Starting phenix.real_space_refine on Thu Mar 5 02:11:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plm_13493/03_2026/7plm_13493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plm_13493/03_2026/7plm_13493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7plm_13493/03_2026/7plm_13493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plm_13493/03_2026/7plm_13493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plm_13493/03_2026/7plm_13493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plm_13493/03_2026/7plm_13493.map" } resolution = 2.9 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= 0.007 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 24 7.16 5 P 4 5.49 5 Mg 2 5.21 5 S 145 5.16 5 C 11424 2.51 5 N 3078 2.21 5 O 3546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s 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: 18225 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1177, 8996 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1177, 8996 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 8 bond proxies already assigned to first conformer: 9174 Chain: "B" Number of atoms: 9005 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1177, 8996 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1177, 8996 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 8 bond proxies already assigned to first conformer: 9170 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {' CA': 1, ' MG': 1, 'SF4': 3, 'TPP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {' CA': 1, ' MG': 1, 'SF4': 3, 'TPP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5544 SG CYS A 755 81.996 27.505 78.240 1.00 39.15 S ATOM 5127 SG CYS A 695 77.454 27.520 73.988 1.00 28.18 S ATOM 5098 SG ACYS A 692 75.981 28.432 79.862 0.50 16.14 S ATOM 5075 SG CYS A 689 77.888 22.405 78.212 1.00 19.33 S ATOM 5517 SG CYS A 751 82.062 30.513 70.769 1.00 10.27 S ATOM 5156 SG CYS A 699 77.767 32.048 66.797 1.00 7.85 S ATOM 5481 SG CYS A 745 83.607 29.890 64.453 1.00 13.08 S ATOM 5499 SG CYS A 748 82.408 35.798 67.548 1.00 12.03 S ATOM 6197 SG CYS A 840 76.727 47.644 59.041 1.00 31.03 S ATOM 5988 SG CYS A 812 81.818 43.969 59.819 1.00 20.30 S ATOM 6004 SG CYS A 815 76.751 42.993 63.616 1.00 12.97 S ATOM 7912 SG CYS A1071 80.527 48.775 63.306 1.00 17.38 S ATOM 14546 SG CYS B 755 42.062 100.160 78.236 1.00 42.28 S ATOM 14129 SG CYS B 695 46.567 100.182 73.962 1.00 30.47 S ATOM 14100 SG ACYS B 692 48.078 99.224 79.862 0.50 14.76 S ATOM 14077 SG CYS B 689 46.178 105.253 78.212 1.00 20.78 S ATOM 14519 SG CYS B 751 41.993 97.148 70.767 1.00 9.78 S ATOM 14158 SG CYS B 699 46.291 95.625 66.795 1.00 7.42 S ATOM 14483 SG CYS B 745 40.454 97.772 64.454 1.00 10.82 S ATOM 14501 SG CYS B 748 41.650 91.859 67.546 1.00 11.41 S ATOM 15199 SG CYS B 840 47.333 80.010 59.037 1.00 29.38 S ATOM 14990 SG CYS B 812 42.245 83.689 59.819 1.00 21.48 S ATOM 15006 SG CYS B 815 47.311 84.665 63.614 1.00 12.97 S ATOM 16914 SG CYS B1071 43.538 78.883 63.307 1.00 20.63 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS A 692 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 692 " occ=0.50 residue: pdb=" N ACYS B 692 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 692 " occ=0.50 Time building chain proxies: 7.19, per 1000 atoms: 0.39 Number of scatterers: 18225 At special positions: 0 Unit cell: (124.961, 128.557, 100.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 24 26.01 Ca 2 19.99 S 145 16.00 P 4 15.00 Mg 2 11.99 O 3546 8.00 N 3078 7.00 C 11424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1212 " distance=2.04 Simple disulfide: pdb=" SG CYS B1195 " - pdb=" SG ACYS B1212 " distance=2.04 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: 1.53 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE3 SF4 A1301 " - pdb=" SG ACYS A 692 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 689 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 755 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 695 " pdb=" SF4 A1302 " pdb="FE3 SF4 A1302 " - pdb=" SG CYS A 745 " pdb="FE4 SF4 A1302 " - pdb=" SG CYS A 748 " pdb="FE2 SF4 A1302 " - pdb=" SG CYS A 699 " pdb="FE1 SF4 A1302 " - pdb=" SG CYS A 751 " pdb=" SF4 A1303 " pdb="FE4 SF4 A1303 " - pdb=" SG CYS A1071 " pdb="FE1 SF4 A1303 " - pdb=" SG CYS A 840 " pdb="FE2 SF4 A1303 " - pdb=" SG CYS A 812 " pdb="FE3 SF4 A1303 " - pdb=" SG CYS A 815 " pdb=" SF4 B1301 " pdb="FE3 SF4 B1301 " - pdb=" SG ACYS B 692 " pdb="FE4 SF4 B1301 " - pdb=" SG CYS B 689 " pdb="FE1 SF4 B1301 " - pdb=" SG CYS B 755 " pdb="FE2 SF4 B1301 " - pdb=" SG CYS B 695 " pdb=" SF4 B1302 " pdb="FE3 SF4 B1302 " - pdb=" SG CYS B 745 " pdb="FE4 SF4 B1302 " - pdb=" SG CYS B 748 " pdb="FE2 SF4 B1302 " - pdb=" SG CYS B 699 " pdb="FE1 SF4 B1302 " - pdb=" SG CYS B 751 " pdb=" SF4 B1303 " pdb="FE4 SF4 B1303 " - pdb=" SG CYS B1071 " pdb="FE2 SF4 B1303 " - pdb=" SG CYS B 812 " pdb="FE1 SF4 B1303 " - pdb=" SG CYS B 840 " pdb="FE3 SF4 B1303 " - pdb=" SG CYS B 815 " Number of angles added : 72 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 14 sheets defined 47.7% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.624A pdb=" N VAL A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 47 removed outlier: 3.877A pdb=" N GLY A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 86 through 103 Proline residue: A 95 - end of helix removed outlier: 3.679A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 145 through 164 Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.523A pdb=" N SER A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 232 through 255 removed outlier: 3.950A pdb=" N TYR A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.633A pdb=" N LEU A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 removed outlier: 3.659A pdb=" N THR A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 338 through 352 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 493 through 498 removed outlier: 3.671A pdb=" N ILE A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 526 Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.660A pdb=" N ILE A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 642 through 648 Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.615A pdb=" N ALA A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 659 " --> pdb=" O VAL A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 655 through 659' Processing helix chain 'A' and resid 669 through 673 removed outlier: 3.575A pdb=" N PHE A 672 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 699 removed outlier: 3.553A pdb=" N PHE A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 755 Processing helix chain 'A' and resid 774 through 782 Processing helix chain 'A' and resid 795 through 801 Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 871 through 898 Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 919 through 934 Processing helix chain 'A' and resid 939 through 948 removed outlier: 3.638A pdb=" N MET A 948 " --> pdb=" O GLN A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 952 removed outlier: 3.812A pdb=" N TYR A 952 " --> pdb=" O SER A 949 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 949 through 952' Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 970 through 978 Processing helix chain 'A' and resid 1024 through 1031 removed outlier: 3.637A pdb=" N THR A1031 " --> pdb=" O ARG A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1058 removed outlier: 3.996A pdb=" N PHE A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1075 Processing helix chain 'A' and resid 1079 through 1081 No H-bonds generated for 'chain 'A' and resid 1079 through 1081' Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1123 through 1130 Processing helix chain 'A' and resid 1131 through 1141 Processing helix chain 'A' and resid 1141 through 1168 Processing helix chain 'A' and resid 1200 through 1204 removed outlier: 3.563A pdb=" N ALA A1204 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1230 Processing helix chain 'B' and resid 9 through 22 removed outlier: 3.620A pdb=" N VAL B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.874A pdb=" N GLY B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 77 Processing helix chain 'B' and resid 86 through 103 Proline residue: B 95 - end of helix removed outlier: 3.672A pdb=" N LYS B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 164 Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.530A pdb=" N SER B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 232 through 255 removed outlier: 3.953A pdb=" N TYR B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.649A pdb=" N LEU B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.662A pdb=" N THR B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 338 through 352 Processing helix chain 'B' and resid 371 through 384 Processing helix chain 'B' and resid 429 through 445 Processing helix chain 'B' and resid 493 through 498 removed outlier: 3.682A pdb=" N ILE B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 526 Processing helix chain 'B' and resid 527 through 537 Processing helix chain 'B' and resid 545 through 553 removed outlier: 3.668A pdb=" N ILE B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 599 through 613 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 642 through 648 Processing helix chain 'B' and resid 650 through 654 Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.618A pdb=" N ALA B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 659 " --> pdb=" O VAL B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 659' Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.579A pdb=" N PHE B 672 " --> pdb=" O THR B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 699 removed outlier: 3.548A pdb=" N PHE B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 755 Processing helix chain 'B' and resid 774 through 782 Processing helix chain 'B' and resid 795 through 801 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 839 through 846 Processing helix chain 'B' and resid 871 through 898 Processing helix chain 'B' and resid 904 through 916 Processing helix chain 'B' and resid 919 through 934 Processing helix chain 'B' and resid 939 through 948 removed outlier: 3.651A pdb=" N MET B 948 " --> pdb=" O GLN B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 952 removed outlier: 3.808A pdb=" N TYR B 952 " --> pdb=" O SER B 949 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 949 through 952' Processing helix chain 'B' and resid 963 through 968 Processing helix chain 'B' and resid 970 through 978 Processing helix chain 'B' and resid 1024 through 1031 removed outlier: 3.634A pdb=" N THR B1031 " --> pdb=" O ARG B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1058 removed outlier: 4.001A pdb=" N PHE B1049 " --> pdb=" O SER B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1071 through 1075 Processing helix chain 'B' and resid 1079 through 1081 No H-bonds generated for 'chain 'B' and resid 1079 through 1081' Processing helix chain 'B' and resid 1082 through 1093 Processing helix chain 'B' and resid 1123 through 1130 Processing helix chain 'B' and resid 1131 through 1141 Processing helix chain 'B' and resid 1141 through 1168 Processing helix chain 'B' and resid 1200 through 1204 removed outlier: 3.564A pdb=" N ALA B1204 " --> pdb=" O PRO B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1230 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 6.595A pdb=" N VAL A 24 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N PHE A 84 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA A 26 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR A 81 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N HIS A 110 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR A 83 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR A 112 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR A 85 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE A 109 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 171 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 111 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA A 139 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE A 170 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 141 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ASP A 172 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N SER A 143 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET A 140 " --> pdb=" O TYR A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 216 removed outlier: 5.898A pdb=" N PHE B 833 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE B 960 " --> pdb=" O PHE B 833 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA B 835 " --> pdb=" O PHE B 960 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY B 962 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 957 " --> pdb=" O ASN B 985 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE B 987 " --> pdb=" O VAL B 957 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 959 " --> pdb=" O PHE B 987 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET B 989 " --> pdb=" O ILE B 959 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY B 961 " --> pdb=" O MET B 989 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR B1036 " --> pdb=" O LEU B1064 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B1066 " --> pdb=" O TYR B1036 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B1038 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR B1068 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL B1040 " --> pdb=" O TYR B1068 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B1099 " --> pdb=" O THR B1039 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.559A pdb=" N ARG A 271 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 300 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 273 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 302 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 275 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N PHE A 390 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA A 360 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 392 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG A 362 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.538A pdb=" N VAL A 487 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASN A 513 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N CYS A 489 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 544 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU A 512 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 680 through 684 Processing sheet with id=AA7, first strand: chain 'A' and resid 704 through 710 Processing sheet with id=AA8, first strand: chain 'A' and resid 1113 through 1115 removed outlier: 3.863A pdb=" N PHE A1099 " --> pdb=" O THR A1039 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR A1036 " --> pdb=" O LEU A1064 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE A1066 " --> pdb=" O TYR A1036 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A1038 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR A1068 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A1040 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 957 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE A 987 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 959 " --> pdb=" O PHE A 987 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N MET A 989 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY A 961 " --> pdb=" O MET A 989 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 833 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE A 960 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA A 835 " --> pdb=" O PHE A 960 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLY A 962 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP A 864 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 8 Processing sheet with id=AB1, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.597A pdb=" N VAL B 24 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N PHE B 84 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ALA B 26 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 81 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS B 110 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 83 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR B 112 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR B 85 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 109 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE B 171 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 111 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA B 139 " --> pdb=" O MET B 168 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE B 170 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 141 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ASP B 172 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N SER B 143 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET B 140 " --> pdb=" O TYR B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 261 through 265 removed outlier: 6.552A pdb=" N ARG B 271 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE B 300 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 273 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 302 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER B 275 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N PHE B 390 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 360 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 392 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG B 362 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 448 through 454 removed outlier: 6.554A pdb=" N VAL B 487 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASN B 513 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS B 489 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 510 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE B 544 " --> pdb=" O PHE B 510 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU B 512 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 680 through 684 Processing sheet with id=AB5, first strand: chain 'B' and resid 704 through 710 817 hydrogen bonds defined for protein. 2361 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: 3.97 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 7804 1.43 - 1.65: 10427 1.65 - 1.86: 203 1.86 - 2.07: 0 2.07 - 2.29: 72 Bond restraints: 18506 Sorted by residual: bond pdb=" C PHE A 174 " pdb=" N ARG A 175 " ideal model delta sigma weight residual 1.332 1.304 0.029 1.40e-02 5.10e+03 4.21e+00 bond pdb=" C PHE B 174 " pdb=" N ARG B 175 " ideal model delta sigma weight residual 1.332 1.306 0.027 1.40e-02 5.10e+03 3.65e+00 bond pdb=" O3B TPP B1304 " pdb=" PB TPP B1304 " ideal model delta sigma weight residual 1.532 1.485 0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" O3B TPP A1304 " pdb=" PB TPP A1304 " ideal model delta sigma weight residual 1.532 1.485 0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" CB THR A 112 " pdb=" CG2 THR A 112 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 ... (remaining 18501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 23936 1.46 - 2.93: 950 2.93 - 4.39: 126 4.39 - 5.86: 29 5.86 - 7.32: 14 Bond angle restraints: 25055 Sorted by residual: angle pdb=" O3A TPP B1304 " pdb=" PB TPP B1304 " pdb=" O3B TPP B1304 " ideal model delta sigma weight residual 104.26 110.51 -6.25 1.33e+00 5.64e-01 2.20e+01 angle pdb=" O3A TPP A1304 " pdb=" PB TPP A1304 " pdb=" O3B TPP A1304 " ideal model delta sigma weight residual 104.26 110.47 -6.21 1.33e+00 5.64e-01 2.17e+01 angle pdb=" O1B TPP A1304 " pdb=" PB TPP A1304 " pdb=" O3A TPP A1304 " ideal model delta sigma weight residual 111.16 104.34 6.82 1.82e+00 3.03e-01 1.41e+01 angle pdb=" O1B TPP B1304 " pdb=" PB TPP B1304 " pdb=" O3A TPP B1304 " ideal model delta sigma weight residual 111.16 104.34 6.82 1.82e+00 3.03e-01 1.41e+01 angle pdb=" CA TRP A 844 " pdb=" CB TRP A 844 " pdb=" CG TRP A 844 " ideal model delta sigma weight residual 113.60 119.79 -6.19 1.90e+00 2.77e-01 1.06e+01 ... (remaining 25050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9987 17.94 - 35.87: 833 35.87 - 53.81: 184 53.81 - 71.74: 42 71.74 - 89.68: 17 Dihedral angle restraints: 11063 sinusoidal: 4335 harmonic: 6728 Sorted by residual: dihedral pdb=" CA PHE B 124 " pdb=" C PHE B 124 " pdb=" N GLY B 125 " pdb=" CA GLY B 125 " ideal model delta harmonic sigma weight residual 180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA PHE A 124 " pdb=" C PHE A 124 " pdb=" N GLY A 125 " pdb=" CA GLY A 125 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CB CYS A1195 " pdb=" SG CYS A1195 " pdb=" SG CYS A1212 " pdb=" CB CYS A1212 " ideal model delta sinusoidal sigma weight residual -86.00 -121.63 35.63 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 11060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1537 0.033 - 0.067: 809 0.067 - 0.100: 271 0.100 - 0.134: 109 0.134 - 0.167: 11 Chirality restraints: 2737 Sorted by residual: chirality pdb=" CA VAL A 239 " pdb=" N VAL A 239 " pdb=" C VAL A 239 " pdb=" CB VAL A 239 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA VAL B 239 " pdb=" N VAL B 239 " pdb=" C VAL B 239 " pdb=" CB VAL B 239 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA THR B 818 " pdb=" N THR B 818 " pdb=" C THR B 818 " pdb=" CB THR B 818 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 2734 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 755 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 756 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 756 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 756 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 755 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 756 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 756 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 756 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B1087 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C MET B1087 " 0.029 2.00e-02 2.50e+03 pdb=" O MET B1087 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN B1088 " -0.010 2.00e-02 2.50e+03 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 166 2.42 - 3.04: 11577 3.04 - 3.66: 29520 3.66 - 4.28: 46960 4.28 - 4.90: 76456 Nonbonded interactions: 164679 Sorted by model distance: nonbonded pdb=" O2B TPP B1304 " pdb="MG MG B1306 " model vdw 1.802 2.170 nonbonded pdb=" O2B TPP A1304 " pdb="MG MG A1306 " model vdw 1.807 2.170 nonbonded pdb=" OD2 ASP B 963 " pdb=" O VAL B 993 " model vdw 1.893 3.040 nonbonded pdb=" OD2 ASP A 963 " pdb=" O VAL A 993 " model vdw 1.896 3.040 nonbonded pdb=" O VAL B 993 " pdb="MG MG B1306 " model vdw 1.931 2.170 ... (remaining 164674 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 'A' and (resid 2 through 691 or resid 693 through 1211 or resid 1213 thro \ ugh 1306)) selection = (chain 'B' and (resid 2 through 691 or resid 693 through 1211 or resid 1213 thro \ ugh 1306)) } 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=0.01 max=1.00 mean=0.99 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: 1.230 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.010 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18532 Z= 0.249 Angle : 0.816 20.580 25131 Z= 0.386 Chirality : 0.046 0.167 2737 Planarity : 0.006 0.052 3245 Dihedral : 14.622 89.678 6751 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.98 % Allowed : 10.60 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2325 helix: 0.06 (0.15), residues: 1048 sheet: -0.62 (0.25), residues: 374 loop : -1.20 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1027 TYR 0.017 0.003 TYR A 820 PHE 0.017 0.002 PHE B 697 TRP 0.024 0.003 TRP B 844 HIS 0.006 0.002 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00567 (18506) covalent geometry : angle 0.69538 (25055) SS BOND : bond 0.00756 ( 2) SS BOND : angle 1.64172 ( 4) hydrogen bonds : bond 0.13297 ( 817) hydrogen bonds : angle 6.24993 ( 2361) metal coordination : bond 0.01322 ( 24) metal coordination : angle 7.98880 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 305 time to evaluate : 0.601 Fit side-chains REVERT: A 3 LYS cc_start: 0.5870 (mtmt) cc_final: 0.5658 (mttt) REVERT: A 36 MET cc_start: 0.8143 (mtm) cc_final: 0.7820 (mtm) REVERT: A 211 GLU cc_start: 0.7265 (mp0) cc_final: 0.6988 (mp0) REVERT: A 253 LEU cc_start: 0.7659 (mp) cc_final: 0.7390 (mp) REVERT: A 328 ASP cc_start: 0.7711 (m-30) cc_final: 0.7465 (m-30) REVERT: A 332 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: A 604 ASP cc_start: 0.5661 (m-30) cc_final: 0.5455 (m-30) REVERT: A 640 LYS cc_start: 0.6675 (tmtt) cc_final: 0.6440 (tmtm) REVERT: A 770 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6642 (tt0) REVERT: A 771 ARG cc_start: 0.7008 (ptm160) cc_final: 0.6234 (ptm-80) REVERT: A 926 TYR cc_start: 0.7076 (m-80) cc_final: 0.6683 (m-80) REVERT: A 942 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6706 (mp) REVERT: A 1151 GLN cc_start: 0.5103 (mm110) cc_final: 0.4640 (mm110) REVERT: A 1165 HIS cc_start: 0.4451 (t70) cc_final: 0.3687 (t-170) REVERT: A 1197 ARG cc_start: 0.5618 (mmt-90) cc_final: 0.5339 (mmt180) REVERT: B 3 LYS cc_start: 0.5875 (mtmt) cc_final: 0.5662 (mttt) REVERT: B 36 MET cc_start: 0.8186 (mtm) cc_final: 0.7888 (mtm) REVERT: B 211 GLU cc_start: 0.7233 (mp0) cc_final: 0.6879 (mp0) REVERT: B 328 ASP cc_start: 0.7770 (m-30) cc_final: 0.7543 (m-30) REVERT: B 770 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: B 771 ARG cc_start: 0.7002 (ptm160) cc_final: 0.6242 (ptm-80) REVERT: B 926 TYR cc_start: 0.7143 (m-80) cc_final: 0.6753 (m-80) REVERT: B 942 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6764 (mp) REVERT: B 971 TYR cc_start: 0.7449 (t80) cc_final: 0.7052 (t80) REVERT: B 1132 ASN cc_start: 0.7620 (t0) cc_final: 0.7313 (t0) REVERT: B 1151 GLN cc_start: 0.5128 (mm110) cc_final: 0.4682 (mm110) REVERT: B 1165 HIS cc_start: 0.4805 (t70) cc_final: 0.4159 (t70) REVERT: B 1197 ARG cc_start: 0.5676 (mmt-90) cc_final: 0.5412 (mmt180) outliers start: 93 outliers final: 42 residues processed: 383 average time/residue: 0.5895 time to fit residues: 254.0126 Evaluate side-chains 298 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 770 GLN Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1212 CYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1198 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 720 ASN A 770 GLN A 866 ASN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 GLN ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN B 720 ASN B 866 ASN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 GLN ** B1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.185125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.161227 restraints weight = 49285.828| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.92 r_work: 0.3485 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 110 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18532 Z= 0.135 Angle : 0.713 18.461 25131 Z= 0.303 Chirality : 0.042 0.149 2737 Planarity : 0.004 0.050 3245 Dihedral : 7.821 77.139 2608 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.23 % Allowed : 15.63 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2325 helix: 0.85 (0.16), residues: 1034 sheet: -0.55 (0.26), residues: 374 loop : -0.96 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 783 TYR 0.013 0.002 TYR A 875 PHE 0.016 0.002 PHE A 124 TRP 0.015 0.002 TRP A 844 HIS 0.005 0.001 HIS A 976 Details of bonding type rmsd covalent geometry : bond 0.00300 (18506) covalent geometry : angle 0.56470 (25055) SS BOND : bond 0.00511 ( 2) SS BOND : angle 1.41434 ( 4) hydrogen bonds : bond 0.04203 ( 817) hydrogen bonds : angle 4.78476 ( 2361) metal coordination : bond 0.00715 ( 24) metal coordination : angle 8.15874 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.808 Fit side-chains REVERT: A 36 MET cc_start: 0.8043 (mtm) cc_final: 0.7749 (mtm) REVERT: A 135 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: A 211 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 502 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.5211 (pm20) REVERT: A 604 ASP cc_start: 0.5594 (m-30) cc_final: 0.5311 (m-30) REVERT: A 640 LYS cc_start: 0.6914 (tmtt) cc_final: 0.6687 (tmtm) REVERT: A 653 LYS cc_start: 0.7216 (mttt) cc_final: 0.6697 (mmtt) REVERT: A 771 ARG cc_start: 0.6906 (ptm160) cc_final: 0.6419 (ptm-80) REVERT: A 831 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7342 (ppt-90) REVERT: A 926 TYR cc_start: 0.7447 (m-80) cc_final: 0.7038 (m-80) REVERT: A 1032 TYR cc_start: 0.6565 (m-80) cc_final: 0.6325 (m-80) REVERT: A 1100 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6743 (mtp-110) REVERT: A 1151 GLN cc_start: 0.5007 (mm-40) cc_final: 0.4678 (mm110) REVERT: A 1165 HIS cc_start: 0.4991 (t70) cc_final: 0.4234 (t-170) REVERT: B 36 MET cc_start: 0.8066 (mtm) cc_final: 0.7782 (mtm) REVERT: B 135 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: B 211 GLU cc_start: 0.7488 (mp0) cc_final: 0.7103 (mp0) REVERT: B 502 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5233 (pm20) REVERT: B 653 LYS cc_start: 0.7229 (mttt) cc_final: 0.6755 (mmtt) REVERT: B 771 ARG cc_start: 0.7004 (ptm160) cc_final: 0.6490 (ptm-80) REVERT: B 831 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7338 (ppt-90) REVERT: B 926 TYR cc_start: 0.7481 (m-80) cc_final: 0.7256 (m-80) REVERT: B 971 TYR cc_start: 0.7340 (t80) cc_final: 0.6904 (t80) REVERT: B 1032 TYR cc_start: 0.6485 (m-80) cc_final: 0.6155 (m-80) REVERT: B 1100 ARG cc_start: 0.6994 (mtm110) cc_final: 0.6743 (mtp-110) REVERT: B 1151 GLN cc_start: 0.4964 (mm-40) cc_final: 0.4610 (mm110) REVERT: B 1165 HIS cc_start: 0.4983 (t70) cc_final: 0.4220 (t-170) REVERT: B 1197 ARG cc_start: 0.5846 (mmt-90) cc_final: 0.5597 (mmt180) outliers start: 60 outliers final: 19 residues processed: 299 average time/residue: 0.5856 time to fit residues: 197.2924 Evaluate side-chains 254 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 831 ARG Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 122 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 119 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 720 ASN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 720 ASN B 770 GLN ** B1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.186345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.163546 restraints weight = 35113.284| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.86 r_work: 0.3603 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18532 Z= 0.111 Angle : 0.648 17.231 25131 Z= 0.276 Chirality : 0.040 0.146 2737 Planarity : 0.004 0.047 3245 Dihedral : 6.259 72.564 2560 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.28 % Allowed : 18.02 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2325 helix: 1.17 (0.16), residues: 1028 sheet: -0.60 (0.25), residues: 382 loop : -0.75 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 114 TYR 0.025 0.001 TYR A 971 PHE 0.022 0.001 PHE A1099 TRP 0.019 0.001 TRP B 516 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00245 (18506) covalent geometry : angle 0.52135 (25055) SS BOND : bond 0.00532 ( 2) SS BOND : angle 1.26195 ( 4) hydrogen bonds : bond 0.03628 ( 817) hydrogen bonds : angle 4.52313 ( 2361) metal coordination : bond 0.00466 ( 24) metal coordination : angle 7.19922 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.7888 (mtm) cc_final: 0.7588 (mtm) REVERT: A 135 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: A 202 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: A 211 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: A 413 THR cc_start: 0.7045 (m) cc_final: 0.6371 (p) REVERT: A 522 MET cc_start: 0.4478 (mtt) cc_final: 0.4029 (mtt) REVERT: A 561 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5887 (mpt) REVERT: A 604 ASP cc_start: 0.5566 (m-30) cc_final: 0.5326 (m-30) REVERT: A 640 LYS cc_start: 0.6789 (tmtt) cc_final: 0.6568 (tmtm) REVERT: A 653 LYS cc_start: 0.7199 (mttt) cc_final: 0.6776 (mmtt) REVERT: A 771 ARG cc_start: 0.6893 (ptm160) cc_final: 0.6320 (ptm-80) REVERT: A 1032 TYR cc_start: 0.6290 (m-80) cc_final: 0.5813 (m-80) REVERT: A 1100 ARG cc_start: 0.6730 (mtm110) cc_final: 0.6443 (mtp-110) REVERT: B 36 MET cc_start: 0.7904 (mtm) cc_final: 0.7568 (mtm) REVERT: B 211 GLU cc_start: 0.7368 (mp0) cc_final: 0.6911 (mp0) REVERT: B 413 THR cc_start: 0.7058 (m) cc_final: 0.6352 (p) REVERT: B 485 ASP cc_start: 0.6742 (m-30) cc_final: 0.6007 (t0) REVERT: B 561 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5955 (mpt) REVERT: B 604 ASP cc_start: 0.6195 (m-30) cc_final: 0.5899 (m-30) REVERT: B 653 LYS cc_start: 0.7183 (mttt) cc_final: 0.6789 (mmtt) REVERT: B 771 ARG cc_start: 0.6876 (ptm160) cc_final: 0.5967 (ptp90) REVERT: B 971 TYR cc_start: 0.7331 (t80) cc_final: 0.6961 (t80) REVERT: B 1032 TYR cc_start: 0.6186 (m-80) cc_final: 0.5667 (m-80) REVERT: B 1100 ARG cc_start: 0.6745 (mtm110) cc_final: 0.6458 (mtp-110) outliers start: 42 outliers final: 16 residues processed: 279 average time/residue: 0.5976 time to fit residues: 187.2050 Evaluate side-chains 265 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 201 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A1073 ASN ** A1165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN B1073 ASN ** B1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.180962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.157702 restraints weight = 45531.742| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.93 r_work: 0.3454 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 18532 Z= 0.218 Angle : 0.764 18.687 25131 Z= 0.342 Chirality : 0.045 0.162 2737 Planarity : 0.005 0.051 3245 Dihedral : 6.516 76.197 2546 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.07 % Allowed : 18.34 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2325 helix: 0.73 (0.16), residues: 1034 sheet: -0.76 (0.26), residues: 372 loop : -0.99 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 831 TYR 0.017 0.002 TYR A 820 PHE 0.024 0.002 PHE A1099 TRP 0.025 0.002 TRP A 844 HIS 0.006 0.002 HIS B 976 Details of bonding type rmsd covalent geometry : bond 0.00512 (18506) covalent geometry : angle 0.63971 (25055) SS BOND : bond 0.00803 ( 2) SS BOND : angle 1.24262 ( 4) hydrogen bonds : bond 0.04634 ( 817) hydrogen bonds : angle 4.86157 ( 2361) metal coordination : bond 0.01247 ( 24) metal coordination : angle 7.83077 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.524 Fit side-chains REVERT: A 36 MET cc_start: 0.8014 (mtm) cc_final: 0.7652 (mtm) REVERT: A 202 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: A 211 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: A 519 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6797 (mp) REVERT: A 561 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5777 (mpt) REVERT: A 604 ASP cc_start: 0.5778 (m-30) cc_final: 0.5467 (m-30) REVERT: A 640 LYS cc_start: 0.6850 (tmtt) cc_final: 0.6640 (tmtm) REVERT: A 653 LYS cc_start: 0.7288 (mttt) cc_final: 0.6773 (mmtt) REVERT: A 770 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: A 771 ARG cc_start: 0.6925 (ptm160) cc_final: 0.6301 (ptm-80) REVERT: A 831 ARG cc_start: 0.7450 (ppt-90) cc_final: 0.7223 (ppt-90) REVERT: A 942 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6646 (mp) REVERT: A 1032 TYR cc_start: 0.6497 (m-80) cc_final: 0.6182 (m-80) REVERT: A 1100 ARG cc_start: 0.6933 (mtm110) cc_final: 0.6685 (mtp-110) REVERT: A 1151 GLN cc_start: 0.5026 (mm-40) cc_final: 0.4661 (mm110) REVERT: A 1197 ARG cc_start: 0.5924 (mmt-90) cc_final: 0.5679 (mmt180) REVERT: B 36 MET cc_start: 0.8039 (mtm) cc_final: 0.7715 (mtm) REVERT: B 202 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: B 211 GLU cc_start: 0.7359 (mp0) cc_final: 0.6924 (mp0) REVERT: B 561 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.5926 (mpt) REVERT: B 653 LYS cc_start: 0.7271 (mttt) cc_final: 0.6788 (mmtt) REVERT: B 771 ARG cc_start: 0.6907 (ptm160) cc_final: 0.6254 (ptm-80) REVERT: B 942 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6702 (mp) REVERT: B 971 TYR cc_start: 0.7425 (t80) cc_final: 0.6978 (t80) REVERT: B 1032 TYR cc_start: 0.6337 (m-80) cc_final: 0.5798 (m-80) REVERT: B 1100 ARG cc_start: 0.6913 (mtm110) cc_final: 0.6672 (mtp-110) REVERT: B 1151 GLN cc_start: 0.5060 (mm-40) cc_final: 0.4665 (mm110) REVERT: B 1197 ARG cc_start: 0.5934 (mmt-90) cc_final: 0.5702 (mmt180) outliers start: 57 outliers final: 17 residues processed: 262 average time/residue: 0.6043 time to fit residues: 176.7397 Evaluate side-chains 248 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 770 GLN Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 98 optimal weight: 0.0370 chunk 33 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.184742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.162908 restraints weight = 43881.035| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.71 r_work: 0.3519 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18532 Z= 0.125 Angle : 0.673 17.149 25131 Z= 0.290 Chirality : 0.041 0.152 2737 Planarity : 0.004 0.049 3245 Dihedral : 6.253 74.917 2546 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.44 % Allowed : 19.77 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2325 helix: 1.01 (0.16), residues: 1038 sheet: -0.72 (0.26), residues: 374 loop : -0.90 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 783 TYR 0.018 0.001 TYR A 971 PHE 0.025 0.002 PHE A1099 TRP 0.018 0.001 TRP A 844 HIS 0.004 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00287 (18506) covalent geometry : angle 0.54670 (25055) SS BOND : bond 0.00543 ( 2) SS BOND : angle 1.35921 ( 4) hydrogen bonds : bond 0.03780 ( 817) hydrogen bonds : angle 4.58683 ( 2361) metal coordination : bond 0.00516 ( 24) metal coordination : angle 7.36088 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.683 Fit side-chains REVERT: A 36 MET cc_start: 0.7908 (mtm) cc_final: 0.7599 (mtm) REVERT: A 202 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: A 211 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 332 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6032 (mt-10) REVERT: A 395 GLU cc_start: 0.6770 (mm-30) cc_final: 0.5865 (tt0) REVERT: A 413 THR cc_start: 0.6902 (m) cc_final: 0.6231 (p) REVERT: A 485 ASP cc_start: 0.6915 (m-30) cc_final: 0.6166 (t0) REVERT: A 604 ASP cc_start: 0.5735 (m-30) cc_final: 0.5435 (m-30) REVERT: A 640 LYS cc_start: 0.6828 (tmtt) cc_final: 0.6615 (tmtm) REVERT: A 653 LYS cc_start: 0.7248 (mttt) cc_final: 0.6750 (mmtt) REVERT: A 771 ARG cc_start: 0.6902 (ptm160) cc_final: 0.6334 (ptm-80) REVERT: A 783 ARG cc_start: 0.6373 (mpt-90) cc_final: 0.5917 (mpt-90) REVERT: A 1032 TYR cc_start: 0.6248 (m-80) cc_final: 0.5690 (m-80) REVERT: A 1100 ARG cc_start: 0.6789 (mtm110) cc_final: 0.6520 (mtp-110) REVERT: A 1197 ARG cc_start: 0.5903 (mmt-90) cc_final: 0.5686 (mmt180) REVERT: B 36 MET cc_start: 0.7957 (mtm) cc_final: 0.7599 (mtm) REVERT: B 202 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: B 211 GLU cc_start: 0.7374 (mp0) cc_final: 0.6942 (mp0) REVERT: B 353 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: B 413 THR cc_start: 0.6880 (m) cc_final: 0.6211 (p) REVERT: B 485 ASP cc_start: 0.6840 (m-30) cc_final: 0.6128 (t0) REVERT: B 561 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.5928 (mpt) REVERT: B 653 LYS cc_start: 0.7260 (mttt) cc_final: 0.6769 (mmtt) REVERT: B 771 ARG cc_start: 0.6874 (ptm160) cc_final: 0.6294 (ptm-80) REVERT: B 783 ARG cc_start: 0.6228 (mpt-90) cc_final: 0.5875 (mmt180) REVERT: B 942 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6701 (mp) REVERT: B 971 TYR cc_start: 0.7360 (t80) cc_final: 0.7154 (t80) REVERT: B 1032 TYR cc_start: 0.6156 (m-80) cc_final: 0.5581 (m-80) REVERT: B 1100 ARG cc_start: 0.6802 (mtm110) cc_final: 0.6546 (mtp-110) REVERT: B 1151 GLN cc_start: 0.4966 (mm-40) cc_final: 0.4635 (mm110) REVERT: B 1165 HIS cc_start: 0.6205 (OUTLIER) cc_final: 0.5971 (t-170) outliers start: 45 outliers final: 16 residues processed: 276 average time/residue: 0.6169 time to fit residues: 190.5502 Evaluate side-chains 258 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1165 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 191 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 39 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A1165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.184012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.160220 restraints weight = 42460.556| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.55 r_work: 0.3516 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18532 Z= 0.141 Angle : 0.678 17.666 25131 Z= 0.298 Chirality : 0.042 0.162 2737 Planarity : 0.004 0.049 3245 Dihedral : 6.266 75.160 2546 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.96 % Allowed : 20.61 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2325 helix: 1.03 (0.16), residues: 1026 sheet: -0.66 (0.26), residues: 366 loop : -0.86 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 831 TYR 0.015 0.002 TYR A 971 PHE 0.019 0.002 PHE A 124 TRP 0.019 0.002 TRP A 844 HIS 0.004 0.001 HIS B 976 Details of bonding type rmsd covalent geometry : bond 0.00327 (18506) covalent geometry : angle 0.56248 (25055) SS BOND : bond 0.00662 ( 2) SS BOND : angle 1.34165 ( 4) hydrogen bonds : bond 0.03901 ( 817) hydrogen bonds : angle 4.61910 ( 2361) metal coordination : bond 0.00699 ( 24) metal coordination : angle 7.07769 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.574 Fit side-chains REVERT: A 36 MET cc_start: 0.7940 (mtm) cc_final: 0.7630 (mtm) REVERT: A 202 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: A 211 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: A 332 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6021 (mt-10) REVERT: A 413 THR cc_start: 0.6907 (m) cc_final: 0.6222 (p) REVERT: A 485 ASP cc_start: 0.6945 (m-30) cc_final: 0.6244 (t0) REVERT: A 604 ASP cc_start: 0.5694 (m-30) cc_final: 0.5438 (m-30) REVERT: A 640 LYS cc_start: 0.6857 (tmtt) cc_final: 0.6650 (tmtm) REVERT: A 653 LYS cc_start: 0.7316 (mttt) cc_final: 0.6807 (mmtt) REVERT: A 771 ARG cc_start: 0.6872 (ptm160) cc_final: 0.5928 (ptp90) REVERT: A 1032 TYR cc_start: 0.6279 (m-80) cc_final: 0.5634 (m-80) REVERT: A 1100 ARG cc_start: 0.6820 (mtm110) cc_final: 0.6565 (mtp-110) REVERT: A 1197 ARG cc_start: 0.5920 (mmt-90) cc_final: 0.5704 (mmt180) REVERT: B 36 MET cc_start: 0.7971 (mtm) cc_final: 0.7614 (mtm) REVERT: B 202 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: B 208 MET cc_start: 0.6529 (ttp) cc_final: 0.6135 (ptm) REVERT: B 211 GLU cc_start: 0.7396 (mp0) cc_final: 0.6971 (mp0) REVERT: B 413 THR cc_start: 0.6835 (m) cc_final: 0.6141 (p) REVERT: B 485 ASP cc_start: 0.6899 (m-30) cc_final: 0.6172 (t0) REVERT: B 561 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5797 (mpt) REVERT: B 653 LYS cc_start: 0.7262 (mttt) cc_final: 0.6786 (mmtt) REVERT: B 771 ARG cc_start: 0.6899 (ptm160) cc_final: 0.6317 (ptm-80) REVERT: B 783 ARG cc_start: 0.6324 (mpt-90) cc_final: 0.5960 (mmt180) REVERT: B 942 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6695 (mp) REVERT: B 971 TYR cc_start: 0.7430 (t80) cc_final: 0.7223 (t80) REVERT: B 1032 TYR cc_start: 0.6106 (m-80) cc_final: 0.5449 (m-80) REVERT: B 1100 ARG cc_start: 0.6814 (mtm110) cc_final: 0.6560 (mtp-110) REVERT: B 1165 HIS cc_start: 0.6214 (OUTLIER) cc_final: 0.5985 (t-170) outliers start: 36 outliers final: 19 residues processed: 259 average time/residue: 0.6104 time to fit residues: 177.0324 Evaluate side-chains 257 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1165 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 161 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 168 optimal weight: 0.0030 chunk 181 optimal weight: 0.3980 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 96 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** A1165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 96 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.185557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.163057 restraints weight = 32528.218| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.72 r_work: 0.3612 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18532 Z= 0.112 Angle : 0.639 16.530 25131 Z= 0.279 Chirality : 0.041 0.157 2737 Planarity : 0.004 0.047 3245 Dihedral : 6.061 71.377 2546 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.28 % Allowed : 20.93 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2325 helix: 1.23 (0.16), residues: 1026 sheet: -0.59 (0.26), residues: 366 loop : -0.76 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 783 TYR 0.010 0.001 TYR A 971 PHE 0.018 0.001 PHE A 638 TRP 0.015 0.001 TRP A 844 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00253 (18506) covalent geometry : angle 0.53198 (25055) SS BOND : bond 0.00622 ( 2) SS BOND : angle 1.39187 ( 4) hydrogen bonds : bond 0.03503 ( 817) hydrogen bonds : angle 4.49006 ( 2361) metal coordination : bond 0.00449 ( 24) metal coordination : angle 6.63503 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 0.719 Fit side-chains REVERT: A 3 LYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4987 (mttm) REVERT: A 36 MET cc_start: 0.7922 (mtm) cc_final: 0.7581 (mtm) REVERT: A 202 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: A 211 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: A 395 GLU cc_start: 0.6786 (mm-30) cc_final: 0.5848 (tt0) REVERT: A 413 THR cc_start: 0.6768 (OUTLIER) cc_final: 0.6172 (p) REVERT: A 485 ASP cc_start: 0.6942 (m-30) cc_final: 0.6246 (t0) REVERT: A 604 ASP cc_start: 0.5742 (m-30) cc_final: 0.5508 (m-30) REVERT: A 640 LYS cc_start: 0.6883 (tmtt) cc_final: 0.6673 (tmtm) REVERT: A 653 LYS cc_start: 0.7340 (mttt) cc_final: 0.6818 (mmtt) REVERT: A 771 ARG cc_start: 0.6824 (ptm160) cc_final: 0.5881 (ptp90) REVERT: A 1032 TYR cc_start: 0.6169 (m-80) cc_final: 0.5358 (m-80) REVERT: A 1100 ARG cc_start: 0.6756 (mtm110) cc_final: 0.6448 (mtp-110) REVERT: B 3 LYS cc_start: 0.5270 (OUTLIER) cc_final: 0.5039 (mttm) REVERT: B 36 MET cc_start: 0.7894 (mtm) cc_final: 0.7603 (mtm) REVERT: B 211 GLU cc_start: 0.7452 (mp0) cc_final: 0.7031 (mp0) REVERT: B 413 THR cc_start: 0.6726 (OUTLIER) cc_final: 0.6054 (p) REVERT: B 485 ASP cc_start: 0.6988 (m-30) cc_final: 0.6265 (t0) REVERT: B 771 ARG cc_start: 0.6885 (ptm160) cc_final: 0.6327 (ptm-80) REVERT: B 918 ASN cc_start: 0.6308 (m110) cc_final: 0.6079 (m110) REVERT: B 971 TYR cc_start: 0.7489 (t80) cc_final: 0.7153 (t80) REVERT: B 1032 TYR cc_start: 0.6052 (m-80) cc_final: 0.5213 (m-80) REVERT: B 1100 ARG cc_start: 0.6747 (mtm110) cc_final: 0.6443 (mtp-110) outliers start: 42 outliers final: 12 residues processed: 274 average time/residue: 0.6142 time to fit residues: 189.0347 Evaluate side-chains 261 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1024 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 48 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS A 289 HIS A 421 GLN A 560 ASN A 694 GLN ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 602 ASN B 694 GLN ** B1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.183584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.160379 restraints weight = 36431.157| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.07 r_work: 0.3562 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18532 Z= 0.156 Angle : 0.711 17.929 25131 Z= 0.313 Chirality : 0.043 0.168 2737 Planarity : 0.005 0.049 3245 Dihedral : 6.103 75.567 2541 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.75 % Allowed : 21.99 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2325 helix: 1.09 (0.16), residues: 1026 sheet: -0.70 (0.25), residues: 374 loop : -0.81 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1027 TYR 0.026 0.002 TYR A 971 PHE 0.025 0.002 PHE B1194 TRP 0.023 0.002 TRP A 622 HIS 0.006 0.001 HIS A1165 Details of bonding type rmsd covalent geometry : bond 0.00364 (18506) covalent geometry : angle 0.59619 (25055) SS BOND : bond 0.00737 ( 2) SS BOND : angle 1.31016 ( 4) hydrogen bonds : bond 0.04026 ( 817) hydrogen bonds : angle 4.65196 ( 2361) metal coordination : bond 0.00843 ( 24) metal coordination : angle 7.24862 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.652 Fit side-chains REVERT: A 3 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.5136 (mttm) REVERT: A 36 MET cc_start: 0.7915 (mtm) cc_final: 0.7604 (mtm) REVERT: A 202 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: A 208 MET cc_start: 0.6652 (ptm) cc_final: 0.6379 (ptm) REVERT: A 211 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: A 413 THR cc_start: 0.6898 (m) cc_final: 0.6226 (p) REVERT: A 485 ASP cc_start: 0.6955 (m-30) cc_final: 0.6236 (t0) REVERT: A 502 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5028 (pt0) REVERT: A 533 THR cc_start: 0.7553 (p) cc_final: 0.7087 (t) REVERT: A 604 ASP cc_start: 0.5697 (m-30) cc_final: 0.5461 (m-30) REVERT: A 640 LYS cc_start: 0.6704 (tmtt) cc_final: 0.6491 (tmtm) REVERT: A 771 ARG cc_start: 0.6867 (ptm160) cc_final: 0.6264 (ptm-80) REVERT: A 942 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6602 (mp) REVERT: A 1032 TYR cc_start: 0.6185 (m-80) cc_final: 0.5628 (m-80) REVERT: A 1100 ARG cc_start: 0.6726 (mtm110) cc_final: 0.6444 (mtp-110) REVERT: B 3 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.5122 (mttm) REVERT: B 36 MET cc_start: 0.7944 (mtm) cc_final: 0.7700 (mtm) REVERT: B 202 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: B 211 GLU cc_start: 0.7348 (mp0) cc_final: 0.6915 (mp0) REVERT: B 413 THR cc_start: 0.6897 (m) cc_final: 0.6199 (p) REVERT: B 485 ASP cc_start: 0.6829 (m-30) cc_final: 0.6145 (t0) REVERT: B 533 THR cc_start: 0.7573 (p) cc_final: 0.7097 (t) REVERT: B 606 VAL cc_start: 0.6766 (t) cc_final: 0.6543 (t) REVERT: B 771 ARG cc_start: 0.6937 (ptm160) cc_final: 0.6366 (ptm-80) REVERT: B 918 ASN cc_start: 0.6199 (m110) cc_final: 0.5995 (m110) REVERT: B 942 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6707 (mp) REVERT: B 971 TYR cc_start: 0.7425 (t80) cc_final: 0.7147 (t80) REVERT: B 1032 TYR cc_start: 0.5957 (m-80) cc_final: 0.5361 (m-80) REVERT: B 1100 ARG cc_start: 0.6734 (mtm110) cc_final: 0.6456 (mtp-110) REVERT: B 1132 ASN cc_start: 0.7543 (t0) cc_final: 0.6524 (t0) outliers start: 32 outliers final: 15 residues processed: 258 average time/residue: 0.5935 time to fit residues: 172.0066 Evaluate side-chains 251 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.183953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.159885 restraints weight = 43570.641| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.63 r_work: 0.3508 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18532 Z= 0.148 Angle : 0.706 17.773 25131 Z= 0.311 Chirality : 0.043 0.167 2737 Planarity : 0.004 0.048 3245 Dihedral : 6.141 74.864 2541 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.70 % Allowed : 22.05 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2325 helix: 1.07 (0.16), residues: 1026 sheet: -0.72 (0.25), residues: 384 loop : -0.80 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 831 TYR 0.031 0.002 TYR A 971 PHE 0.022 0.002 PHE A 638 TRP 0.020 0.002 TRP B 622 HIS 0.005 0.001 HIS A1165 Details of bonding type rmsd covalent geometry : bond 0.00345 (18506) covalent geometry : angle 0.59300 (25055) SS BOND : bond 0.00693 ( 2) SS BOND : angle 1.29505 ( 4) hydrogen bonds : bond 0.03948 ( 817) hydrogen bonds : angle 4.65217 ( 2361) metal coordination : bond 0.00745 ( 24) metal coordination : angle 7.17092 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.616 Fit side-chains REVERT: A 3 LYS cc_start: 0.5380 (OUTLIER) cc_final: 0.4982 (mttm) REVERT: A 36 MET cc_start: 0.7968 (mtm) cc_final: 0.7677 (mtm) REVERT: A 202 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: A 208 MET cc_start: 0.6804 (ptm) cc_final: 0.6533 (ptm) REVERT: A 211 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 413 THR cc_start: 0.6847 (m) cc_final: 0.6154 (p) REVERT: A 485 ASP cc_start: 0.7028 (m-30) cc_final: 0.6305 (t0) REVERT: A 533 THR cc_start: 0.7609 (p) cc_final: 0.7126 (t) REVERT: A 604 ASP cc_start: 0.5689 (m-30) cc_final: 0.5438 (m-30) REVERT: A 640 LYS cc_start: 0.6771 (tmtt) cc_final: 0.6559 (tmtm) REVERT: A 921 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5811 (mm) REVERT: A 942 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6642 (mp) REVERT: A 1032 TYR cc_start: 0.6310 (m-80) cc_final: 0.5594 (m-80) REVERT: A 1100 ARG cc_start: 0.6799 (mtm110) cc_final: 0.6498 (mtp-110) REVERT: B 3 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.5102 (mttm) REVERT: B 36 MET cc_start: 0.7996 (mtm) cc_final: 0.7754 (mtm) REVERT: B 211 GLU cc_start: 0.7416 (mp0) cc_final: 0.7006 (mp0) REVERT: B 413 THR cc_start: 0.6719 (m) cc_final: 0.5993 (p) REVERT: B 485 ASP cc_start: 0.6903 (m-30) cc_final: 0.6208 (t0) REVERT: B 533 THR cc_start: 0.7515 (p) cc_final: 0.7050 (t) REVERT: B 563 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6489 (mmt) REVERT: B 606 VAL cc_start: 0.6750 (t) cc_final: 0.6516 (t) REVERT: B 771 ARG cc_start: 0.6919 (ptm160) cc_final: 0.6354 (ptm-80) REVERT: B 918 ASN cc_start: 0.6235 (m110) cc_final: 0.6019 (m110) REVERT: B 942 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6722 (mp) REVERT: B 971 TYR cc_start: 0.7410 (t80) cc_final: 0.7005 (t80) REVERT: B 1027 ARG cc_start: 0.6033 (mtp180) cc_final: 0.5273 (ttp-110) REVERT: B 1032 TYR cc_start: 0.6032 (m-80) cc_final: 0.5321 (m-80) REVERT: B 1100 ARG cc_start: 0.6810 (mtm110) cc_final: 0.6515 (mtp-110) REVERT: B 1132 ASN cc_start: 0.7597 (t0) cc_final: 0.6537 (t0) outliers start: 31 outliers final: 16 residues processed: 250 average time/residue: 0.6022 time to fit residues: 169.1610 Evaluate side-chains 252 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 138 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 31 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 918 ASN ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.186703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.164312 restraints weight = 40898.551| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.33 r_work: 0.3583 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18532 Z= 0.112 Angle : 0.650 16.207 25131 Z= 0.286 Chirality : 0.041 0.166 2737 Planarity : 0.004 0.046 3245 Dihedral : 5.849 69.138 2541 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.27 % Allowed : 22.58 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 2325 helix: 1.30 (0.16), residues: 1026 sheet: -0.64 (0.25), residues: 378 loop : -0.66 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.028 0.001 TYR A 971 PHE 0.020 0.001 PHE B 638 TRP 0.015 0.002 TRP A 844 HIS 0.006 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00252 (18506) covalent geometry : angle 0.55069 (25055) SS BOND : bond 0.00626 ( 2) SS BOND : angle 1.52345 ( 4) hydrogen bonds : bond 0.03421 ( 817) hydrogen bonds : angle 4.50386 ( 2361) metal coordination : bond 0.00400 ( 24) metal coordination : angle 6.46324 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.591 Fit side-chains REVERT: A 36 MET cc_start: 0.7845 (mtm) cc_final: 0.7503 (mtm) REVERT: A 211 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: A 395 GLU cc_start: 0.6643 (mm-30) cc_final: 0.5799 (tt0) REVERT: A 413 THR cc_start: 0.6732 (m) cc_final: 0.6147 (p) REVERT: A 485 ASP cc_start: 0.6860 (m-30) cc_final: 0.6157 (t0) REVERT: A 533 THR cc_start: 0.7597 (p) cc_final: 0.7044 (t) REVERT: A 561 MET cc_start: 0.5818 (mmm) cc_final: 0.5536 (mpm) REVERT: A 604 ASP cc_start: 0.5737 (m-30) cc_final: 0.5527 (m-30) REVERT: A 640 LYS cc_start: 0.6713 (tmtt) cc_final: 0.6497 (tmtm) REVERT: A 771 ARG cc_start: 0.6975 (ptm160) cc_final: 0.6469 (ptm-80) REVERT: A 1032 TYR cc_start: 0.5942 (m-80) cc_final: 0.5230 (m-80) REVERT: A 1100 ARG cc_start: 0.6669 (mtm110) cc_final: 0.6437 (mtp-110) REVERT: B 36 MET cc_start: 0.7773 (mtm) cc_final: 0.7502 (mtm) REVERT: B 211 GLU cc_start: 0.7427 (mp0) cc_final: 0.6968 (mp0) REVERT: B 413 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6069 (p) REVERT: B 485 ASP cc_start: 0.6837 (m-30) cc_final: 0.6198 (t0) REVERT: B 533 THR cc_start: 0.7571 (p) cc_final: 0.7009 (t) REVERT: B 563 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6460 (mmt) REVERT: B 771 ARG cc_start: 0.6901 (ptm160) cc_final: 0.6350 (ptm-80) REVERT: B 918 ASN cc_start: 0.6238 (m110) cc_final: 0.6021 (m110) REVERT: B 971 TYR cc_start: 0.7330 (t80) cc_final: 0.6974 (t80) REVERT: B 1032 TYR cc_start: 0.5839 (m-80) cc_final: 0.5199 (m-80) REVERT: B 1100 ARG cc_start: 0.6678 (mtm110) cc_final: 0.6373 (mtp-110) outliers start: 23 outliers final: 12 residues processed: 246 average time/residue: 0.5950 time to fit residues: 164.7007 Evaluate side-chains 238 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 204 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 97 optimal weight: 0.3980 chunk 186 optimal weight: 0.0970 chunk 220 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 918 ASN ** A1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 128 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN B 694 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.184772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162686 restraints weight = 41500.326| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.63 r_work: 0.3546 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18532 Z= 0.144 Angle : 0.698 17.442 25131 Z= 0.307 Chirality : 0.043 0.168 2737 Planarity : 0.004 0.048 3245 Dihedral : 5.856 73.701 2539 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.32 % Allowed : 22.84 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2325 helix: 1.20 (0.16), residues: 1026 sheet: -0.68 (0.26), residues: 374 loop : -0.74 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 831 TYR 0.017 0.002 TYR A 971 PHE 0.023 0.002 PHE B 638 TRP 0.018 0.002 TRP A 844 HIS 0.004 0.001 HIS A 976 Details of bonding type rmsd covalent geometry : bond 0.00335 (18506) covalent geometry : angle 0.58915 (25055) SS BOND : bond 0.00727 ( 2) SS BOND : angle 1.38227 ( 4) hydrogen bonds : bond 0.03835 ( 817) hydrogen bonds : angle 4.60052 ( 2361) metal coordination : bond 0.00743 ( 24) metal coordination : angle 7.00504 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5347.06 seconds wall clock time: 92 minutes 36.14 seconds (5556.14 seconds total)