Starting phenix.real_space_refine on Sat Jul 4 04:21:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7plm_13493/07_2026/7plm_13493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plm_13493/07_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_13493/07_2026/7plm_13493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plm_13493/07_2026/7plm_13493.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7plm_13493/07_2026/7plm_13493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7plm_13493/07_2026/7plm_13493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plm_13493/07_2026/7plm_13493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plm_13493/07_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-6108/lib/python3.11/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: 6.40, per 1000 atoms: 0.35 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: 1.36 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: 0.87 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: 3.71 Time building geometry restraints manager: 1.83 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: 9985 17.94 - 35.87: 829 35.87 - 53.81: 184 53.81 - 71.74: 42 71.74 - 89.68: 15 Dihedral angle restraints: 11055 sinusoidal: 4327 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 11052 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: 1.160 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.240 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 14.550 89.678 6743 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/Z covalent geometry : bond 0.00567 / 0.25 (18506) covalent geometry : angle 0.69538 / 0.38 (25055) SS BOND : bond 0.00756 / 0.45 ( 2) SS BOND : angle 1.64172 / 0.81 ( 4) hydrogen bonds : bond 0.13297 / 9.07 ( 817) hydrogen bonds : angle 6.24993 / 4.50 ( 2361) metal coordination : bond 0.01322 / 0.86 ( 24) metal coordination : angle 7.98880 / 5.14 ( 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 : 0.794 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: 0.5613 time to fit residues: 242.5200 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 : 0.414 ------------------------------------------------------------------------------- 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... 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 = 0.4008 r_free = 0.4008 target = 0.184948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.161026 restraints weight = 49263.188| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.93 r_work: 0.3478 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 110 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (17 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1274 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= 0.138 Angle : 0.714 18.539 25131 Z= 0.304 Chirality : 0.042 0.150 2737 Planarity : 0.004 0.050 3245 Dihedral : 7.587 77.449 2600 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.18 % Allowed : 15.79 % Favored : 81.03 % 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: 0.85 (0.16), residues: 1034 sheet: -0.54 (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 0.001 TRP A 844 HIS 0.005 0.001 HIS A 976 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (18506) covalent geometry : angle 0.56560 / 0.30 (25055) SS BOND : bond 0.00524 / 0.29 ( 2) SS BOND : angle 1.39554 / 0.68 ( 4) hydrogen bonds : bond 0.04219 / 2.89 ( 817) hydrogen bonds : angle 4.79888 / 3.49 ( 2361) metal coordination : bond 0.00697 / 0.49 ( 24) metal coordination : angle 8.15826 / 5.34 ( 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 319 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 0.550 Fit side-chains REVERT: A 36 MET cc_start: 0.8034 (mtm) cc_final: 0.7736 (mtm) REVERT: A 135 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7160 (mp10) REVERT: A 211 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: A 502 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.5216 (pm20) REVERT: A 604 ASP cc_start: 0.5595 (m-30) cc_final: 0.5308 (m-30) REVERT: A 640 LYS cc_start: 0.6907 (tmtt) cc_final: 0.6678 (tmtm) REVERT: A 653 LYS cc_start: 0.7225 (mttt) cc_final: 0.6685 (mmtt) REVERT: A 771 ARG cc_start: 0.6914 (ptm160) cc_final: 0.6436 (ptm-80) REVERT: A 831 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7335 (ppt-90) REVERT: A 926 TYR cc_start: 0.7466 (m-80) cc_final: 0.7048 (m-80) REVERT: A 1032 TYR cc_start: 0.6576 (m-80) cc_final: 0.6351 (m-80) REVERT: A 1100 ARG cc_start: 0.6992 (mtm110) cc_final: 0.6746 (mtp-110) REVERT: A 1151 GLN cc_start: 0.4968 (mm-40) cc_final: 0.4633 (mm110) REVERT: A 1165 HIS cc_start: 0.4964 (t70) cc_final: 0.4204 (t-170) REVERT: B 36 MET cc_start: 0.8059 (mtm) cc_final: 0.7774 (mtm) REVERT: B 135 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: B 211 GLU cc_start: 0.7474 (mp0) cc_final: 0.7092 (mp0) REVERT: B 653 LYS cc_start: 0.7242 (mttt) cc_final: 0.6747 (mmtt) REVERT: B 771 ARG cc_start: 0.7002 (ptm160) cc_final: 0.6489 (ptm-80) REVERT: B 831 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7335 (ppt-90) REVERT: B 926 TYR cc_start: 0.7483 (m-80) cc_final: 0.7257 (m-80) REVERT: B 971 TYR cc_start: 0.7344 (t80) cc_final: 0.6964 (t80) REVERT: B 1032 TYR cc_start: 0.6498 (m-80) cc_final: 0.6226 (m-80) REVERT: B 1100 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6748 (mtp-110) REVERT: B 1151 GLN cc_start: 0.4963 (mm-40) cc_final: 0.4620 (mm110) REVERT: B 1165 HIS cc_start: 0.4993 (t70) cc_final: 0.4236 (t-170) REVERT: B 1197 ARG cc_start: 0.5855 (mmt-90) cc_final: 0.5598 (mmt180) outliers start: 59 outliers final: 19 residues processed: 297 average time/residue: 0.5803 time to fit residues: 194.5859 Evaluate side-chains 255 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 152 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 168 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 119 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4017 r_free = 0.4017 target = 0.185809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.163223 restraints weight = 35170.376| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.98 r_work: 0.3580 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18532 Z= 0.115 Angle : 0.654 17.331 25131 Z= 0.280 Chirality : 0.041 0.147 2737 Planarity : 0.004 0.048 3245 Dihedral : 5.916 58.712 2552 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.44 % Allowed : 17.86 % 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: 0.09 (0.17), residues: 2325 helix: 1.13 (0.16), residues: 1028 sheet: -0.61 (0.25), residues: 382 loop : -0.78 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 114 TYR 0.013 0.001 TYR B 875 PHE 0.022 0.001 PHE A1099 TRP 0.019 0.001 TRP B 516 HIS 0.004 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (18506) covalent geometry : angle 0.52727 / 0.28 (25055) SS BOND : bond 0.00530 / 0.30 ( 2) SS BOND : angle 1.23092 / 0.61 ( 4) hydrogen bonds : bond 0.03708 / 2.55 ( 817) hydrogen bonds : angle 4.55010 / 3.30 ( 2361) metal coordination : bond 0.00482 / 0.33 ( 24) metal coordination : angle 7.23900 / 4.68 ( 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: 45 poor density : 251 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.7906 (mtm) cc_final: 0.7609 (mtm) REVERT: A 135 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7132 (mp10) REVERT: A 202 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: A 211 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: A 522 MET cc_start: 0.4440 (mtt) cc_final: 0.3992 (mtt) REVERT: A 561 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5866 (mpt) REVERT: A 604 ASP cc_start: 0.5574 (m-30) cc_final: 0.5329 (m-30) REVERT: A 640 LYS cc_start: 0.6798 (tmtt) cc_final: 0.6577 (tmtm) REVERT: A 653 LYS cc_start: 0.7214 (mttt) cc_final: 0.6771 (mmtt) REVERT: A 771 ARG cc_start: 0.6899 (ptm160) cc_final: 0.6317 (ptm-80) REVERT: A 1032 TYR cc_start: 0.6256 (m-80) cc_final: 0.5793 (m-80) REVERT: A 1080 MET cc_start: 0.5945 (mmp) cc_final: 0.5726 (mmp) REVERT: A 1100 ARG cc_start: 0.6759 (mtm110) cc_final: 0.6477 (mtp-110) REVERT: A 1197 ARG cc_start: 0.5825 (mmt-90) cc_final: 0.5557 (mmt180) REVERT: B 36 MET cc_start: 0.7920 (mtm) cc_final: 0.7583 (mtm) REVERT: B 202 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: B 211 GLU cc_start: 0.7349 (mp0) cc_final: 0.6895 (mp0) REVERT: B 485 ASP cc_start: 0.6749 (m-30) cc_final: 0.6002 (t0) REVERT: B 502 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5316 (pm20) REVERT: B 561 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5928 (mpt) REVERT: B 604 ASP cc_start: 0.6162 (m-30) cc_final: 0.5890 (m-30) REVERT: B 653 LYS cc_start: 0.7197 (mttt) cc_final: 0.6786 (mmtt) REVERT: B 771 ARG cc_start: 0.6897 (ptm160) cc_final: 0.5973 (ptp90) REVERT: B 971 TYR cc_start: 0.7351 (t80) cc_final: 0.6965 (t80) REVERT: B 1032 TYR cc_start: 0.6157 (m-80) cc_final: 0.5628 (m-80) REVERT: B 1100 ARG cc_start: 0.6750 (mtm110) cc_final: 0.6469 (mtp-110) REVERT: B 1197 ARG cc_start: 0.5833 (mmt-90) cc_final: 0.5581 (mmt180) outliers start: 45 outliers final: 15 residues processed: 278 average time/residue: 0.6031 time to fit residues: 188.2989 Evaluate side-chains 259 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 187 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 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 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 502 GLU 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: 8.9990 chunk 219 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.178662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.154343 restraints weight = 45100.097| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.74 r_work: 0.3430 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 18532 Z= 0.301 Angle : 0.863 19.567 25131 Z= 0.396 Chirality : 0.049 0.175 2737 Planarity : 0.006 0.057 3245 Dihedral : 6.490 58.832 2538 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.71 % Allowed : 18.12 % Favored : 78.17 % 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: -0.72 (0.17), residues: 2325 helix: 0.35 (0.15), residues: 1036 sheet: -0.81 (0.25), residues: 372 loop : -1.17 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1149 TYR 0.020 0.003 TYR A 820 PHE 0.028 0.003 PHE A1099 TRP 0.030 0.003 TRP B 844 HIS 0.008 0.002 HIS A 976 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.30 (18506) covalent geometry : angle 0.74041 / 0.39 (25055) SS BOND : bond 0.01004 / 0.57 ( 2) SS BOND : angle 1.31029 / 0.64 ( 4) hydrogen bonds : bond 0.05319 / 3.68 ( 817) hydrogen bonds : angle 5.14521 / 3.74 ( 2361) metal coordination : bond 0.01747 / 1.17 ( 24) metal coordination : angle 8.32334 / 5.35 ( 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 302 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 233 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.7996 (mtm) cc_final: 0.7668 (mtm) REVERT: A 202 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: A 211 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: A 353 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: A 519 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6693 (mp) REVERT: A 561 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.5879 (mpt) REVERT: A 604 ASP cc_start: 0.5899 (m-30) cc_final: 0.5601 (m-30) REVERT: A 653 LYS cc_start: 0.7331 (mttt) cc_final: 0.6808 (mmtt) REVERT: A 770 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: A 771 ARG cc_start: 0.6911 (ptm160) cc_final: 0.5946 (ptp90) REVERT: A 942 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6682 (mp) REVERT: A 1032 TYR cc_start: 0.6501 (m-80) cc_final: 0.6183 (m-80) REVERT: A 1100 ARG cc_start: 0.6971 (mtm110) cc_final: 0.6743 (mtp-110) REVERT: A 1197 ARG cc_start: 0.5954 (mmt-90) cc_final: 0.5714 (mmt180) REVERT: B 36 MET cc_start: 0.8027 (mtm) cc_final: 0.7767 (mtm) REVERT: B 202 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: B 211 GLU cc_start: 0.7360 (mp0) cc_final: 0.6922 (mp0) REVERT: B 353 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: B 519 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6770 (mp) REVERT: B 561 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.6011 (mpt) REVERT: B 653 LYS cc_start: 0.7270 (mttt) cc_final: 0.6811 (mmtt) REVERT: B 771 ARG cc_start: 0.6893 (ptm160) cc_final: 0.5947 (ptp90) REVERT: B 797 LYS cc_start: 0.6926 (tttp) cc_final: 0.6714 (tttt) REVERT: B 942 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6657 (mp) REVERT: B 971 TYR cc_start: 0.7435 (t80) cc_final: 0.6858 (t80) REVERT: B 1100 ARG cc_start: 0.6980 (mtm110) cc_final: 0.6761 (mtp-110) REVERT: B 1132 ASN cc_start: 0.7736 (t0) cc_final: 0.6686 (t0) REVERT: B 1151 GLN cc_start: 0.5068 (mm-40) cc_final: 0.4704 (mm110) REVERT: B 1197 ARG cc_start: 0.5976 (mmt-90) cc_final: 0.5487 (mmp80) outliers start: 69 outliers final: 22 residues processed: 274 average time/residue: 0.6126 time to fit residues: 189.1109 Evaluate side-chains 258 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 270 GLU Chi-restraints excluded: chain A residue 353 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 681 VAL 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 353 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 698 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 98 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 720 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.184077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.161856 restraints weight = 41673.470| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.42 r_work: 0.3538 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 18532 Z= 0.127 Angle : 0.688 17.561 25131 Z= 0.296 Chirality : 0.041 0.153 2737 Planarity : 0.004 0.050 3245 Dihedral : 6.028 60.299 2538 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.02 % Allowed : 19.40 % Favored : 77.58 % 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: 0.93 (0.16), residues: 1034 sheet: -0.77 (0.25), residues: 374 loop : -0.96 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 831 TYR 0.021 0.002 TYR A 971 PHE 0.027 0.002 PHE B1099 TRP 0.018 0.001 TRP B 516 HIS 0.004 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (18506) covalent geometry : angle 0.55731 / 0.29 (25055) SS BOND : bond 0.00614 / 0.34 ( 2) SS BOND : angle 1.40982 / 0.70 ( 4) hydrogen bonds : bond 0.03839 / 2.63 ( 817) hydrogen bonds : angle 4.65324 / 3.39 ( 2361) metal coordination : bond 0.00457 / 0.32 ( 24) metal coordination : angle 7.55313 / 4.90 ( 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 302 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 0.686 Fit side-chains REVERT: A 3 LYS cc_start: 0.5480 (OUTLIER) cc_final: 0.5263 (mttm) REVERT: A 36 MET cc_start: 0.7921 (mtm) cc_final: 0.7609 (mtm) REVERT: A 202 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: A 211 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: A 353 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: A 395 GLU cc_start: 0.6787 (mm-30) cc_final: 0.5883 (tt0) REVERT: A 413 THR cc_start: 0.7014 (m) cc_final: 0.6345 (p) REVERT: A 561 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5739 (mpt) REVERT: A 604 ASP cc_start: 0.5742 (m-30) cc_final: 0.5449 (m-30) REVERT: A 653 LYS cc_start: 0.7318 (mttt) cc_final: 0.6797 (mmtt) REVERT: A 771 ARG cc_start: 0.6918 (ptm160) cc_final: 0.6011 (ptp90) REVERT: A 942 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6664 (mp) REVERT: A 1032 TYR cc_start: 0.6284 (m-80) cc_final: 0.5735 (m-80) REVERT: A 1100 ARG cc_start: 0.6769 (mtm110) cc_final: 0.6507 (mtp-110) REVERT: A 1197 ARG cc_start: 0.5824 (mmt-90) cc_final: 0.5607 (mmt180) REVERT: B 3 LYS cc_start: 0.5357 (OUTLIER) cc_final: 0.5079 (mttm) REVERT: B 36 MET cc_start: 0.7939 (mtm) cc_final: 0.7677 (mtm) REVERT: B 202 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: B 211 GLU cc_start: 0.7353 (mp0) cc_final: 0.6920 (mp0) REVERT: B 353 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: B 413 THR cc_start: 0.6844 (m) cc_final: 0.6173 (p) REVERT: B 519 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6765 (mp) REVERT: B 561 MET cc_start: 0.6332 (OUTLIER) cc_final: 0.5911 (mpt) REVERT: B 653 LYS cc_start: 0.7272 (mttt) cc_final: 0.6815 (mmtt) REVERT: B 771 ARG cc_start: 0.6909 (ptm160) cc_final: 0.5980 (ptp90) REVERT: B 783 ARG cc_start: 0.6235 (mpt-90) cc_final: 0.5905 (mmt180) REVERT: B 831 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6865 (ppt-90) REVERT: B 942 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6677 (mp) REVERT: B 971 TYR cc_start: 0.7291 (t80) cc_final: 0.6894 (t80) REVERT: B 1032 TYR cc_start: 0.5847 (m-80) cc_final: 0.5375 (m-80) REVERT: B 1100 ARG cc_start: 0.6778 (mtm110) cc_final: 0.6525 (mtp-110) REVERT: B 1165 HIS cc_start: 0.6161 (OUTLIER) cc_final: 0.5890 (t-170) REVERT: B 1197 ARG cc_start: 0.5922 (mmt-90) cc_final: 0.5721 (mmt180) outliers start: 56 outliers final: 18 residues processed: 278 average time/residue: 0.6187 time to fit residues: 193.7092 Evaluate side-chains 266 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 202 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 353 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 669 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 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 353 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 831 ARG 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 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: 4.9990 chunk 46 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 86 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 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 96 ASN ** B 128 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 = 0.4015 r_free = 0.4015 target = 0.185446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.163282 restraints weight = 43049.580| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.46 r_work: 0.3554 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 18532 Z= 0.112 Angle : 0.637 16.831 25131 Z= 0.280 Chirality : 0.041 0.157 2737 Planarity : 0.004 0.046 3245 Dihedral : 5.710 56.873 2538 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.44 % Allowed : 20.67 % Favored : 76.89 % 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: 0.13 (0.17), residues: 2325 helix: 1.19 (0.16), residues: 1026 sheet: -0.60 (0.26), residues: 366 loop : -0.80 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 783 TYR 0.036 0.001 TYR A 971 PHE 0.015 0.001 PHE A 422 TRP 0.016 0.001 TRP A 516 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (18506) covalent geometry : angle 0.53109 / 0.28 (25055) SS BOND : bond 0.00570 / 0.32 ( 2) SS BOND : angle 1.36998 / 0.68 ( 4) hydrogen bonds : bond 0.03511 / 2.41 ( 817) hydrogen bonds : angle 4.52130 / 3.29 ( 2361) metal coordination : bond 0.00487 / 0.33 ( 24) metal coordination : angle 6.60145 / 4.21 ( 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 298 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.688 Fit side-chains REVERT: A 3 LYS cc_start: 0.5353 (OUTLIER) cc_final: 0.5022 (mttm) REVERT: A 36 MET cc_start: 0.7870 (mtm) cc_final: 0.7508 (mtm) REVERT: A 202 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: A 211 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: A 270 GLU cc_start: 0.7231 (pt0) cc_final: 0.6953 (pt0) REVERT: A 353 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: A 395 GLU cc_start: 0.6672 (mm-30) cc_final: 0.5777 (tt0) REVERT: A 413 THR cc_start: 0.6817 (OUTLIER) cc_final: 0.6244 (p) REVERT: A 485 ASP cc_start: 0.6828 (m-30) cc_final: 0.6116 (t0) REVERT: A 604 ASP cc_start: 0.5641 (m-30) cc_final: 0.5416 (m-30) REVERT: A 653 LYS cc_start: 0.7300 (mttt) cc_final: 0.6829 (mmtt) REVERT: A 771 ARG cc_start: 0.6836 (ptm160) cc_final: 0.5906 (ptp90) REVERT: A 832 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7131 (ttp) REVERT: A 1032 TYR cc_start: 0.6160 (m-80) cc_final: 0.5498 (m-80) REVERT: A 1100 ARG cc_start: 0.6677 (mtm110) cc_final: 0.6408 (mtp-110) REVERT: B 3 LYS cc_start: 0.5172 (OUTLIER) cc_final: 0.4904 (mttm) REVERT: B 36 MET cc_start: 0.7834 (mtm) cc_final: 0.7528 (mtm) REVERT: B 202 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: B 211 GLU cc_start: 0.7448 (mp0) cc_final: 0.7013 (mp0) REVERT: B 395 GLU cc_start: 0.6621 (mm-30) cc_final: 0.5747 (tt0) REVERT: B 413 THR cc_start: 0.6840 (OUTLIER) cc_final: 0.6173 (p) REVERT: B 485 ASP cc_start: 0.6841 (m-30) cc_final: 0.6153 (t0) REVERT: B 519 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6779 (mp) REVERT: B 653 LYS cc_start: 0.7263 (mttt) cc_final: 0.6817 (mmtt) REVERT: B 771 ARG cc_start: 0.6913 (ptm160) cc_final: 0.6001 (ptp90) REVERT: B 832 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7064 (ttp) REVERT: B 971 TYR cc_start: 0.7356 (t80) cc_final: 0.7006 (t80) REVERT: B 1032 TYR cc_start: 0.5744 (m-80) cc_final: 0.5118 (m-80) REVERT: B 1100 ARG cc_start: 0.6647 (mtm110) cc_final: 0.6375 (mtp-110) outliers start: 45 outliers final: 16 residues processed: 276 average time/residue: 0.6425 time to fit residues: 199.2584 Evaluate side-chains 268 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 353 GLU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1024 ASP 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 202 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 986 VAL 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: 2.9990 chunk 141 optimal weight: 2.9990 chunk 168 optimal weight: 0.0270 chunk 181 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 107 optimal weight: 0.0000 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 289 HIS A 421 GLN A 560 ASN A 602 ASN A 680 ASN ** A1165 HIS ** 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 197 GLN B 289 HIS B 421 GLN B 602 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.188188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.165880 restraints weight = 31793.778| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.74 r_work: 0.3636 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 18532 Z= 0.104 Angle : 0.630 15.389 25131 Z= 0.278 Chirality : 0.040 0.154 2737 Planarity : 0.004 0.045 3245 Dihedral : 5.396 59.024 2536 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.59 % Allowed : 22.05 % Favored : 76.36 % 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: 0.26 (0.18), residues: 2325 helix: 1.30 (0.16), residues: 1040 sheet: -0.58 (0.26), residues: 362 loop : -0.74 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1149 TYR 0.032 0.001 TYR A 971 PHE 0.018 0.001 PHE A 422 TRP 0.018 0.001 TRP A 622 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (18506) covalent geometry : angle 0.53619 / 0.28 (25055) SS BOND : bond 0.00641 / 0.36 ( 2) SS BOND : angle 1.47025 / 0.73 ( 4) hydrogen bonds : bond 0.03307 / 2.26 ( 817) hydrogen bonds : angle 4.45015 / 3.23 ( 2361) metal coordination : bond 0.00357 / 0.23 ( 24) metal coordination : angle 6.20896 / 3.97 ( 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 293 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.706 Fit side-chains REVERT: A 36 MET cc_start: 0.7789 (mtm) cc_final: 0.7478 (mtm) REVERT: A 211 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 270 GLU cc_start: 0.7122 (pt0) cc_final: 0.6869 (pm20) REVERT: A 350 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6329 (mp0) REVERT: A 353 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: A 395 GLU cc_start: 0.6568 (mm-30) cc_final: 0.5784 (tt0) REVERT: A 413 THR cc_start: 0.6743 (OUTLIER) cc_final: 0.6202 (p) REVERT: A 485 ASP cc_start: 0.6693 (m-30) cc_final: 0.6077 (t0) REVERT: A 533 THR cc_start: 0.7592 (p) cc_final: 0.7072 (t) REVERT: A 560 ASN cc_start: 0.5832 (OUTLIER) cc_final: 0.5439 (p0) REVERT: A 771 ARG cc_start: 0.6830 (ptm160) cc_final: 0.6588 (ptm160) REVERT: A 779 GLU cc_start: 0.7255 (tp30) cc_final: 0.6222 (tm-30) REVERT: A 1032 TYR cc_start: 0.5889 (m-80) cc_final: 0.5275 (m-80) REVERT: A 1100 ARG cc_start: 0.6611 (mtm110) cc_final: 0.6274 (mtp-110) REVERT: B 36 MET cc_start: 0.7725 (mtm) cc_final: 0.7391 (mtm) REVERT: B 208 MET cc_start: 0.6589 (ttp) cc_final: 0.6272 (ptm) REVERT: B 211 GLU cc_start: 0.7394 (mp0) cc_final: 0.7004 (mp0) REVERT: B 350 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6328 (mp0) REVERT: B 353 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: B 395 GLU cc_start: 0.6548 (mm-30) cc_final: 0.5773 (tt0) REVERT: B 413 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6203 (p) REVERT: B 485 ASP cc_start: 0.6701 (m-30) cc_final: 0.6101 (t0) REVERT: B 519 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6816 (mp) REVERT: B 533 THR cc_start: 0.7569 (p) cc_final: 0.7033 (t) REVERT: B 604 ASP cc_start: 0.6036 (m-30) cc_final: 0.5738 (m-30) REVERT: B 606 VAL cc_start: 0.6640 (t) cc_final: 0.6440 (t) REVERT: B 771 ARG cc_start: 0.6742 (ptm160) cc_final: 0.6258 (ptm-80) REVERT: B 779 GLU cc_start: 0.7150 (tp30) cc_final: 0.6117 (tm-30) REVERT: B 783 ARG cc_start: 0.6346 (mpt-90) cc_final: 0.6140 (mpt-90) REVERT: B 832 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7118 (ttt) REVERT: B 971 TYR cc_start: 0.7330 (t80) cc_final: 0.6950 (t80) REVERT: B 1032 TYR cc_start: 0.5533 (m-80) cc_final: 0.5014 (m-80) REVERT: B 1100 ARG cc_start: 0.6567 (mtm110) cc_final: 0.6250 (mtp-110) REVERT: B 1165 HIS cc_start: 0.6062 (t-170) cc_final: 0.5663 (t70) outliers start: 29 outliers final: 9 residues processed: 280 average time/residue: 0.6410 time to fit residues: 201.5625 Evaluate side-chains 251 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR 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 353 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 611 THR 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 353 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 986 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 48 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 421 GLN A 694 GLN ** 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 421 GLN B 680 ASN B 694 GLN B 918 ASN ** B1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.183375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.160583 restraints weight = 35844.700| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.11 r_work: 0.3549 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- 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: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18532 Z= 0.178 Angle : 0.732 17.715 25131 Z= 0.326 Chirality : 0.045 0.192 2737 Planarity : 0.005 0.050 3245 Dihedral : 5.216 55.404 2525 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.85 % Allowed : 22.31 % 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: 0.05 (0.17), residues: 2325 helix: 1.11 (0.16), residues: 1026 sheet: -0.67 (0.25), residues: 386 loop : -0.81 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1149 TYR 0.020 0.002 TYR A 971 PHE 0.031 0.002 PHE B 124 TRP 0.022 0.002 TRP B 844 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (18506) covalent geometry : angle 0.61953 / 0.33 (25055) SS BOND : bond 0.00770 / 0.43 ( 2) SS BOND : angle 1.32987 / 0.65 ( 4) hydrogen bonds : bond 0.04140 / 2.87 ( 817) hydrogen bonds : angle 4.66133 / 3.38 ( 2361) metal coordination : bond 0.00969 / 0.65 ( 24) metal coordination : angle 7.31812 / 4.64 ( 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: 34 poor density : 233 time to evaluate : 0.843 Fit side-chains REVERT: A 3 LYS cc_start: 0.5426 (OUTLIER) cc_final: 0.5126 (mttp) REVERT: A 36 MET cc_start: 0.7935 (mtm) cc_final: 0.7624 (mtm) REVERT: A 208 MET cc_start: 0.6578 (ptm) cc_final: 0.6322 (ptm) REVERT: A 211 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 270 GLU cc_start: 0.7299 (pt0) cc_final: 0.6932 (pt0) REVERT: A 353 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: A 413 THR cc_start: 0.6929 (m) cc_final: 0.6247 (p) REVERT: A 485 ASP cc_start: 0.6944 (m-30) cc_final: 0.6242 (t0) REVERT: A 533 THR cc_start: 0.7579 (p) cc_final: 0.7103 (t) REVERT: A 771 ARG cc_start: 0.6822 (ptm160) cc_final: 0.5905 (ptp90) REVERT: A 921 ILE cc_start: 0.6031 (OUTLIER) cc_final: 0.5797 (mm) REVERT: A 942 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6614 (mp) REVERT: A 1032 TYR cc_start: 0.6202 (m-80) cc_final: 0.5645 (m-80) REVERT: A 1100 ARG cc_start: 0.6807 (mtm110) cc_final: 0.6526 (mtp-110) REVERT: B 3 LYS cc_start: 0.5323 (OUTLIER) cc_final: 0.5025 (mttm) REVERT: B 36 MET cc_start: 0.7963 (mtm) cc_final: 0.7610 (mtm) REVERT: B 197 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: B 211 GLU cc_start: 0.7419 (mp0) cc_final: 0.6998 (mp0) REVERT: B 353 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: B 413 THR cc_start: 0.6837 (m) cc_final: 0.6131 (p) REVERT: B 485 ASP cc_start: 0.6816 (m-30) cc_final: 0.6169 (t0) REVERT: B 519 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6796 (mp) REVERT: B 533 THR cc_start: 0.7508 (p) cc_final: 0.7046 (t) REVERT: B 771 ARG cc_start: 0.6800 (ptm160) cc_final: 0.5868 (ptp90) REVERT: B 942 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6686 (mp) REVERT: B 971 TYR cc_start: 0.7400 (t80) cc_final: 0.7072 (t80) REVERT: B 1027 ARG cc_start: 0.5948 (mtp180) cc_final: 0.5173 (ttm170) REVERT: B 1032 TYR cc_start: 0.5882 (m-80) cc_final: 0.5384 (m-80) REVERT: B 1100 ARG cc_start: 0.6771 (mtm110) cc_final: 0.6498 (mtp-110) REVERT: B 1132 ASN cc_start: 0.7557 (t0) cc_final: 0.6615 (t0) outliers start: 34 outliers final: 9 residues processed: 253 average time/residue: 0.6414 time to fit residues: 182.4219 Evaluate side-chains 249 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 942 LEU 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 130 ILE Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 942 LEU 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: 10.0000 chunk 39 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 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 214 HIS B 918 ASN ** B1214 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 = 0.4006 r_free = 0.4006 target = 0.184816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.161615 restraints weight = 43699.246| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.79 r_work: 0.3534 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 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 = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18532 Z= 0.140 Angle : 0.701 17.282 25131 Z= 0.308 Chirality : 0.043 0.171 2737 Planarity : 0.004 0.048 3245 Dihedral : 5.168 55.273 2525 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.59 % Allowed : 22.58 % 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: 0.06 (0.17), residues: 2325 helix: 1.14 (0.16), residues: 1026 sheet: -0.66 (0.25), residues: 374 loop : -0.82 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1149 TYR 0.029 0.002 TYR A 971 PHE 0.035 0.002 PHE A 124 TRP 0.020 0.002 TRP B 844 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (18506) covalent geometry : angle 0.58976 / 0.31 (25055) SS BOND : bond 0.00667 / 0.37 ( 2) SS BOND : angle 1.41541 / 0.69 ( 4) hydrogen bonds : bond 0.03849 / 2.66 ( 817) hydrogen bonds : angle 4.60065 / 3.33 ( 2361) metal coordination : bond 0.00647 / 0.44 ( 24) metal coordination : angle 7.08526 / 4.56 ( 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 258 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.673 Fit side-chains REVERT: A 3 LYS cc_start: 0.5442 (OUTLIER) cc_final: 0.5017 (mttm) REVERT: A 36 MET cc_start: 0.7938 (mtm) cc_final: 0.7639 (mtm) REVERT: A 208 MET cc_start: 0.6820 (ptm) cc_final: 0.6584 (ptm) REVERT: A 211 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 270 GLU cc_start: 0.7371 (pt0) cc_final: 0.7102 (pt0) REVERT: A 353 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7384 (mm-30) REVERT: A 413 THR cc_start: 0.6832 (m) cc_final: 0.6241 (p) REVERT: A 485 ASP cc_start: 0.6979 (m-30) cc_final: 0.6271 (t0) REVERT: A 533 THR cc_start: 0.7544 (p) cc_final: 0.7069 (t) REVERT: A 560 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.5867 (p0) REVERT: A 831 ARG cc_start: 0.7353 (ppt170) cc_final: 0.7076 (ppt-90) REVERT: A 921 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5860 (mm) REVERT: A 942 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6615 (mp) REVERT: A 1032 TYR cc_start: 0.6159 (m-80) cc_final: 0.5514 (m-80) REVERT: A 1100 ARG cc_start: 0.6732 (mtm110) cc_final: 0.6449 (mtp-110) REVERT: B 3 LYS cc_start: 0.5263 (OUTLIER) cc_final: 0.4962 (mttm) REVERT: B 36 MET cc_start: 0.7966 (mtm) cc_final: 0.7620 (mtm) REVERT: B 197 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: B 211 GLU cc_start: 0.7493 (mp0) cc_final: 0.7068 (mp0) REVERT: B 353 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: B 413 THR cc_start: 0.6823 (m) cc_final: 0.6112 (p) REVERT: B 485 ASP cc_start: 0.6861 (m-30) cc_final: 0.6201 (t0) REVERT: B 519 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6778 (mp) REVERT: B 533 THR cc_start: 0.7592 (p) cc_final: 0.7130 (t) REVERT: B 771 ARG cc_start: 0.6839 (ptm160) cc_final: 0.6309 (ptm-80) REVERT: B 921 ILE cc_start: 0.6087 (OUTLIER) cc_final: 0.5835 (mm) REVERT: B 942 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6709 (mp) REVERT: B 971 TYR cc_start: 0.7369 (t80) cc_final: 0.6967 (t80) REVERT: B 1027 ARG cc_start: 0.6036 (mtp180) cc_final: 0.5405 (ttp-110) REVERT: B 1032 TYR cc_start: 0.5968 (m-80) cc_final: 0.5323 (m-80) REVERT: B 1100 ARG cc_start: 0.6728 (mtm110) cc_final: 0.6447 (mtp-110) outliers start: 29 outliers final: 9 residues processed: 252 average time/residue: 0.6280 time to fit residues: 177.2384 Evaluate side-chains 247 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 669 THR 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 197 GLN Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 942 LEU 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: 5.9990 chunk 90 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 31 optimal weight: 0.0170 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** B 918 ASN ** B1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.184889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.161867 restraints weight = 37084.471| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.13 r_work: 0.3572 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 18532 Z= 0.168 Angle : 0.841 59.193 25131 Z= 0.427 Chirality : 0.045 0.811 2737 Planarity : 0.005 0.072 3245 Dihedral : 5.168 55.280 2525 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.38 % Allowed : 23.00 % Favored : 75.62 % Cbeta Deviations : 0.05 % 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: 0.05 (0.17), residues: 2325 helix: 1.12 (0.16), residues: 1026 sheet: -0.66 (0.25), residues: 374 loop : -0.81 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1149 TYR 0.026 0.002 TYR A 971 PHE 0.032 0.002 PHE A 124 TRP 0.019 0.002 TRP A 844 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (18506) covalent geometry : angle 0.75189 / 0.43 (25055) SS BOND : bond 0.00744 / 0.43 ( 2) SS BOND : angle 1.62073 / 0.76 ( 4) hydrogen bonds : bond 0.03859 / 2.66 ( 817) hydrogen bonds : angle 4.60497 / 3.34 ( 2361) metal coordination : bond 0.00635 / 0.43 ( 24) metal coordination : angle 7.08235 / 4.56 ( 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 250 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.678 Fit side-chains REVERT: A 3 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.5025 (mttm) REVERT: A 36 MET cc_start: 0.7906 (mtm) cc_final: 0.7599 (mtm) REVERT: A 208 MET cc_start: 0.6779 (ptm) cc_final: 0.6505 (ptm) REVERT: A 211 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: A 353 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: A 413 THR cc_start: 0.6879 (m) cc_final: 0.6286 (p) REVERT: A 485 ASP cc_start: 0.6914 (m-30) cc_final: 0.6211 (t0) REVERT: A 533 THR cc_start: 0.7546 (p) cc_final: 0.7079 (t) REVERT: A 831 ARG cc_start: 0.7312 (ppt170) cc_final: 0.7045 (ppt-90) REVERT: A 921 ILE cc_start: 0.6105 (OUTLIER) cc_final: 0.5857 (mm) REVERT: A 942 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6607 (mp) REVERT: A 1032 TYR cc_start: 0.6077 (m-80) cc_final: 0.5514 (m-80) REVERT: A 1100 ARG cc_start: 0.6683 (mtm110) cc_final: 0.6405 (mtp-110) REVERT: B 3 LYS cc_start: 0.5236 (OUTLIER) cc_final: 0.4980 (mttm) REVERT: B 36 MET cc_start: 0.7927 (mtm) cc_final: 0.7571 (mtm) REVERT: B 197 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: B 211 GLU cc_start: 0.7447 (mp0) cc_final: 0.7014 (mp0) REVERT: B 353 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: B 413 THR cc_start: 0.6861 (m) cc_final: 0.6159 (p) REVERT: B 485 ASP cc_start: 0.6798 (m-30) cc_final: 0.6148 (t0) REVERT: B 519 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6792 (mp) REVERT: B 533 THR cc_start: 0.7587 (p) cc_final: 0.7144 (t) REVERT: B 771 ARG cc_start: 0.6863 (ptm160) cc_final: 0.6330 (ptm-80) REVERT: B 921 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5831 (mm) REVERT: B 942 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6686 (mp) REVERT: B 971 TYR cc_start: 0.7311 (t80) cc_final: 0.6933 (t80) REVERT: B 1032 TYR cc_start: 0.5902 (m-80) cc_final: 0.5322 (m-80) REVERT: B 1100 ARG cc_start: 0.6682 (mtm110) cc_final: 0.6407 (mtp-110) outliers start: 25 outliers final: 10 residues processed: 244 average time/residue: 0.6670 time to fit residues: 182.1898 Evaluate side-chains 247 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 669 THR 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 A residue 1042 MET Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 942 LEU 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: 10.0000 chunk 57 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** 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** B 918 ASN ** B1214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.184917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162685 restraints weight = 41166.222| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.32 r_work: 0.3552 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 18532 Z= 0.167 Angle : 0.841 59.200 25131 Z= 0.427 Chirality : 0.045 0.802 2737 Planarity : 0.005 0.072 3245 Dihedral : 5.168 55.280 2525 Min Nonbonded Distance : 1.360 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.32 % Allowed : 23.05 % Favored : 75.62 % Cbeta Deviations : 0.05 % 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: 0.05 (0.17), residues: 2325 helix: 1.12 (0.16), residues: 1026 sheet: -0.66 (0.25), residues: 374 loop : -0.81 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1149 TYR 0.026 0.002 TYR A 971 PHE 0.032 0.002 PHE A 124 TRP 0.019 0.002 TRP A 844 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (18506) covalent geometry : angle 0.75178 / 0.43 (25055) SS BOND : bond 0.00743 / 0.43 ( 2) SS BOND : angle 1.62066 / 0.76 ( 4) hydrogen bonds : bond 0.03859 / 2.66 ( 817) hydrogen bonds : angle 4.60495 / 3.34 ( 2361) metal coordination : bond 0.00635 / 0.43 ( 24) metal coordination : angle 7.08234 / 4.56 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5461.46 seconds wall clock time: 94 minutes 22.33 seconds (5662.33 seconds total)