Starting phenix.real_space_refine on Wed Mar 4 08:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yet_33777/03_2026/7yet_33777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yet_33777/03_2026/7yet_33777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yet_33777/03_2026/7yet_33777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yet_33777/03_2026/7yet_33777.map" model { file = "/net/cci-nas-00/data/ceres_data/7yet_33777/03_2026/7yet_33777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yet_33777/03_2026/7yet_33777.cif" } resolution = 3.3 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= 0.002 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7588 2.51 5 N 1981 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11862 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 8038 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 945} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1990 Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 733 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 515 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'SVR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'SVR:plan-3': 1, 'SVR:plan-4': 1, 'SVR:plan-7': 1, 'SVR:plan-9': 1} Unresolved non-hydrogen planarities: 31 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN B 244 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 244 " occ=0.50 residue: pdb=" N ASER B 266 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.50 residue: pdb=" N ACYS B 275 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 275 " occ=0.50 residue: pdb=" N ATHR B 335 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 335 " occ=0.50 Time building chain proxies: 2.51, per 1000 atoms: 0.21 Number of scatterers: 11862 At special positions: 0 Unit cell: (177.84, 132.08, 102.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2227 8.00 N 1981 7.00 C 7588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 635.8 milliseconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 6 sheets defined 60.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.587A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.574A pdb=" N THR A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.605A pdb=" N LYS A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 112 removed outlier: 3.533A pdb=" N ASP A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 146 through 166 removed outlier: 3.664A pdb=" N ASN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.816A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 235 through 261 removed outlier: 3.719A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.655A pdb=" N ILE A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.620A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.716A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 436 " --> pdb=" O ARG A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 436' Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.835A pdb=" N MET A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.695A pdb=" N LEU A 464 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.615A pdb=" N TRP A 494 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP A 495 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA A 496 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.614A pdb=" N LEU A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 584 Processing helix chain 'A' and resid 634 through 640 removed outlier: 3.875A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.604A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.668A pdb=" N ARG A 691 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 692 " --> pdb=" O GLU A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.611A pdb=" N TRP A 716 " --> pdb=" O GLN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.809A pdb=" N GLU A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.791A pdb=" N THR A 792 " --> pdb=" O PRO A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 removed outlier: 3.569A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.664A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.714A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.868A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 3.580A pdb=" N ILE A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 Processing helix chain 'A' and resid 949 through 954 removed outlier: 3.613A pdb=" N ILE A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 949 through 954' Processing helix chain 'A' and resid 963 through 968 removed outlier: 3.998A pdb=" N LEU A 967 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 1069 through 1085 Processing helix chain 'A' and resid 1315 through 1331 removed outlier: 3.937A pdb=" N ILE A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A1321 " --> pdb=" O GLN A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1339 Processing helix chain 'B' and resid 82 through 117 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.117A pdb=" N TYR B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 148 removed outlier: 3.987A pdb=" N SER B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.774A pdb=" N GLU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.547A pdb=" N GLU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 removed outlier: 4.263A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 230 Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.759A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 306 through 309 removed outlier: 4.123A pdb=" N LYS B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'C' and resid 82 through 118 removed outlier: 4.232A pdb=" N LEU C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.739A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.725A pdb=" N GLU C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 112 Processing helix chain 'D' and resid 114 through 146 Proline residue: D 120 - end of helix removed outlier: 4.028A pdb=" N SER D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 144 removed outlier: 4.842A pdb=" N LYS E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Proline residue: E 120 - end of helix removed outlier: 3.717A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 562 through 565 Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 632 removed outlier: 3.819A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 799 through 801 Processing sheet with id=AA6, first strand: chain 'B' and resid 294 through 297 removed outlier: 6.560A pdb=" N ILE B 295 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B 326 " --> pdb=" O LEU B 338 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1831 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: 1.82 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3803 1.34 - 1.46: 2046 1.46 - 1.58: 6196 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 12138 Sorted by residual: bond pdb=" O25 SVR A2301 " pdb=" S17 SVR A2301 " ideal model delta sigma weight residual 1.469 1.566 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O30 SVR A2301 " pdb=" S21 SVR A2301 " ideal model delta sigma weight residual 1.472 1.566 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C13 SVR A2301 " pdb=" C20 SVR A2301 " ideal model delta sigma weight residual 1.401 1.482 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" O24 SVR A2301 " pdb=" S17 SVR A2301 " ideal model delta sigma weight residual 1.485 1.429 0.056 2.00e-02 2.50e+03 7.84e+00 bond pdb=" O29 SVR A2301 " pdb=" S21 SVR A2301 " ideal model delta sigma weight residual 1.473 1.418 0.055 2.00e-02 2.50e+03 7.53e+00 ... (remaining 12133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 16069 1.68 - 3.35: 360 3.35 - 5.03: 55 5.03 - 6.71: 21 6.71 - 8.38: 6 Bond angle restraints: 16511 Sorted by residual: angle pdb=" N ILE A 963 " pdb=" CA ILE A 963 " pdb=" C ILE A 963 " ideal model delta sigma weight residual 112.96 109.00 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" N PHE A 113 " pdb=" CA PHE A 113 " pdb=" C PHE A 113 " ideal model delta sigma weight residual 110.80 118.23 -7.43 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N ASN A 87 " pdb=" CA ASN A 87 " pdb=" C ASN A 87 " ideal model delta sigma weight residual 114.75 110.40 4.35 1.26e+00 6.30e-01 1.19e+01 angle pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 angle pdb=" N GLN B 100 " pdb=" CA GLN B 100 " pdb=" CB GLN B 100 " ideal model delta sigma weight residual 110.28 115.23 -4.95 1.55e+00 4.16e-01 1.02e+01 ... (remaining 16506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6551 17.89 - 35.79: 587 35.79 - 53.68: 108 53.68 - 71.57: 25 71.57 - 89.46: 7 Dihedral angle restraints: 7278 sinusoidal: 2872 harmonic: 4406 Sorted by residual: dihedral pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N ALA A 111 " pdb=" CA ALA A 111 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LEU A 112 " pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta harmonic sigma weight residual 180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 7275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1484 0.047 - 0.093: 322 0.093 - 0.139: 70 0.139 - 0.186: 3 0.186 - 0.232: 1 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CB ILE A 454 " pdb=" CA ILE A 454 " pdb=" CG1 ILE A 454 " pdb=" CG2 ILE A 454 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN A 681 " pdb=" N ASN A 681 " pdb=" C ASN A 681 " pdb=" CB ASN A 681 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA GLN B 99 " pdb=" N GLN B 99 " pdb=" C GLN B 99 " pdb=" CB GLN B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1877 not shown) Planarity restraints: 2111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 SVR A2301 " 0.316 2.00e-02 2.50e+03 2.60e-01 8.43e+02 pdb=" C26 SVR A2301 " -0.092 2.00e-02 2.50e+03 pdb=" C33 SVR A2301 " 0.194 2.00e-02 2.50e+03 pdb=" N19 SVR A2301 " -0.437 2.00e-02 2.50e+03 pdb=" O32 SVR A2301 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 SVR A2301 " 0.235 2.00e-02 2.50e+03 2.33e-01 8.17e+02 pdb=" C43 SVR A2301 " -0.016 2.00e-02 2.50e+03 pdb=" C46 SVR A2301 " -0.146 2.00e-02 2.50e+03 pdb=" N41 SVR A2301 " -0.335 2.00e-02 2.50e+03 pdb=" N44 SVR A2301 " 0.359 2.00e-02 2.50e+03 pdb=" O45 SVR A2301 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 SVR A2301 " 0.050 2.00e-02 2.50e+03 1.96e-01 4.80e+02 pdb=" C3 SVR A2301 " -0.229 2.00e-02 2.50e+03 pdb=" C5 SVR A2301 " 0.010 2.00e-02 2.50e+03 pdb=" N1 SVR A2301 " 0.332 2.00e-02 2.50e+03 pdb=" O4 SVR A2301 " -0.163 2.00e-02 2.50e+03 ... (remaining 2108 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1150 2.74 - 3.28: 11973 3.28 - 3.82: 19536 3.82 - 4.36: 21928 4.36 - 4.90: 39195 Nonbonded interactions: 93782 Sorted by model distance: nonbonded pdb=" OG1 THR A 70 " pdb=" O VAL A 229 " model vdw 2.204 3.040 nonbonded pdb=" O TYR A 667 " pdb=" NE2 GLN A 671 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 687 " pdb=" OD1 ASN A 690 " model vdw 2.217 3.040 nonbonded pdb=" OD2 ASP A 20 " pdb=" ND2 ASN A 681 " model vdw 2.287 3.120 nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.302 3.040 ... (remaining 93777 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 82 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 146)) } 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=0.50 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: 1.350 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.010 Find NCS groups from input model: 0.050 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.004 0.097 12138 Z= 0.168 Angle : 0.612 8.382 16511 Z= 0.318 Chirality : 0.039 0.232 1880 Planarity : 0.010 0.260 2111 Dihedral : 14.412 89.464 4422 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.90 % Favored : 93.69 % Rotamer: Outliers : 0.23 % Allowed : 0.15 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.31 (0.23), residues: 1487 helix: 2.07 (0.19), residues: 837 sheet: 0.65 (0.55), residues: 73 loop : -0.94 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.019 0.001 TYR A 667 PHE 0.015 0.001 PHE A 867 TRP 0.023 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00354 (12138) covalent geometry : angle 0.61235 (16511) hydrogen bonds : bond 0.13548 ( 640) hydrogen bonds : angle 4.31909 ( 1831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.433 Fit side-chains REVERT: A 108 MET cc_start: 0.8654 (mpp) cc_final: 0.7927 (mpp) REVERT: A 238 ILE cc_start: 0.8458 (mm) cc_final: 0.7851 (mm) REVERT: A 314 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 559 VAL cc_start: 0.7457 (t) cc_final: 0.7181 (t) REVERT: A 663 ASN cc_start: 0.8741 (p0) cc_final: 0.8488 (p0) REVERT: A 846 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7567 (mtt-85) REVERT: B 201 ASN cc_start: 0.8813 (m-40) cc_final: 0.8388 (m110) REVERT: B 309 LYS cc_start: 0.8380 (pttm) cc_final: 0.8118 (tttt) REVERT: B 324 TRP cc_start: 0.6812 (m-90) cc_final: 0.5925 (m-90) REVERT: C 144 LEU cc_start: 0.8790 (mt) cc_final: 0.8378 (pp) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 0.1000 time to fit residues: 27.1984 Evaluate side-chains 151 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107437 restraints weight = 50330.376| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 6.06 r_work: 0.2865 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12138 Z= 0.207 Angle : 0.673 15.483 16511 Z= 0.331 Chirality : 0.042 0.159 1880 Planarity : 0.005 0.090 2111 Dihedral : 4.902 71.715 1615 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.37 % Favored : 93.15 % Rotamer: Outliers : 1.14 % Allowed : 8.00 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.18 (0.23), residues: 1487 helix: 2.02 (0.18), residues: 843 sheet: 0.59 (0.55), residues: 73 loop : -1.13 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.014 0.001 TYR A 427 PHE 0.021 0.002 PHE A 99 TRP 0.018 0.001 TRP A 191 HIS 0.007 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00500 (12138) covalent geometry : angle 0.67292 (16511) hydrogen bonds : bond 0.04271 ( 640) hydrogen bonds : angle 3.66972 ( 1831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8497 (mm) cc_final: 0.8296 (mm) REVERT: A 238 ILE cc_start: 0.8814 (mm) cc_final: 0.8263 (mm) REVERT: A 242 ASP cc_start: 0.9023 (m-30) cc_final: 0.8779 (m-30) REVERT: A 314 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 201 ASN cc_start: 0.8920 (m-40) cc_final: 0.8547 (m110) REVERT: B 309 LYS cc_start: 0.8378 (pttm) cc_final: 0.8076 (tmtt) REVERT: C 144 LEU cc_start: 0.8877 (mt) cc_final: 0.8357 (pp) REVERT: D 138 MET cc_start: 0.8439 (tmm) cc_final: 0.7823 (tmm) outliers start: 14 outliers final: 12 residues processed: 169 average time/residue: 0.1031 time to fit residues: 24.8164 Evaluate side-chains 159 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 134 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109331 restraints weight = 61881.783| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 6.90 r_work: 0.2864 rms_B_bonded: 6.00 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12138 Z= 0.131 Angle : 0.608 15.011 16511 Z= 0.298 Chirality : 0.040 0.189 1880 Planarity : 0.004 0.080 2111 Dihedral : 4.720 61.504 1615 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.17 % Favored : 93.42 % Rotamer: Outliers : 1.14 % Allowed : 11.04 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.29 (0.23), residues: 1487 helix: 2.12 (0.18), residues: 835 sheet: 0.51 (0.55), residues: 73 loop : -1.03 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 151 TYR 0.019 0.001 TYR E 142 PHE 0.015 0.001 PHE A 369 TRP 0.013 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00303 (12138) covalent geometry : angle 0.60808 (16511) hydrogen bonds : bond 0.03604 ( 640) hydrogen bonds : angle 3.49212 ( 1831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 238 ILE cc_start: 0.8813 (mm) cc_final: 0.8314 (mm) REVERT: A 314 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8297 (tm-30) REVERT: A 1073 ARG cc_start: 0.6674 (ttt180) cc_final: 0.6004 (ttp-170) REVERT: B 138 MET cc_start: 0.9112 (tmm) cc_final: 0.8882 (ttp) REVERT: B 147 MET cc_start: 0.9235 (tmm) cc_final: 0.9015 (tmm) REVERT: B 201 ASN cc_start: 0.8947 (m-40) cc_final: 0.8694 (m110) REVERT: B 216 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7793 (mmmt) REVERT: B 309 LYS cc_start: 0.8388 (pttm) cc_final: 0.8095 (tmtt) REVERT: C 144 LEU cc_start: 0.8879 (mt) cc_final: 0.8367 (pp) REVERT: D 138 MET cc_start: 0.8432 (tmm) cc_final: 0.7831 (tmm) outliers start: 14 outliers final: 10 residues processed: 167 average time/residue: 0.1064 time to fit residues: 25.6095 Evaluate side-chains 158 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 43 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 120 optimal weight: 0.1980 chunk 133 optimal weight: 0.0040 chunk 25 optimal weight: 0.7980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.155747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109677 restraints weight = 51265.690| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 5.74 r_work: 0.2923 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12138 Z= 0.111 Angle : 0.585 13.855 16511 Z= 0.286 Chirality : 0.039 0.155 1880 Planarity : 0.004 0.073 2111 Dihedral : 4.594 60.520 1615 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.90 % Favored : 93.69 % Rotamer: Outliers : 1.07 % Allowed : 12.03 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.34 (0.23), residues: 1487 helix: 2.17 (0.18), residues: 836 sheet: 0.58 (0.55), residues: 71 loop : -1.04 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.016 0.001 TYR E 142 PHE 0.014 0.001 PHE A 369 TRP 0.010 0.001 TRP A 191 HIS 0.004 0.000 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00239 (12138) covalent geometry : angle 0.58460 (16511) hydrogen bonds : bond 0.03226 ( 640) hydrogen bonds : angle 3.42172 ( 1831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 578 GLU cc_start: 0.8423 (tp30) cc_final: 0.7558 (tp30) REVERT: A 1073 ARG cc_start: 0.6617 (ttt180) cc_final: 0.5992 (ttp-170) REVERT: B 138 MET cc_start: 0.9036 (tmm) cc_final: 0.8791 (ttp) REVERT: B 147 MET cc_start: 0.9206 (tmm) cc_final: 0.8955 (tmm) REVERT: B 201 ASN cc_start: 0.8899 (m-40) cc_final: 0.8665 (m110) REVERT: B 309 LYS cc_start: 0.8377 (pttm) cc_final: 0.8093 (tmtt) REVERT: C 144 LEU cc_start: 0.8825 (mt) cc_final: 0.8307 (pp) REVERT: D 138 MET cc_start: 0.8417 (tmm) cc_final: 0.7754 (tmm) outliers start: 13 outliers final: 10 residues processed: 162 average time/residue: 0.1082 time to fit residues: 25.0936 Evaluate side-chains 155 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106543 restraints weight = 46980.368| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 5.33 r_work: 0.2910 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12138 Z= 0.162 Angle : 0.614 16.002 16511 Z= 0.298 Chirality : 0.041 0.174 1880 Planarity : 0.004 0.070 2111 Dihedral : 4.604 59.406 1615 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.44 % Favored : 93.15 % Rotamer: Outliers : 1.68 % Allowed : 11.88 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.40 (0.23), residues: 1487 helix: 2.20 (0.18), residues: 829 sheet: 0.60 (0.56), residues: 71 loop : -0.94 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.014 0.001 TYR E 142 PHE 0.017 0.002 PHE A 99 TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00392 (12138) covalent geometry : angle 0.61435 (16511) hydrogen bonds : bond 0.03470 ( 640) hydrogen bonds : angle 3.45260 ( 1831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 391 LYS cc_start: 0.8389 (tttp) cc_final: 0.7890 (ttmt) REVERT: A 811 GLN cc_start: 0.8230 (tp40) cc_final: 0.8024 (tp40) REVERT: A 1073 ARG cc_start: 0.6610 (ttt180) cc_final: 0.5996 (ttp-170) REVERT: B 200 PHE cc_start: 0.9129 (t80) cc_final: 0.8924 (t80) REVERT: B 201 ASN cc_start: 0.8911 (m-40) cc_final: 0.8668 (m110) REVERT: B 213 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8709 (p0) REVERT: B 309 LYS cc_start: 0.8381 (pttm) cc_final: 0.8092 (tmtt) REVERT: D 138 MET cc_start: 0.8455 (tmm) cc_final: 0.7739 (tmm) outliers start: 21 outliers final: 14 residues processed: 162 average time/residue: 0.1080 time to fit residues: 25.2233 Evaluate side-chains 157 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 135 optimal weight: 40.0000 chunk 103 optimal weight: 0.3980 chunk 64 optimal weight: 0.0070 chunk 96 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107280 restraints weight = 43869.200| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.75 r_work: 0.2942 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12138 Z= 0.114 Angle : 0.590 14.996 16511 Z= 0.286 Chirality : 0.039 0.156 1880 Planarity : 0.004 0.067 2111 Dihedral : 4.509 58.177 1615 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.44 % Favored : 93.08 % Rotamer: Outliers : 1.22 % Allowed : 13.40 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.43 (0.23), residues: 1487 helix: 2.23 (0.18), residues: 829 sheet: 0.70 (0.57), residues: 71 loop : -0.95 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 182 TYR 0.010 0.001 TYR A 153 PHE 0.014 0.001 PHE A 369 TRP 0.010 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00260 (12138) covalent geometry : angle 0.59039 (16511) hydrogen bonds : bond 0.03170 ( 640) hydrogen bonds : angle 3.41499 ( 1831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 742 ASP cc_start: 0.8128 (p0) cc_final: 0.7791 (p0) REVERT: A 811 GLN cc_start: 0.8157 (tp40) cc_final: 0.7936 (tp40) REVERT: A 1073 ARG cc_start: 0.6622 (ttt180) cc_final: 0.6038 (ttp-170) REVERT: B 138 MET cc_start: 0.9000 (tmm) cc_final: 0.8332 (ttp) REVERT: B 309 LYS cc_start: 0.8364 (pttm) cc_final: 0.8051 (tmtt) REVERT: D 138 MET cc_start: 0.8369 (tmm) cc_final: 0.7862 (tmm) outliers start: 15 outliers final: 12 residues processed: 158 average time/residue: 0.1085 time to fit residues: 24.8133 Evaluate side-chains 154 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 77 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 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 = 0.3803 r_free = 0.3803 target = 0.152511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106277 restraints weight = 50988.722| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 5.50 r_work: 0.2887 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12138 Z= 0.169 Angle : 0.615 13.754 16511 Z= 0.301 Chirality : 0.041 0.155 1880 Planarity : 0.004 0.066 2111 Dihedral : 4.563 57.573 1615 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.37 % Favored : 93.15 % Rotamer: Outliers : 1.52 % Allowed : 13.40 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.37 (0.23), residues: 1487 helix: 2.18 (0.18), residues: 830 sheet: 0.68 (0.57), residues: 71 loop : -0.99 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.013 0.001 TYR C 142 PHE 0.018 0.002 PHE A 99 TRP 0.013 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00412 (12138) covalent geometry : angle 0.61460 (16511) hydrogen bonds : bond 0.03480 ( 640) hydrogen bonds : angle 3.46551 ( 1831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 391 LYS cc_start: 0.8400 (tttp) cc_final: 0.7899 (ttmt) REVERT: A 916 ASN cc_start: 0.8454 (p0) cc_final: 0.7958 (p0) REVERT: A 1073 ARG cc_start: 0.6665 (ttt180) cc_final: 0.6066 (ttp-170) REVERT: B 138 MET cc_start: 0.9050 (tmm) cc_final: 0.8664 (ttp) REVERT: B 201 ASN cc_start: 0.8978 (m-40) cc_final: 0.8658 (m110) REVERT: B 213 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8659 (p0) REVERT: B 309 LYS cc_start: 0.8387 (pttm) cc_final: 0.8104 (tmtt) REVERT: D 138 MET cc_start: 0.8397 (tmm) cc_final: 0.7933 (tmm) outliers start: 18 outliers final: 15 residues processed: 159 average time/residue: 0.1061 time to fit residues: 24.1764 Evaluate side-chains 157 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 107 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106439 restraints weight = 46702.428| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 5.10 r_work: 0.2914 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12138 Z= 0.134 Angle : 0.607 15.857 16511 Z= 0.295 Chirality : 0.040 0.150 1880 Planarity : 0.004 0.064 2111 Dihedral : 4.524 56.732 1615 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.92 % Favored : 92.68 % Rotamer: Outliers : 1.52 % Allowed : 13.79 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.37 (0.23), residues: 1487 helix: 2.19 (0.18), residues: 829 sheet: 0.69 (0.58), residues: 71 loop : -0.99 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.011 0.001 TYR A 153 PHE 0.015 0.001 PHE A 369 TRP 0.011 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00315 (12138) covalent geometry : angle 0.60709 (16511) hydrogen bonds : bond 0.03290 ( 640) hydrogen bonds : angle 3.44943 ( 1831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.369 Fit side-chains REVERT: A 314 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 391 LYS cc_start: 0.8388 (tttp) cc_final: 0.7859 (ttmt) REVERT: A 916 ASN cc_start: 0.8395 (p0) cc_final: 0.7854 (p0) REVERT: A 927 ASP cc_start: 0.7732 (t70) cc_final: 0.7425 (t70) REVERT: A 1073 ARG cc_start: 0.6639 (ttt180) cc_final: 0.6062 (ttp-170) REVERT: B 138 MET cc_start: 0.9017 (tmm) cc_final: 0.8803 (ttp) REVERT: B 309 LYS cc_start: 0.8357 (pttm) cc_final: 0.8045 (tmtt) REVERT: D 138 MET cc_start: 0.8437 (tmm) cc_final: 0.7783 (tmm) outliers start: 18 outliers final: 15 residues processed: 156 average time/residue: 0.1083 time to fit residues: 24.2534 Evaluate side-chains 154 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 0.0040 chunk 58 optimal weight: 0.6980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108070 restraints weight = 60786.648| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 6.42 r_work: 0.2874 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12138 Z= 0.125 Angle : 0.603 15.462 16511 Z= 0.293 Chirality : 0.040 0.251 1880 Planarity : 0.004 0.064 2111 Dihedral : 4.492 56.437 1615 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.58 % Favored : 93.02 % Rotamer: Outliers : 1.29 % Allowed : 14.39 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.40 (0.23), residues: 1487 helix: 2.21 (0.18), residues: 829 sheet: 0.76 (0.59), residues: 71 loop : -0.98 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.011 0.001 TYR A 153 PHE 0.014 0.001 PHE A 369 TRP 0.011 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00292 (12138) covalent geometry : angle 0.60338 (16511) hydrogen bonds : bond 0.03214 ( 640) hydrogen bonds : angle 3.43037 ( 1831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.370 Fit side-chains REVERT: A 314 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 391 LYS cc_start: 0.8382 (tttp) cc_final: 0.7846 (ttmt) REVERT: A 434 ASN cc_start: 0.8108 (m-40) cc_final: 0.7799 (t0) REVERT: A 578 GLU cc_start: 0.8416 (tp30) cc_final: 0.7496 (tp30) REVERT: A 916 ASN cc_start: 0.8405 (p0) cc_final: 0.7860 (p0) REVERT: A 927 ASP cc_start: 0.7732 (t70) cc_final: 0.7439 (t70) REVERT: A 1073 ARG cc_start: 0.6879 (ttt180) cc_final: 0.6207 (ttp-170) REVERT: B 138 MET cc_start: 0.9045 (tmm) cc_final: 0.8840 (ttp) REVERT: B 309 LYS cc_start: 0.8358 (pttm) cc_final: 0.8049 (tmtt) REVERT: D 138 MET cc_start: 0.8394 (tmm) cc_final: 0.7701 (tmm) outliers start: 15 outliers final: 14 residues processed: 151 average time/residue: 0.1029 time to fit residues: 22.3639 Evaluate side-chains 155 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 54 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 19 optimal weight: 0.0170 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 0.0060 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107524 restraints weight = 50350.671| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 5.20 r_work: 0.2932 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12138 Z= 0.112 Angle : 0.593 15.303 16511 Z= 0.288 Chirality : 0.039 0.241 1880 Planarity : 0.004 0.063 2111 Dihedral : 4.406 55.836 1615 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.85 % Favored : 92.75 % Rotamer: Outliers : 1.22 % Allowed : 14.39 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.46 (0.23), residues: 1487 helix: 2.27 (0.18), residues: 829 sheet: 0.78 (0.59), residues: 71 loop : -0.97 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.010 0.001 TYR A 153 PHE 0.014 0.001 PHE A 369 TRP 0.011 0.001 TRP A 191 HIS 0.004 0.000 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00252 (12138) covalent geometry : angle 0.59316 (16511) hydrogen bonds : bond 0.03042 ( 640) hydrogen bonds : angle 3.38465 ( 1831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.425 Fit side-chains REVERT: A 314 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 391 LYS cc_start: 0.8305 (tttp) cc_final: 0.7788 (ttmt) REVERT: A 578 GLU cc_start: 0.8352 (tp30) cc_final: 0.7425 (tp30) REVERT: A 916 ASN cc_start: 0.8324 (p0) cc_final: 0.7816 (p0) REVERT: A 927 ASP cc_start: 0.7783 (t70) cc_final: 0.7494 (t70) REVERT: A 1073 ARG cc_start: 0.6845 (ttt180) cc_final: 0.6295 (ttp-170) REVERT: B 138 MET cc_start: 0.8968 (tmm) cc_final: 0.8648 (ttp) REVERT: B 147 MET cc_start: 0.9256 (tmm) cc_final: 0.8933 (tmm) REVERT: B 151 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7733 (ttm170) REVERT: B 216 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7704 (mmmt) REVERT: B 309 LYS cc_start: 0.8348 (pttm) cc_final: 0.8045 (tmtt) outliers start: 14 outliers final: 12 residues processed: 157 average time/residue: 0.1122 time to fit residues: 24.8846 Evaluate side-chains 153 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 GLN ** A1318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105094 restraints weight = 50417.976| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 5.55 r_work: 0.2885 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12138 Z= 0.180 Angle : 0.638 14.981 16511 Z= 0.310 Chirality : 0.042 0.247 1880 Planarity : 0.004 0.064 2111 Dihedral : 4.497 55.645 1615 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.51 % Favored : 93.08 % Rotamer: Outliers : 1.29 % Allowed : 14.32 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.32 (0.23), residues: 1487 helix: 2.13 (0.18), residues: 836 sheet: 0.73 (0.59), residues: 71 loop : -1.04 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 858 TYR 0.014 0.001 TYR C 142 PHE 0.024 0.002 PHE B 214 TRP 0.012 0.001 TRP A 191 HIS 0.006 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00439 (12138) covalent geometry : angle 0.63769 (16511) hydrogen bonds : bond 0.03442 ( 640) hydrogen bonds : angle 3.44711 ( 1831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3165.50 seconds wall clock time: 54 minutes 49.69 seconds (3289.69 seconds total)