ( 2) hydrogen bonds : bond 0.14062 / 9.40 ( 389) hydrogen bonds : angle 6.12532 / 4.30 ( 1107) Misc. bond : bond 0.08241 / 4.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8215 (t70) cc_final: 0.7975 (t0) REVERT: B 315 MET cc_start: 0.7317 (ptt) cc_final: 0.6950 (mpp) REVERT: C 42 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6986 (tppt) outliers start: 17 outliers final: 5 residues processed: 133 average time/residue: 0.1110 time to fit residues: 21.0647 Evaluate side-chains 125 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.183938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140898 restraints weight = 11119.026| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.35 r_work: 0.2906 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11107 Z= 0.162 Angle : 0.627 11.400 15060 Z= 0.299 Chirality : 0.044 0.299 1691 Planarity : 0.004 0.054 1924 Dihedral : 10.655 83.888 1514 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.24 % Favored : 92.47 % Rotamer: Outliers : 4.31 % Allowed : 25.79 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1354 helix: 0.92 (0.24), residues: 497 sheet: -0.11 (0.41), residues: 187 loop : -1.33 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 48 TYR 0.014 0.001 TYR A 994 PHE 0.019 0.001 PHE A 510 TRP 0.015 0.001 TRP A 735 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (11105) covalent geometry : angle 0.62672 / 0.30 (15058) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 0.36292 / 0.18 ( 2) hydrogen bonds : bond 0.04148 / 2.79 ( 389) hydrogen bonds : angle 4.90388 / 3.44 ( 1107) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 0.411 Fit side-chains REVERT: A 153 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8377 (pttp) REVERT: A 515 HIS cc_start: 0.6415 (OUTLIER) cc_final: 0.6150 (m170) REVERT: A 572 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7375 (pp20) REVERT: A 922 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8716 (ptpp) REVERT: A 991 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.5938 (tttt) REVERT: B 297 MET cc_start: 0.6808 (mmt) cc_final: 0.6605 (mmm) outliers start: 52 outliers final: 25 residues processed: 162 average time/residue: 0.1126 time to fit residues: 26.0974 Evaluate side-chains 150 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 132 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 107 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 76 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 HIS A 543 ASN ** A 736 GLN ** 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 = 0.3810 r_free = 0.3810 target = 0.169736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122957 restraints weight = 11389.844| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.17 r_work: 0.3149 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11107 Z= 0.112 Angle : 0.601 13.266 15060 Z= 0.280 Chirality : 0.043 0.310 1691 Planarity : 0.004 0.048 1924 Dihedral : 9.964 79.143 1506 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.94 % Favored : 92.76 % Rotamer: Outliers : 4.15 % Allowed : 26.37 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1354 helix: 1.05 (0.24), residues: 494 sheet: -0.40 (0.39), residues: 200 loop : -1.22 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 316 TYR 0.012 0.001 TYR A 994 PHE 0.019 0.001 PHE A 510 TRP 0.013 0.001 TRP A 735 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (11105) covalent geometry : angle 0.60115 / 0.28 (15058) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.27623 / 0.14 ( 2) hydrogen bonds : bond 0.03473 / 2.34 ( 389) hydrogen bonds : angle 4.58778 / 3.21 ( 1107) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8313 (pttp) REVERT: A 510 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7828 (p90) REVERT: A 572 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: A 663 TYR cc_start: 0.7056 (m-10) cc_final: 0.6741 (m-10) REVERT: A 764 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8507 (mm) REVERT: A 836 GLU cc_start: 0.0354 (OUTLIER) cc_final: 0.0029 (pm20) REVERT: A 991 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.6057 (tttt) REVERT: B 186 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7329 (mttm) REVERT: B 297 MET cc_start: 0.6851 (mmt) cc_final: 0.6630 (mmm) REVERT: B 315 MET cc_start: 0.7387 (ptt) cc_final: 0.6820 (mpp) outliers start: 50 outliers final: 33 residues processed: 164 average time/residue: 0.0980 time to fit residues: 23.6303 Evaluate side-chains 158 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 147 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 119 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.183277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139850 restraints weight = 11213.529| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.59 r_work: 0.2907 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11107 Z= 0.166 Angle : 0.625 13.782 15060 Z= 0.292 Chirality : 0.044 0.311 1691 Planarity : 0.004 0.048 1924 Dihedral : 9.634 76.156 1506 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.39 % Favored : 92.32 % Rotamer: Outliers : 5.47 % Allowed : 26.20 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1354 helix: 0.93 (0.24), residues: 495 sheet: -0.51 (0.39), residues: 199 loop : -1.27 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 316 TYR 0.014 0.001 TYR A 994 PHE 0.021 0.001 PHE A 510 TRP 0.011 0.001 TRP A 735 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (11105) covalent geometry : angle 0.62478 / 0.29 (15058) SS BOND : bond 0.00207 / 0.11 ( 1) SS BOND : angle 0.44143 / 0.26 ( 2) hydrogen bonds : bond 0.03731 / 2.48 ( 389) hydrogen bonds : angle 4.61501 / 3.23 ( 1107) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 121 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8336 (pttp) REVERT: A 510 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7574 (p90) REVERT: A 515 HIS cc_start: 0.6328 (OUTLIER) cc_final: 0.6040 (m170) REVERT: A 572 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: A 687 LYS cc_start: 0.6827 (tptt) cc_final: 0.6493 (ttmt) REVERT: A 736 GLN cc_start: 0.7388 (mt0) cc_final: 0.7069 (mt0) REVERT: A 764 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 836 GLU cc_start: 0.0353 (OUTLIER) cc_final: 0.0022 (pm20) REVERT: A 991 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.5862 (tttt) REVERT: A 992 MET cc_start: 0.8654 (mmt) cc_final: 0.7925 (mmm) REVERT: B 186 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7301 (mttm) REVERT: B 297 MET cc_start: 0.6718 (mmt) cc_final: 0.6511 (mmm) REVERT: B 315 MET cc_start: 0.7675 (ptt) cc_final: 0.6975 (mpp) outliers start: 66 outliers final: 46 residues processed: 170 average time/residue: 0.0969 time to fit residues: 24.0984 Evaluate side-chains 171 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.184523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141674 restraints weight = 11198.809| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.35 r_work: 0.2913 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11107 Z= 0.124 Angle : 0.596 11.436 15060 Z= 0.278 Chirality : 0.043 0.326 1691 Planarity : 0.004 0.048 1924 Dihedral : 9.264 73.676 1504 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.02 % Favored : 92.69 % Rotamer: Outliers : 5.31 % Allowed : 26.45 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 (0.23), residues: 1354 helix: 1.01 (0.24), residues: 495 sheet: -0.50 (0.39), residues: 200 loop : -1.27 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 316 TYR 0.013 0.001 TYR A 994 PHE 0.020 0.001 PHE A 510 TRP 0.012 0.001 TRP A 735 HIS 0.005 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 (11105) covalent geometry : angle 0.59593 / 0.28 (15058) SS BOND : bond 0.00148 / 0.08 ( 1) SS BOND : angle 0.30563 / 0.17 ( 2) hydrogen bonds : bond 0.03376 / 2.25 ( 389) hydrogen bonds : angle 4.47709 / 3.13 ( 1107) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 121 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8366 (pttp) REVERT: A 510 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7656 (p90) REVERT: A 515 HIS cc_start: 0.6328 (OUTLIER) cc_final: 0.6018 (m170) REVERT: A 572 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7384 (pp20) REVERT: A 687 LYS cc_start: 0.6917 (tptt) cc_final: 0.6571 (ttmt) REVERT: A 736 GLN cc_start: 0.7399 (mt0) cc_final: 0.7198 (mt0) REVERT: A 764 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8442 (mm) REVERT: A 991 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.6020 (tttt) REVERT: A 992 MET cc_start: 0.8670 (mmt) cc_final: 0.7997 (mmm) REVERT: B 186 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7451 (mttm) REVERT: B 297 MET cc_start: 0.6824 (mmt) cc_final: 0.6595 (mmm) REVERT: B 315 MET cc_start: 0.7644 (ptt) cc_final: 0.7218 (mpp) outliers start: 64 outliers final: 47 residues processed: 169 average time/residue: 0.1025 time to fit residues: 25.0613 Evaluate side-chains 171 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 147 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.186450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.148106 restraints weight = 11167.859| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.06 r_work: 0.2965 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11107 Z= 0.108 Angle : 0.589 15.036 15060 Z= 0.273 Chirality : 0.042 0.342 1691 Planarity : 0.004 0.048 1924 Dihedral : 8.875 70.289 1504 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.16 % Favored : 92.54 % Rotamer: Outliers : 5.31 % Allowed : 26.45 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.32 (0.24), residues: 1354 helix: 1.16 (0.24), residues: 490 sheet: -0.49 (0.39), residues: 200 loop : -1.17 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 316 TYR 0.032 0.001 TYR B 158 PHE 0.019 0.001 PHE A 510 TRP 0.011 0.001 TRP A 735 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (11105) covalent geometry : angle 0.58861 / 0.27 (15058) SS BOND : bond 0.00108 / 0.06 ( 1) SS BOND : angle 0.22413 / 0.12 ( 2) hydrogen bonds : bond 0.03111 / 2.08 ( 389) hydrogen bonds : angle 4.35763 / 3.05 ( 1107) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7665 (p90) REVERT: A 515 HIS cc_start: 0.6406 (OUTLIER) cc_final: 0.6080 (m170) REVERT: A 572 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7328 (pp20) REVERT: A 736 GLN cc_start: 0.7424 (mt0) cc_final: 0.7142 (mt0) REVERT: A 764 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8444 (mm) REVERT: A 991 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.6069 (tttt) REVERT: A 992 MET cc_start: 0.8604 (mmt) cc_final: 0.7939 (mmm) REVERT: B 186 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7355 (mttm) REVERT: B 297 MET cc_start: 0.6829 (mmt) cc_final: 0.6609 (mmm) REVERT: B 315 MET cc_start: 0.7499 (ptt) cc_final: 0.7013 (mpp) outliers start: 64 outliers final: 43 residues processed: 178 average time/residue: 0.1046 time to fit residues: 26.9659 Evaluate side-chains 169 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 147 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 460 ASN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN B 180 ASN C 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.185360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.147075 restraints weight = 11106.077| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.02 r_work: 0.2977 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11107 Z= 0.139 Angle : 0.601 13.365 15060 Z= 0.282 Chirality : 0.043 0.341 1691 Planarity : 0.004 0.048 1924 Dihedral : 8.606 67.396 1504 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.61 % Favored : 92.10 % Rotamer: Outliers : 5.39 % Allowed : 26.04 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1354 helix: 1.06 (0.24), residues: 491 sheet: -0.32 (0.40), residues: 190 loop : -1.23 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 289 TYR 0.047 0.001 TYR B 158 PHE 0.020 0.001 PHE A 510 TRP 0.010 0.001 TRP A 735 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (11105) covalent geometry : angle 0.60104 / 0.28 (15058) SS BOND : bond 0.00256 / 0.13 ( 1) SS BOND : angle 0.52139 / 0.30 ( 2) hydrogen bonds : bond 0.03398 / 2.25 ( 389) hydrogen bonds : angle 4.43471 / 3.10 ( 1107) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 125 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7714 (p90) REVERT: A 515 HIS cc_start: 0.6474 (OUTLIER) cc_final: 0.6130 (m170) REVERT: A 572 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: A 687 LYS cc_start: 0.6928 (tptt) cc_final: 0.6588 (ttmt) REVERT: A 736 GLN cc_start: 0.7464 (mt0) cc_final: 0.7156 (mt0) REVERT: A 764 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8492 (mm) REVERT: A 991 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.6249 (tttt) REVERT: B 186 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7474 (mttm) REVERT: B 297 MET cc_start: 0.6849 (mmt) cc_final: 0.6626 (mmm) REVERT: B 315 MET cc_start: 0.7552 (ptt) cc_final: 0.7075 (mpp) outliers start: 65 outliers final: 48 residues processed: 178 average time/residue: 0.1005 time to fit residues: 26.0287 Evaluate side-chains 178 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 460 ASN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** 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 = 0.3953 r_free = 0.3953 target = 0.180251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138292 restraints weight = 11150.085| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.33 r_work: 0.2931 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11107 Z= 0.129 Angle : 0.599 15.794 15060 Z= 0.280 Chirality : 0.043 0.341 1691 Planarity : 0.004 0.042 1924 Dihedral : 8.472 66.281 1504 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.39 % Favored : 92.32 % Rotamer: Outliers : 4.81 % Allowed : 26.62 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.35 (0.24), residues: 1354 helix: 1.10 (0.24), residues: 491 sheet: -0.32 (0.40), residues: 190 loop : -1.22 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 289 TYR 0.040 0.001 TYR B 158 PHE 0.019 0.001 PHE A 510 TRP 0.012 0.001 TRP A 660 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (11105) covalent geometry : angle 0.59892 / 0.28 (15058) SS BOND : bond 0.00282 / 0.15 ( 1) SS BOND : angle 0.29950 / 0.17 ( 2) hydrogen bonds : bond 0.03289 / 2.18 ( 389) hydrogen bonds : angle 4.40152 / 3.08 ( 1107) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7660 (p90) REVERT: A 515 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6060 (m170) REVERT: A 572 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: A 687 LYS cc_start: 0.6883 (tptt) cc_final: 0.6543 (ttmt) REVERT: A 736 GLN cc_start: 0.7425 (mt0) cc_final: 0.6929 (mt0) REVERT: A 764 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8448 (mm) REVERT: A 991 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.6214 (tttt) REVERT: B 186 LYS cc_start: 0.8440 (mtpt) cc_final: 0.7461 (mttm) REVERT: B 297 MET cc_start: 0.6806 (mmt) cc_final: 0.6584 (mmm) REVERT: B 315 MET cc_start: 0.7650 (ptt) cc_final: 0.7201 (mpp) outliers start: 58 outliers final: 46 residues processed: 170 average time/residue: 0.1034 time to fit residues: 25.4915 Evaluate side-chains 172 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 94 optimal weight: 0.0870 chunk 109 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.182438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137139 restraints weight = 11038.849| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.32 r_work: 0.2947 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11107 Z= 0.101 Angle : 0.590 15.009 15060 Z= 0.272 Chirality : 0.042 0.344 1691 Planarity : 0.004 0.045 1924 Dihedral : 7.992 63.223 1504 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.72 % Favored : 92.98 % Rotamer: Outliers : 4.15 % Allowed : 27.28 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.25 (0.24), residues: 1354 helix: 1.22 (0.24), residues: 494 sheet: -0.47 (0.39), residues: 200 loop : -1.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 183 TYR 0.040 0.001 TYR B 158 PHE 0.019 0.001 PHE A 510 TRP 0.012 0.001 TRP A 735 HIS 0.003 0.000 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (11105) covalent geometry : angle 0.59046 / 0.27 (15058) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 0.28335 / 0.17 ( 2) hydrogen bonds : bond 0.02866 / 1.92 ( 389) hydrogen bonds : angle 4.23582 / 2.96 ( 1107) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 510 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7553 (p90) REVERT: A 572 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7267 (pp20) REVERT: A 736 GLN cc_start: 0.7362 (mt0) cc_final: 0.6952 (mt0) REVERT: A 764 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 991 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.5948 (tttt) REVERT: B 186 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7203 (mttm) REVERT: B 297 MET cc_start: 0.6715 (mmt) cc_final: 0.6501 (mmm) outliers start: 50 outliers final: 40 residues processed: 166 average time/residue: 0.1052 time to fit residues: 25.3305 Evaluate side-chains 167 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 147 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 93 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 73 optimal weight: 0.0370 chunk 43 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.184982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142427 restraints weight = 11070.746| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.23 r_work: 0.3078 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11107 Z= 0.107 Angle : 0.599 14.915 15060 Z= 0.278 Chirality : 0.042 0.340 1691 Planarity : 0.004 0.045 1924 Dihedral : 7.838 61.985 1504 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.79 % Favored : 92.91 % Rotamer: Outliers : 4.06 % Allowed : 27.78 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.21 (0.24), residues: 1354 helix: 1.25 (0.24), residues: 494 sheet: -0.45 (0.39), residues: 200 loop : -1.11 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 316 TYR 0.037 0.001 TYR B 158 PHE 0.019 0.001 PHE A 510 TRP 0.010 0.001 TRP A 735 HIS 0.005 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11105) covalent geometry : angle 0.59890 / 0.28 (15058) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 0.18285 / 0.11 ( 2) hydrogen bonds : bond 0.02903 / 1.93 ( 389) hydrogen bonds : angle 4.24018 / 2.96 ( 1107) Misc. bond : bond 0.00016 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 510 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7667 (p90) REVERT: A 572 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7387 (pp20) REVERT: A 764 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8421 (mm) REVERT: A 991 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.6083 (tttt) REVERT: B 186 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7226 (mttm) REVERT: B 297 MET cc_start: 0.6767 (mmt) cc_final: 0.6549 (mmm) outliers start: 49 outliers final: 43 residues processed: 163 average time/residue: 0.1053 time to fit residues: 24.7787 Evaluate side-chains 169 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 147 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.181471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139588 restraints weight = 11209.050| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.70 r_work: 0.2914 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11107 Z= 0.123 Angle : 0.596 14.745 15060 Z= 0.277 Chirality : 0.042 0.332 1691 Planarity : 0.004 0.045 1924 Dihedral : 7.728 61.075 1504 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.79 % Favored : 92.91 % Rotamer: Outliers : 4.31 % Allowed : 27.36 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.24 (0.24), residues: 1354 helix: 1.29 (0.24), residues: 488 sheet: -0.26 (0.40), residues: 189 loop : -1.23 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 947 TYR 0.035 0.001 TYR B 158 PHE 0.019 0.001 PHE A 510 TRP 0.011 0.001 TRP A 735 HIS 0.006 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 (11105) covalent geometry : angle 0.59626 / 0.28 (15058) SS BOND : bond 0.00185 / 0.10 ( 1) SS BOND : angle 0.16672 / 0.10 ( 2) hydrogen bonds : bond 0.03067 / 2.03 ( 389) hydrogen bonds : angle 4.29040 / 3.00 ( 1107) Misc. bond : bond 0.00022 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3068.96 seconds wall clock time: 53 minutes 17.18 seconds (3197.18 seconds total)