Starting phenix.real_space_refine on Mon Mar 18 01:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2024/7awt_11930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2024/7awt_11930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2024/7awt_11930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2024/7awt_11930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2024/7awt_11930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2024/7awt_11930_updated.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.244 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 673 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Fe 32 7.16 5 P 1 5.49 5 Mg 8 5.21 5 S 146 5.16 5 C 11815 2.51 5 N 3292 2.21 5 O 3597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D ARG 298": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D ARG 386": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D GLU 444": "OE1" <-> "OE2" Residue "D GLU 502": "OE1" <-> "OE2" Residue "D GLU 509": "OE1" <-> "OE2" Residue "D ARG 558": "NH1" <-> "NH2" Residue "D ARG 573": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F ARG 144": "NH1" <-> "NH2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 194": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F ARG 282": "NH1" <-> "NH2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F ARG 348": "NH1" <-> "NH2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 183": "NH1" <-> "NH2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ARG 242": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G ARG 248": "NH1" <-> "NH2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G ARG 265": "NH1" <-> "NH2" Residue "G ARG 278": "NH1" <-> "NH2" Residue "G ARG 329": "NH1" <-> "NH2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G GLU 345": "OE1" <-> "OE2" Residue "G ARG 357": "NH1" <-> "NH2" Residue "G GLU 368": "OE1" <-> "OE2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "G ARG 388": "NH1" <-> "NH2" Residue "G ARG 424": "NH1" <-> "NH2" Residue "G GLU 476": "OE1" <-> "OE2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "G ARG 560": "NH1" <-> "NH2" Residue "G ARG 597": "NH1" <-> "NH2" Residue "G TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 650": "NH1" <-> "NH2" Residue "G ARG 662": "NH1" <-> "NH2" Residue "G GLU 682": "OE1" <-> "OE2" Residue "G ARG 696": "NH1" <-> "NH2" Residue "G ARG 698": "NH1" <-> "NH2" Residue "G GLU 705": "OE1" <-> "OE2" Residue "G ARG 712": "NH1" <-> "NH2" Residue "G ARG 716": "NH1" <-> "NH2" Residue "G GLU 723": "OE1" <-> "OE2" Residue "G GLU 739": "OE1" <-> "OE2" Residue "G ARG 748": "NH1" <-> "NH2" Residue "G ARG 777": "NH1" <-> "NH2" Residue "G ARG 784": "NH1" <-> "NH2" Residue "G ARG 802": "NH1" <-> "NH2" Residue "G ARG 811": "NH1" <-> "NH2" Residue "G ARG 857": "NH1" <-> "NH2" Residue "G GLU 875": "OE1" <-> "OE2" Residue "I ARG 45": "NH1" <-> "NH2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18891 Number of models: 1 Model: "" Number of chains: 17 Chain: "B" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1100 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 130} Chain breaks: 2 Chain: "D" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4760 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 551} Chain: "E" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1219 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "F" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3406 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "G" Number of atoms: 7045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7045 Classifications: {'peptide': 907} Link IDs: {'PTRANS': 41, 'TRANS': 865} Chain: "I" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1133 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 34 Unusual residues: {' MG': 6, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "G" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 567 SG CYS B 129 53.974 72.139 43.114 1.00101.08 S ATOM 104 SG CYS B 64 58.313 75.962 39.701 1.00116.62 S ATOM 98 SG CYS B 63 53.592 78.862 41.752 1.00115.59 S ATOM 784 SG CYS B 158 56.774 76.118 46.112 1.00101.71 S ATOM 6507 SG CYS E 92 59.861 86.615 116.986 1.00 89.33 S ATOM 6541 SG CYS E 97 60.601 89.981 118.905 1.00 87.05 S ATOM 6819 SG CYS E 133 55.629 86.230 118.040 1.00 90.81 S ATOM 6845 SG CYS E 137 54.971 88.887 120.135 1.00 87.76 S ATOM 9784 SG CYS F 351 48.617 74.400 103.858 1.00 81.15 S ATOM 9828 SG CYS F 357 49.173 80.594 101.744 1.00 78.34 S ATOM 10149 SG CYS F 398 44.190 78.576 105.503 1.00 77.70 S ATOM 9808 SG CYS F 354 45.552 78.139 99.116 1.00 77.15 S ATOM 10837 SG CYS G 48 37.698 73.642 90.613 1.00 89.22 S ATOM 10986 SG CYS G 67 37.091 70.953 93.050 1.00 89.22 S ATOM 10735 SG CYS G 34 42.355 70.321 92.820 1.00 89.22 S ATOM 10811 SG CYS G 45 43.005 73.363 91.234 1.00 89.22 S ATOM 11688 SG CYS G 154 48.441 67.645 90.400 1.00 89.22 S ATOM 11669 SG CYS G 151 54.630 68.861 92.128 1.00 89.22 S ATOM 11717 SG CYS G 157 52.035 63.182 93.388 1.00 89.22 S ATOM 12065 SG CYS G 201 52.612 64.723 87.284 1.00 89.22 S ATOM 11274 SG CYS G 103 56.298 73.313 77.403 1.00 89.22 S ATOM 11334 SG CYS G 112 51.844 69.415 80.609 1.00 89.22 S ATOM 11294 SG CYS G 106 57.595 67.782 80.229 1.00 89.22 S ATOM 12290 SG CYS G 228 47.797 43.848 79.438 1.00 89.22 S ATOM 12575 SG CYS G 263 47.787 44.768 86.396 1.00 89.22 S ATOM 12338 SG CYS G 235 43.053 45.655 82.945 1.00 89.22 S ATOM 12314 SG CYS G 231 45.558 39.913 84.340 1.00 89.22 S ATOM 18100 SG CYS I 109 64.739 74.947 66.230 1.00 89.22 S ATOM 17763 SG CYS I 66 62.111 70.349 63.035 1.00 89.22 S ATOM 17723 SG CYS I 60 66.970 68.703 66.380 1.00 89.22 S ATOM 17741 SG CYS I 63 61.809 70.518 69.636 1.00 89.22 S ATOM 18053 SG CYS I 102 57.243 76.097 54.830 1.00 89.22 S ATOM 18028 SG CYS I 99 62.174 72.805 51.893 1.00 89.22 S ATOM 18071 SG CYS I 105 61.932 74.482 58.063 1.00 89.22 S ATOM 17786 SG CYS I 70 57.538 70.403 56.109 1.00 89.22 S ATOM 17810 SG CYS I 74 59.716 69.044 53.986 1.00 83.14 S Residues with excluded nonbonded symmetry interactions: 119 residue: pdb=" N TYR B 65 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR B 65 " occ=0.00 residue: pdb=" N VAL B 66 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 66 " occ=0.00 residue: pdb=" N GLU B 67 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU B 67 " occ=0.00 residue: pdb=" N MET B 68 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET B 68 " occ=0.00 residue: pdb=" N VAL B 69 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 69 " occ=0.00 residue: pdb=" N THR B 70 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 70 " occ=0.00 residue: pdb=" N SER B 71 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER B 71 " occ=0.00 residue: pdb=" N PHE B 72 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE B 72 " occ=0.00 residue: pdb=" N ALA B 74 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 74 " occ=0.00 residue: pdb=" N VAL B 75 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 75 " occ=0.00 residue: pdb=" N HIS B 76 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS B 76 " occ=0.00 residue: pdb=" N ASP B 77 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP B 77 " occ=0.00 ... (remaining 107 not shown) Time building chain proxies: 10.56, per 1000 atoms: 0.56 Number of scatterers: 18891 At special positions: 0 Unit cell: (94.34, 120.84, 155.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 S 146 16.00 P 1 15.00 Mg 8 11.99 O 3597 8.00 N 3292 7.00 C 11815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 7.43 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1001 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 45 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 34 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 48 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 67 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" SF4 F 501 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" SF4 G1002 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 154 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 157 " pdb=" SF4 G1003 " pdb="FE2 SF4 G1003 " - pdb=" NE2 HIS G 99 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 106 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 103 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 112 " pdb=" SF4 G1004 " pdb="FE2 SF4 G1004 " - pdb=" SG CYS G 263 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 228 " pdb="FE3 SF4 G1004 " - pdb=" SG CYS G 235 " pdb="FE4 SF4 G1004 " - pdb=" SG CYS G 231 " pdb=" SF4 I 301 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 60 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 66 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 63 " pdb=" SF4 I 302 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 70 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 105 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 74 " Number of angles added : 96 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 23 sheets defined 33.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.512A pdb=" N ASN B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 131' Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 176 removed outlier: 3.563A pdb=" N SER B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'D' and resid 20 through 29 removed outlier: 3.672A pdb=" N GLU D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 61 removed outlier: 3.676A pdb=" N ASP D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.845A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 200 No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 263 through 272 Proline residue: D 266 - end of helix removed outlier: 3.886A pdb=" N GLU D 272 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 291 Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 297 through 325 Processing helix chain 'D' and resid 333 through 350 removed outlier: 3.554A pdb=" N THR D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 395 removed outlier: 3.651A pdb=" N PHE D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) Proline residue: D 384 - end of helix Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 434 through 437 No H-bonds generated for 'chain 'D' and resid 434 through 437' Processing helix chain 'D' and resid 443 through 445 No H-bonds generated for 'chain 'D' and resid 443 through 445' Processing helix chain 'D' and resid 459 through 482 removed outlier: 3.840A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG D 471 " --> pdb=" O VAL D 467 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN D 472 " --> pdb=" O GLU D 468 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 560 through 566 Processing helix chain 'D' and resid 568 through 571 No H-bonds generated for 'chain 'D' and resid 568 through 571' Processing helix chain 'D' and resid 577 through 586 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'E' and resid 16 through 27 removed outlier: 4.075A pdb=" N HIS E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.512A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.279A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 158 through 164 removed outlier: 3.914A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 50 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.896A pdb=" N ILE F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.588A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 303 through 306 removed outlier: 4.082A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 303 through 306' Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 335 through 348 removed outlier: 3.627A pdb=" N PHE F 345 " --> pdb=" O ASN F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 373 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 381 through 390 removed outlier: 3.546A pdb=" N GLN F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 404 Processing helix chain 'F' and resid 406 through 422 removed outlier: 3.547A pdb=" N TYR F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU F 418 " --> pdb=" O TYR F 414 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 26 Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 82 through 97 removed outlier: 3.625A pdb=" N LEU G 95 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 156 through 163 Processing helix chain 'G' and resid 195 through 200 removed outlier: 3.843A pdb=" N ILE G 200 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 213 Processing helix chain 'G' and resid 218 through 220 No H-bonds generated for 'chain 'G' and resid 218 through 220' Processing helix chain 'G' and resid 295 through 306 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 343 through 357 removed outlier: 3.715A pdb=" N ARG G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 349 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA G 352 " --> pdb=" O ARG G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 371 Processing helix chain 'G' and resid 387 through 408 removed outlier: 3.985A pdb=" N LYS G 398 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS G 400 " --> pdb=" O ALA G 396 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ALA G 401 " --> pdb=" O VAL G 397 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG G 402 " --> pdb=" O LYS G 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN G 408 " --> pdb=" O MET G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 422 Processing helix chain 'G' and resid 453 through 466 Processing helix chain 'G' and resid 477 through 490 removed outlier: 4.088A pdb=" N LYS G 482 " --> pdb=" O GLU G 478 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL G 485 " --> pdb=" O SER G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 523 Processing helix chain 'G' and resid 538 through 544 Processing helix chain 'G' and resid 549 through 557 Processing helix chain 'G' and resid 577 through 585 removed outlier: 3.646A pdb=" N ASN G 581 " --> pdb=" O ALA G 577 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 602 No H-bonds generated for 'chain 'G' and resid 600 through 602' Processing helix chain 'G' and resid 648 through 660 Processing helix chain 'G' and resid 669 through 679 Processing helix chain 'G' and resid 681 through 683 No H-bonds generated for 'chain 'G' and resid 681 through 683' Processing helix chain 'G' and resid 762 through 766 Processing helix chain 'G' and resid 825 through 827 No H-bonds generated for 'chain 'G' and resid 825 through 827' Processing helix chain 'G' and resid 831 through 834 No H-bonds generated for 'chain 'G' and resid 831 through 834' Processing helix chain 'G' and resid 844 through 847 No H-bonds generated for 'chain 'G' and resid 844 through 847' Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing sheet with id= A, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.809A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 59 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL B 97 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'D' and resid 44 through 48 removed outlier: 4.265A pdb=" N ALA D 112 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG D 105 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 119 through 121 removed outlier: 6.680A pdb=" N THR D 144 " --> pdb=" O VAL D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 527 through 534 removed outlier: 3.573A pdb=" N ASN D 540 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 230 through 233 removed outlier: 3.589A pdb=" N ASP D 240 " --> pdb=" O GLN D 232 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 89 through 92 Processing sheet with id= G, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.651A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 260 through 264 Processing sheet with id= I, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= J, first strand: chain 'G' and resid 62 through 65 removed outlier: 4.482A pdb=" N PHE G 76 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 171 through 173 Processing sheet with id= L, first strand: chain 'G' and resid 222 through 227 removed outlier: 3.767A pdb=" N ALA G 224 " --> pdb=" O PRO G 239 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG G 248 " --> pdb=" O GLY G 240 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG G 242 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU G 246 " --> pdb=" O ARG G 242 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 286 removed outlier: 3.598A pdb=" N ASP G 289 " --> pdb=" O ARG G 286 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 337 through 339 removed outlier: 6.171A pdb=" N GLY G 314 " --> pdb=" O TYR G 338 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N MET G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 375 through 378 removed outlier: 6.318A pdb=" N TRP G 445 " --> pdb=" O VAL G 431 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN G 433 " --> pdb=" O TRP G 445 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N TYR G 447 " --> pdb=" O ASN G 433 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 497 through 501 removed outlier: 6.782A pdb=" N GLY G 528 " --> pdb=" O ILE G 498 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N SER G 500 " --> pdb=" O GLY G 528 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N THR G 530 " --> pdb=" O SER G 500 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 618 through 621 removed outlier: 3.511A pdb=" N GLN G 628 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 811 through 816 Processing sheet with id= S, first strand: chain 'G' and resid 839 through 842 removed outlier: 7.598A pdb=" N LEU G 842 " --> pdb=" O PRO G 870 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU G 872 " --> pdb=" O LEU G 842 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'G' and resid 866 through 869 removed outlier: 3.792A pdb=" N ASP G 902 " --> pdb=" O SER G 861 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 47 through 50 removed outlier: 3.683A pdb=" N THR I 117 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 75 through 77 Processing sheet with id= W, first strand: chain 'I' and resid 79 through 81 504 hydrogen bonds defined for protein. 1413 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: 5.65 Time building geometry restraints manager: 8.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.40: 7971 1.40 - 1.67: 10984 1.67 - 1.93: 180 1.93 - 2.19: 7 2.19 - 2.46: 85 Bond restraints: 19227 Sorted by residual: bond pdb=" CA SER G 317 " pdb=" C SER G 317 " ideal model delta sigma weight residual 1.524 1.411 0.113 1.26e-02 6.30e+03 8.07e+01 bond pdb=" C ARG G 394 " pdb=" O ARG G 394 " ideal model delta sigma weight residual 1.237 1.138 0.099 1.17e-02 7.31e+03 7.09e+01 bond pdb=" C VAL G 91 " pdb=" O VAL G 91 " ideal model delta sigma weight residual 1.237 1.140 0.097 1.17e-02 7.31e+03 6.87e+01 bond pdb=" CA ALA G 703 " pdb=" C ALA G 703 " ideal model delta sigma weight residual 1.524 1.428 0.095 1.25e-02 6.40e+03 5.82e+01 bond pdb=" C ILE G 621 " pdb=" O ILE G 621 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.09e-02 8.42e+03 5.79e+01 ... (remaining 19222 not shown) Histogram of bond angle deviations from ideal: 71.83 - 84.77: 88 84.77 - 97.70: 0 97.70 - 110.64: 6324 110.64 - 123.58: 18940 123.58 - 136.51: 761 Bond angle restraints: 26113 Sorted by residual: angle pdb=" N ALA G 44 " pdb=" CA ALA G 44 " pdb=" C ALA G 44 " ideal model delta sigma weight residual 111.07 123.71 -12.64 1.07e+00 8.73e-01 1.40e+02 angle pdb=" N TRP F 353 " pdb=" CA TRP F 353 " pdb=" C TRP F 353 " ideal model delta sigma weight residual 111.07 121.84 -10.77 1.07e+00 8.73e-01 1.01e+02 angle pdb=" N ARG B 205 " pdb=" CA ARG B 205 " pdb=" C ARG B 205 " ideal model delta sigma weight residual 111.28 122.16 -10.88 1.09e+00 8.42e-01 9.97e+01 angle pdb=" N ARG G 834 " pdb=" CA ARG G 834 " pdb=" C ARG G 834 " ideal model delta sigma weight residual 111.36 121.60 -10.24 1.09e+00 8.42e-01 8.82e+01 angle pdb=" N CYS E 137 " pdb=" CA CYS E 137 " pdb=" C CYS E 137 " ideal model delta sigma weight residual 111.28 121.41 -10.13 1.09e+00 8.42e-01 8.64e+01 ... (remaining 26108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.17: 11169 34.17 - 68.34: 272 68.34 - 102.50: 19 102.50 - 136.67: 0 136.67 - 170.84: 1 Dihedral angle restraints: 11461 sinusoidal: 4658 harmonic: 6803 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 86.75 170.84 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C HIS F 431 " pdb=" N HIS F 431 " pdb=" CA HIS F 431 " pdb=" CB HIS F 431 " ideal model delta harmonic sigma weight residual -122.60 -138.53 15.93 0 2.50e+00 1.60e-01 4.06e+01 dihedral pdb=" N HIS F 431 " pdb=" C HIS F 431 " pdb=" CA HIS F 431 " pdb=" CB HIS F 431 " ideal model delta harmonic sigma weight residual 122.80 138.57 -15.77 0 2.50e+00 1.60e-01 3.98e+01 ... (remaining 11458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.414: 2784 4.414 - 8.827: 0 8.827 - 13.241: 0 13.241 - 17.654: 0 17.654 - 22.068: 24 Chirality restraints: 2808 Sorted by residual: chirality pdb="FE4 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S3 SF4 I 302 " both_signs ideal model delta sigma weight residual False 10.55 -11.51 22.07 2.00e-01 2.50e+01 1.22e+04 chirality pdb="FE3 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 2805 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 660 " -0.024 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C LEU G 660 " 0.086 2.00e-02 2.50e+03 pdb=" O LEU G 660 " -0.033 2.00e-02 2.50e+03 pdb=" N SER G 661 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 819 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C PHE G 819 " -0.085 2.00e-02 2.50e+03 pdb=" O PHE G 819 " 0.032 2.00e-02 2.50e+03 pdb=" N GLY G 820 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 317 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C SER G 317 " -0.068 2.00e-02 2.50e+03 pdb=" O SER G 317 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO G 318 " 0.022 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 47 2.27 - 2.93: 8847 2.93 - 3.59: 26414 3.59 - 4.24: 47478 4.24 - 4.90: 81735 Nonbonded interactions: 164521 Sorted by model distance: nonbonded pdb=" OD1 ASP G 177 " pdb=" O HOH G1101 " model vdw 1.618 2.440 nonbonded pdb=" OE2 GLU F 135 " pdb=" O HOH F 601 " model vdw 1.654 2.440 nonbonded pdb=" OE2 GLU D 115 " pdb=" NH2 ARG G 698 " model vdw 1.815 2.520 nonbonded pdb=" OE2 GLU D 85 " pdb=" O HOH D 601 " model vdw 1.841 2.440 nonbonded pdb=" OE2 GLU G 380 " pdb=" ND2 ASN G 503 " model vdw 1.857 2.520 ... (remaining 164516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 5.830 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 55.900 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.012 0.176 19227 Z= 0.777 Angle : 1.119 13.297 26113 Z= 0.732 Chirality : 1.946 22.068 2808 Planarity : 0.007 0.081 3416 Dihedral : 14.797 170.840 7105 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.58 % Allowed : 11.23 % Favored : 87.20 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.15), residues: 2359 helix: -1.89 (0.15), residues: 861 sheet: -2.23 (0.32), residues: 228 loop : -2.53 (0.15), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 15 HIS 0.014 0.001 HIS D 83 PHE 0.018 0.002 PHE G 130 TYR 0.023 0.002 TYR G 638 ARG 0.022 0.001 ARG G 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 337 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.6987 (ptp) cc_final: 0.6775 (ptp) REVERT: B 208 ARG cc_start: -0.3261 (OUTLIER) cc_final: -0.3581 (ptm160) REVERT: D 105 ARG cc_start: 0.7669 (mmt90) cc_final: 0.7360 (mpt180) REVERT: D 123 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: D 272 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: D 273 TYR cc_start: 0.7462 (p90) cc_final: 0.7212 (p90) REVERT: D 390 TYR cc_start: 0.7325 (t80) cc_final: 0.6850 (t80) REVERT: D 449 GLU cc_start: 0.7951 (pt0) cc_final: 0.7254 (mm-30) REVERT: D 468 GLU cc_start: 0.7379 (pt0) cc_final: 0.6839 (tp30) REVERT: D 471 ARG cc_start: 0.6733 (mtp85) cc_final: 0.6449 (mtp-110) REVERT: D 575 SER cc_start: 0.8140 (m) cc_final: 0.7707 (t) REVERT: E 31 ASP cc_start: 0.8617 (t0) cc_final: 0.8390 (t0) REVERT: E 60 ASP cc_start: 0.7876 (m-30) cc_final: 0.7646 (m-30) REVERT: E 164 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7911 (mtm-85) REVERT: F 48 ASP cc_start: 0.7392 (m-30) cc_final: 0.7148 (m-30) REVERT: F 135 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: F 158 LYS cc_start: 0.7657 (mmpt) cc_final: 0.7068 (mmpt) REVERT: F 168 GLU cc_start: 0.7984 (tt0) cc_final: 0.7756 (tt0) REVERT: F 183 GLU cc_start: 0.8702 (tt0) cc_final: 0.8411 (tt0) REVERT: F 241 LYS cc_start: 0.9210 (mmpt) cc_final: 0.8949 (mppt) REVERT: F 258 ASN cc_start: 0.8313 (t0) cc_final: 0.7841 (t0) REVERT: F 275 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 386 GLN cc_start: 0.7466 (tt0) cc_final: 0.7137 (mt0) REVERT: F 424 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8423 (mtmm) REVERT: G 72 SER cc_start: 0.8345 (m) cc_final: 0.8142 (p) REVERT: G 80 ASP cc_start: 0.8481 (m-30) cc_final: 0.8241 (m-30) REVERT: G 276 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8646 (mmpt) REVERT: G 277 ASP cc_start: 0.8207 (p0) cc_final: 0.7989 (p0) REVERT: G 335 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7431 (mp0) REVERT: G 436 ASP cc_start: 0.7740 (p0) cc_final: 0.7471 (p0) REVERT: G 488 GLN cc_start: 0.7700 (tt0) cc_final: 0.7255 (mt0) REVERT: G 494 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7299 (mmtm) REVERT: G 544 MET cc_start: 0.8406 (ttm) cc_final: 0.8109 (ttp) REVERT: G 586 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7772 (ptmt) REVERT: G 642 LYS cc_start: 0.8835 (pttp) cc_final: 0.8539 (ptpp) REVERT: G 725 ARG cc_start: 0.7469 (ptm160) cc_final: 0.7233 (ptm160) REVERT: G 748 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8172 (ppt90) REVERT: G 832 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8189 (mp10) REVERT: G 835 MET cc_start: 0.7735 (ptp) cc_final: 0.7349 (ptm) REVERT: G 849 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8430 (ttpp) REVERT: G 881 GLN cc_start: 0.7818 (mt0) cc_final: 0.7512 (mt0) REVERT: G 888 MET cc_start: 0.7943 (tpp) cc_final: 0.7351 (mmm) REVERT: G 902 ASP cc_start: 0.8080 (t0) cc_final: 0.6511 (p0) REVERT: I 57 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6461 (mm-30) REVERT: I 83 LYS cc_start: 0.7980 (tppt) cc_final: 0.7705 (mptt) REVERT: I 122 MET cc_start: 0.6243 (mmp) cc_final: 0.5453 (ptm) REVERT: I 145 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: I 171 LYS cc_start: 0.8324 (mttt) cc_final: 0.7733 (mptt) outliers start: 31 outliers final: 11 residues processed: 361 average time/residue: 1.5922 time to fit residues: 632.3161 Evaluate side-chains 240 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 698 ARG Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 748 ARG Chi-restraints excluded: chain I residue 145 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 0.3980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 315 HIS D 566 GLN E 103 GLN F 196 ASN F 341 ASN G 101 HIS G 325 ASN G 726 GLN G 769 GLN G 804 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.263 19227 Z= 0.918 Angle : 2.821 50.957 26113 Z= 1.863 Chirality : 0.585 6.473 2808 Planarity : 0.005 0.081 3416 Dihedral : 7.109 168.530 2662 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.59 % Allowed : 16.06 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2359 helix: -0.70 (0.18), residues: 851 sheet: -1.72 (0.33), residues: 228 loop : -2.12 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 15 HIS 0.006 0.001 HIS E 98 PHE 0.023 0.001 PHE D 352 TYR 0.020 0.001 TYR I 44 ARG 0.012 0.000 ARG D 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 244 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6584 (pp20) REVERT: D 48 ILE cc_start: 0.8474 (mm) cc_final: 0.8110 (pt) REVERT: D 58 ASP cc_start: 0.7701 (t0) cc_final: 0.7253 (t0) REVERT: D 62 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8089 (mtpt) REVERT: D 105 ARG cc_start: 0.7544 (mmt90) cc_final: 0.7143 (mpt180) REVERT: D 123 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: D 272 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: D 391 GLU cc_start: 0.3990 (pt0) cc_final: 0.2719 (pp20) REVERT: D 449 GLU cc_start: 0.7966 (pt0) cc_final: 0.7276 (mm-30) REVERT: D 468 GLU cc_start: 0.7167 (pt0) cc_final: 0.6737 (tp30) REVERT: D 469 GLU cc_start: 0.7533 (tt0) cc_final: 0.7244 (mt-10) REVERT: D 471 ARG cc_start: 0.6610 (mtp85) cc_final: 0.6220 (mtt90) REVERT: D 575 SER cc_start: 0.7923 (m) cc_final: 0.7558 (t) REVERT: E 13 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: E 60 ASP cc_start: 0.7923 (m-30) cc_final: 0.7673 (m-30) REVERT: E 111 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8148 (tmmm) REVERT: F 28 GLU cc_start: 0.7989 (tt0) cc_final: 0.7421 (tt0) REVERT: F 31 SER cc_start: 0.8991 (t) cc_final: 0.8740 (p) REVERT: F 48 ASP cc_start: 0.7366 (m-30) cc_final: 0.7114 (m-30) REVERT: F 152 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7889 (tm-30) REVERT: F 241 LYS cc_start: 0.9189 (mmpt) cc_final: 0.8920 (mppt) REVERT: F 243 LYS cc_start: 0.8412 (ptpp) cc_final: 0.7788 (ptmm) REVERT: F 258 ASN cc_start: 0.8216 (t0) cc_final: 0.7558 (t0) REVERT: F 286 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7588 (mtmt) REVERT: F 312 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: F 386 GLN cc_start: 0.7078 (tt0) cc_final: 0.6825 (tt0) REVERT: F 424 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8411 (mtmm) REVERT: G 57 GLU cc_start: 0.7675 (pm20) cc_final: 0.7402 (mp0) REVERT: G 80 ASP cc_start: 0.8342 (m-30) cc_final: 0.8031 (m-30) REVERT: G 108 GLU cc_start: 0.7113 (pt0) cc_final: 0.6902 (pt0) REVERT: G 190 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7758 (mp0) REVERT: G 221 MET cc_start: 0.8969 (tpp) cc_final: 0.8233 (tpp) REVERT: G 276 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8683 (mmpt) REVERT: G 335 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7440 (mp0) REVERT: G 436 ASP cc_start: 0.7608 (p0) cc_final: 0.7392 (p0) REVERT: G 467 ASN cc_start: 0.7515 (m110) cc_final: 0.7123 (t0) REVERT: G 484 ASP cc_start: 0.7258 (m-30) cc_final: 0.6573 (m-30) REVERT: G 488 GLN cc_start: 0.7363 (tt0) cc_final: 0.6924 (mt0) REVERT: G 494 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7325 (mmtm) REVERT: G 544 MET cc_start: 0.8279 (ttm) cc_final: 0.7884 (ttm) REVERT: G 591 MET cc_start: 0.7667 (mtp) cc_final: 0.7450 (ttm) REVERT: G 642 LYS cc_start: 0.8805 (pttp) cc_final: 0.8443 (ptpp) REVERT: G 715 MET cc_start: 0.8902 (ptt) cc_final: 0.8573 (ptm) REVERT: G 771 GLU cc_start: 0.7585 (pt0) cc_final: 0.7180 (pt0) REVERT: G 787 GLU cc_start: 0.7840 (pm20) cc_final: 0.7597 (pm20) REVERT: G 849 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8418 (ttpp) REVERT: G 881 GLN cc_start: 0.7602 (mt0) cc_final: 0.7338 (mt0) REVERT: G 888 MET cc_start: 0.7684 (tpp) cc_final: 0.6961 (mmm) REVERT: I 83 LYS cc_start: 0.7938 (tppt) cc_final: 0.7699 (mptt) REVERT: I 122 MET cc_start: 0.5630 (mmp) cc_final: 0.5072 (ttm) REVERT: I 165 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: I 171 LYS cc_start: 0.8328 (mttt) cc_final: 0.7806 (mptt) outliers start: 51 outliers final: 24 residues processed: 275 average time/residue: 1.5195 time to fit residues: 463.4655 Evaluate side-chains 246 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 769 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 165 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 ASN E 103 GLN F 224 ASN F 341 ASN G 325 ASN G 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.250 19227 Z= 0.942 Angle : 2.820 50.578 26113 Z= 1.862 Chirality : 0.587 6.447 2808 Planarity : 0.005 0.056 3416 Dihedral : 6.782 165.959 2640 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.56 % Allowed : 16.31 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2359 helix: -0.47 (0.18), residues: 856 sheet: -1.38 (0.33), residues: 237 loop : -1.91 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 15 HIS 0.005 0.001 HIS G 113 PHE 0.018 0.002 PHE F 167 TYR 0.015 0.002 TYR F 178 ARG 0.008 0.001 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 221 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 VAL cc_start: 0.3825 (OUTLIER) cc_final: 0.3432 (t) REVERT: B 163 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6614 (pp20) REVERT: B 170 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5888 (mmt) REVERT: D 58 ASP cc_start: 0.7892 (t0) cc_final: 0.7618 (t0) REVERT: D 123 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: D 233 LEU cc_start: 0.8274 (mp) cc_final: 0.8070 (mm) REVERT: D 272 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: D 273 TYR cc_start: 0.7781 (p90) cc_final: 0.7380 (p90) REVERT: D 280 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: D 391 GLU cc_start: 0.3986 (pt0) cc_final: 0.3073 (pp20) REVERT: D 449 GLU cc_start: 0.7966 (pt0) cc_final: 0.7284 (mm-30) REVERT: D 468 GLU cc_start: 0.7133 (pt0) cc_final: 0.6655 (tp30) REVERT: D 471 ARG cc_start: 0.6649 (mtp85) cc_final: 0.6068 (mpt-90) REVERT: D 575 SER cc_start: 0.7942 (m) cc_final: 0.7563 (t) REVERT: E 13 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: E 156 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: E 160 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7513 (tm-30) REVERT: E 164 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7421 (mtt180) REVERT: F 28 GLU cc_start: 0.8025 (tt0) cc_final: 0.7454 (tt0) REVERT: F 31 SER cc_start: 0.9016 (t) cc_final: 0.8747 (p) REVERT: F 152 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7904 (tm-30) REVERT: F 158 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7676 (mmpt) REVERT: F 241 LYS cc_start: 0.9196 (mmpt) cc_final: 0.8951 (mppt) REVERT: F 243 LYS cc_start: 0.8482 (ptpp) cc_final: 0.7809 (ptmm) REVERT: F 286 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7631 (mtmt) REVERT: F 386 GLN cc_start: 0.6982 (tt0) cc_final: 0.6752 (tt0) REVERT: F 424 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8328 (mtpp) REVERT: G 57 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: G 62 ARG cc_start: 0.7346 (ptt-90) cc_final: 0.6625 (ptt-90) REVERT: G 80 ASP cc_start: 0.8234 (m-30) cc_final: 0.7960 (m-30) REVERT: G 185 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6184 (pp20) REVERT: G 221 MET cc_start: 0.8932 (tpp) cc_final: 0.8662 (mtp) REVERT: G 276 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8658 (mmpt) REVERT: G 335 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7458 (mp0) REVERT: G 467 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.6916 (t0) REVERT: G 484 ASP cc_start: 0.7297 (m-30) cc_final: 0.6646 (m-30) REVERT: G 488 GLN cc_start: 0.7495 (tt0) cc_final: 0.7054 (mt0) REVERT: G 494 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7529 (mmtm) REVERT: G 544 MET cc_start: 0.8258 (ttm) cc_final: 0.7642 (ttm) REVERT: G 642 LYS cc_start: 0.8822 (pttp) cc_final: 0.8452 (ptpp) REVERT: G 715 MET cc_start: 0.8891 (ptt) cc_final: 0.8550 (ptm) REVERT: G 771 GLU cc_start: 0.7845 (pt0) cc_final: 0.7397 (pt0) REVERT: G 787 GLU cc_start: 0.7793 (pm20) cc_final: 0.7467 (mp0) REVERT: G 849 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8430 (ttpp) REVERT: G 881 GLN cc_start: 0.7770 (mt0) cc_final: 0.7496 (mt0) REVERT: G 888 MET cc_start: 0.7569 (tpp) cc_final: 0.7251 (mmm) REVERT: I 83 LYS cc_start: 0.8014 (tppt) cc_final: 0.7741 (mptt) REVERT: I 122 MET cc_start: 0.5942 (mmp) cc_final: 0.5151 (ptm) REVERT: I 153 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7380 (mmm) REVERT: I 171 LYS cc_start: 0.8312 (mttt) cc_final: 0.7797 (mptt) outliers start: 70 outliers final: 31 residues processed: 264 average time/residue: 1.4615 time to fit residues: 429.2308 Evaluate side-chains 251 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 226 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 ASN E 98 HIS G 769 GLN G 804 GLN G 908 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.245 19227 Z= 0.918 Angle : 2.808 50.560 26113 Z= 1.857 Chirality : 0.585 6.437 2808 Planarity : 0.004 0.055 3416 Dihedral : 6.540 165.997 2640 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.56 % Allowed : 17.33 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2359 helix: -0.16 (0.18), residues: 860 sheet: -1.32 (0.31), residues: 256 loop : -1.81 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 382 HIS 0.006 0.001 HIS G 176 PHE 0.013 0.001 PHE F 167 TYR 0.015 0.001 TYR I 44 ARG 0.009 0.000 ARG G 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 217 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6563 (ttt) REVERT: B 163 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6610 (pp20) REVERT: B 170 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.5762 (mmt) REVERT: D 48 ILE cc_start: 0.8378 (mm) cc_final: 0.7999 (pt) REVERT: D 58 ASP cc_start: 0.7881 (t70) cc_final: 0.7592 (t0) REVERT: D 103 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6700 (pmm-80) REVERT: D 123 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7176 (m-80) REVERT: D 233 LEU cc_start: 0.8265 (mp) cc_final: 0.8055 (mm) REVERT: D 272 GLU cc_start: 0.7835 (tm-30) cc_final: 0.6908 (tm-30) REVERT: D 391 GLU cc_start: 0.3967 (pt0) cc_final: 0.2829 (pp20) REVERT: D 449 GLU cc_start: 0.7924 (pt0) cc_final: 0.7271 (mm-30) REVERT: D 468 GLU cc_start: 0.7080 (pt0) cc_final: 0.6681 (OUTLIER) REVERT: D 471 ARG cc_start: 0.6625 (mtp85) cc_final: 0.6111 (mpt-90) REVERT: D 575 SER cc_start: 0.7809 (m) cc_final: 0.7440 (t) REVERT: F 28 GLU cc_start: 0.8078 (tt0) cc_final: 0.7530 (tt0) REVERT: F 31 SER cc_start: 0.9003 (t) cc_final: 0.8742 (p) REVERT: F 152 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7880 (tm-30) REVERT: F 158 LYS cc_start: 0.8271 (mmpt) cc_final: 0.7838 (mmpt) REVERT: F 241 LYS cc_start: 0.9216 (mmpt) cc_final: 0.8984 (mppt) REVERT: F 243 LYS cc_start: 0.8479 (ptpp) cc_final: 0.7802 (ptmm) REVERT: F 286 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7666 (mtmt) REVERT: F 386 GLN cc_start: 0.6947 (tt0) cc_final: 0.6661 (tt0) REVERT: F 424 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8359 (mtpp) REVERT: G 57 GLU cc_start: 0.7667 (pm20) cc_final: 0.7330 (mp0) REVERT: G 62 ARG cc_start: 0.7134 (ptt-90) cc_final: 0.6514 (ptt-90) REVERT: G 80 ASP cc_start: 0.8147 (m-30) cc_final: 0.7819 (m-30) REVERT: G 185 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6272 (pp20) REVERT: G 199 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: G 209 LYS cc_start: 0.7617 (mttt) cc_final: 0.7089 (mttp) REVERT: G 221 MET cc_start: 0.8909 (tpp) cc_final: 0.8658 (mtp) REVERT: G 467 ASN cc_start: 0.7408 (OUTLIER) cc_final: 0.7003 (t0) REVERT: G 484 ASP cc_start: 0.7286 (m-30) cc_final: 0.6639 (m-30) REVERT: G 488 GLN cc_start: 0.7570 (tt0) cc_final: 0.7172 (mt0) REVERT: G 494 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7521 (mmtm) REVERT: G 544 MET cc_start: 0.8296 (ttm) cc_final: 0.7800 (ttm) REVERT: G 615 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: G 642 LYS cc_start: 0.8780 (pttp) cc_final: 0.8407 (ptpp) REVERT: G 715 MET cc_start: 0.8854 (ptt) cc_final: 0.8526 (ptm) REVERT: G 771 GLU cc_start: 0.7665 (pt0) cc_final: 0.7203 (pt0) REVERT: G 787 GLU cc_start: 0.7747 (pm20) cc_final: 0.7452 (mp0) REVERT: G 849 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8359 (ttmt) REVERT: G 881 GLN cc_start: 0.7583 (mt0) cc_final: 0.7319 (mt0) REVERT: G 888 MET cc_start: 0.7662 (tpp) cc_final: 0.7132 (mmm) REVERT: I 83 LYS cc_start: 0.8008 (tppt) cc_final: 0.7732 (mptt) REVERT: I 122 MET cc_start: 0.5974 (mmp) cc_final: 0.5207 (ptm) REVERT: I 165 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: I 171 LYS cc_start: 0.8334 (mttt) cc_final: 0.7771 (mptt) outliers start: 70 outliers final: 26 residues processed: 262 average time/residue: 1.4678 time to fit residues: 427.4352 Evaluate side-chains 243 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 44 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 165 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 0.0010 chunk 168 optimal weight: 0.1980 chunk 93 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 ASN G 769 GLN G 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.245 19227 Z= 0.919 Angle : 2.806 50.554 26113 Z= 1.857 Chirality : 0.585 6.413 2808 Planarity : 0.004 0.054 3416 Dihedral : 6.116 165.774 2630 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.20 % Allowed : 18.39 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2359 helix: -0.04 (0.18), residues: 861 sheet: -1.18 (0.31), residues: 258 loop : -1.70 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 382 HIS 0.006 0.001 HIS G 176 PHE 0.014 0.001 PHE F 167 TYR 0.014 0.001 TYR I 44 ARG 0.009 0.000 ARG G 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 217 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6528 (ttt) REVERT: B 163 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6680 (pp20) REVERT: B 170 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5745 (mmt) REVERT: D 48 ILE cc_start: 0.8440 (mm) cc_final: 0.8046 (pt) REVERT: D 58 ASP cc_start: 0.7895 (t70) cc_final: 0.7599 (t0) REVERT: D 103 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6716 (pmm-80) REVERT: D 123 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: D 125 LYS cc_start: 0.8447 (mttt) cc_final: 0.8230 (mttt) REVERT: D 228 ARG cc_start: 0.7202 (ttt-90) cc_final: 0.6997 (ttt180) REVERT: D 272 GLU cc_start: 0.7864 (tm-30) cc_final: 0.6930 (tm-30) REVERT: D 273 TYR cc_start: 0.7747 (p90) cc_final: 0.7354 (p90) REVERT: D 449 GLU cc_start: 0.7906 (pt0) cc_final: 0.7261 (mm-30) REVERT: D 468 GLU cc_start: 0.6941 (pt0) cc_final: 0.6661 (OUTLIER) REVERT: D 575 SER cc_start: 0.7736 (m) cc_final: 0.7365 (t) REVERT: E 156 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: F 28 GLU cc_start: 0.8053 (tt0) cc_final: 0.7520 (tt0) REVERT: F 31 SER cc_start: 0.9007 (t) cc_final: 0.8747 (p) REVERT: F 152 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7865 (tm-30) REVERT: F 158 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7813 (mmpt) REVERT: F 183 GLU cc_start: 0.8510 (tt0) cc_final: 0.8225 (tt0) REVERT: F 241 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8987 (mppt) REVERT: F 286 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7681 (mtmt) REVERT: F 386 GLN cc_start: 0.6933 (tt0) cc_final: 0.6661 (tt0) REVERT: F 424 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8351 (mtpp) REVERT: G 57 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: G 62 ARG cc_start: 0.7209 (ptt-90) cc_final: 0.6634 (ptt-90) REVERT: G 80 ASP cc_start: 0.8152 (m-30) cc_final: 0.7915 (m-30) REVERT: G 185 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6288 (pp20) REVERT: G 199 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: G 209 LYS cc_start: 0.7611 (mttt) cc_final: 0.7066 (mttp) REVERT: G 221 MET cc_start: 0.8893 (tpp) cc_final: 0.8661 (mtp) REVERT: G 335 GLU cc_start: 0.7392 (mp0) cc_final: 0.7153 (pm20) REVERT: G 467 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7006 (t0) REVERT: G 484 ASP cc_start: 0.7280 (m-30) cc_final: 0.6640 (m-30) REVERT: G 488 GLN cc_start: 0.7584 (tt0) cc_final: 0.7186 (mt0) REVERT: G 494 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7522 (mmtm) REVERT: G 531 MET cc_start: 0.8720 (mmt) cc_final: 0.8125 (mmt) REVERT: G 544 MET cc_start: 0.8308 (ttm) cc_final: 0.7809 (ttm) REVERT: G 615 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: G 642 LYS cc_start: 0.8756 (pttp) cc_final: 0.8393 (ptpp) REVERT: G 715 MET cc_start: 0.8765 (ptt) cc_final: 0.8459 (ptm) REVERT: G 771 GLU cc_start: 0.7702 (pt0) cc_final: 0.7308 (pt0) REVERT: G 787 GLU cc_start: 0.7672 (pm20) cc_final: 0.7424 (mp0) REVERT: G 849 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8338 (ttmt) REVERT: G 881 GLN cc_start: 0.7633 (mt0) cc_final: 0.7366 (mt0) REVERT: G 888 MET cc_start: 0.7781 (tpp) cc_final: 0.7096 (mmm) REVERT: I 83 LYS cc_start: 0.8012 (tppt) cc_final: 0.7757 (mptt) REVERT: I 122 MET cc_start: 0.5908 (mmp) cc_final: 0.5165 (ptm) REVERT: I 153 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6049 (mmm) REVERT: I 171 LYS cc_start: 0.8330 (mttt) cc_final: 0.7779 (mptt) outliers start: 63 outliers final: 31 residues processed: 259 average time/residue: 1.5161 time to fit residues: 437.1112 Evaluate side-chains 256 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 769 GLN Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 44 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 ASN G 47 GLN G 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.251 19227 Z= 0.931 Angle : 2.812 50.596 26113 Z= 1.859 Chirality : 0.585 6.425 2808 Planarity : 0.005 0.056 3416 Dihedral : 6.175 165.712 2630 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.71 % Allowed : 18.55 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2359 helix: -0.05 (0.18), residues: 863 sheet: -1.08 (0.32), residues: 250 loop : -1.66 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 15 HIS 0.005 0.001 HIS G 176 PHE 0.016 0.001 PHE F 167 TYR 0.013 0.001 TYR I 44 ARG 0.010 0.000 ARG G 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 213 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6576 (ttt) REVERT: B 163 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6666 (pp20) REVERT: B 170 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.5761 (mmt) REVERT: D 58 ASP cc_start: 0.7968 (t70) cc_final: 0.7638 (t0) REVERT: D 103 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6679 (pmm-80) REVERT: D 272 GLU cc_start: 0.7936 (tm-30) cc_final: 0.6980 (tm-30) REVERT: D 383 MET cc_start: 0.8223 (mmt) cc_final: 0.7805 (mmm) REVERT: D 449 GLU cc_start: 0.7912 (pt0) cc_final: 0.7282 (mm-30) REVERT: D 468 GLU cc_start: 0.6937 (pt0) cc_final: 0.6666 (OUTLIER) REVERT: D 471 ARG cc_start: 0.6563 (mmm-85) cc_final: 0.6203 (mmm-85) REVERT: D 575 SER cc_start: 0.7697 (m) cc_final: 0.7252 (t) REVERT: E 13 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: E 156 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: F 28 GLU cc_start: 0.8011 (tt0) cc_final: 0.7490 (tt0) REVERT: F 31 SER cc_start: 0.9020 (t) cc_final: 0.8662 (p) REVERT: F 152 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7872 (tm-30) REVERT: F 158 LYS cc_start: 0.8245 (mmpt) cc_final: 0.7770 (mmpt) REVERT: F 183 GLU cc_start: 0.8468 (tt0) cc_final: 0.8172 (tt0) REVERT: F 241 LYS cc_start: 0.9233 (mmpt) cc_final: 0.8984 (mppt) REVERT: F 275 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7702 (mt-10) REVERT: F 286 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7675 (mtmt) REVERT: F 386 GLN cc_start: 0.6927 (tt0) cc_final: 0.6695 (tt0) REVERT: F 424 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8365 (mtpp) REVERT: G 57 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: G 62 ARG cc_start: 0.7381 (ptt-90) cc_final: 0.6899 (ptt-90) REVERT: G 80 ASP cc_start: 0.8136 (m-30) cc_final: 0.7909 (m-30) REVERT: G 185 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6244 (pp20) REVERT: G 199 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: G 335 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: G 467 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6839 (t0) REVERT: G 484 ASP cc_start: 0.7274 (m-30) cc_final: 0.6634 (m-30) REVERT: G 488 GLN cc_start: 0.7559 (tt0) cc_final: 0.7153 (mt0) REVERT: G 494 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7522 (mmtm) REVERT: G 544 MET cc_start: 0.8327 (ttm) cc_final: 0.7914 (ttm) REVERT: G 642 LYS cc_start: 0.8714 (pttp) cc_final: 0.8359 (ptpp) REVERT: G 715 MET cc_start: 0.8778 (ptt) cc_final: 0.8470 (ptm) REVERT: G 771 GLU cc_start: 0.7725 (pt0) cc_final: 0.7199 (pt0) REVERT: G 787 GLU cc_start: 0.7673 (pm20) cc_final: 0.7403 (mp0) REVERT: G 849 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8326 (ttmt) REVERT: G 881 GLN cc_start: 0.7694 (mt0) cc_final: 0.7378 (mt0) REVERT: G 888 MET cc_start: 0.7735 (tpp) cc_final: 0.7229 (mmm) REVERT: I 83 LYS cc_start: 0.8094 (tppt) cc_final: 0.7832 (mptt) REVERT: I 122 MET cc_start: 0.6020 (mmp) cc_final: 0.5241 (ptm) REVERT: I 153 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.6055 (mmm) REVERT: I 171 LYS cc_start: 0.8353 (mttt) cc_final: 0.7790 (mptt) outliers start: 73 outliers final: 35 residues processed: 263 average time/residue: 1.4840 time to fit residues: 434.0518 Evaluate side-chains 257 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 211 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 688 ASP Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain I residue 44 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 128 optimal weight: 0.6980 chunk 165 optimal weight: 0.0020 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 GLN G 769 GLN G 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.245 19227 Z= 0.913 Angle : 2.804 50.552 26113 Z= 1.856 Chirality : 0.584 6.390 2808 Planarity : 0.004 0.053 3416 Dihedral : 5.955 166.012 2630 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.00 % Allowed : 19.41 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2359 helix: 0.22 (0.19), residues: 858 sheet: -0.99 (0.32), residues: 258 loop : -1.55 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 651 HIS 0.006 0.001 HIS G 176 PHE 0.011 0.001 PHE F 167 TYR 0.013 0.001 TYR I 44 ARG 0.012 0.000 ARG G 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 223 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6658 (pp20) REVERT: B 170 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5776 (mmt) REVERT: D 48 ILE cc_start: 0.8380 (mm) cc_final: 0.7972 (pt) REVERT: D 58 ASP cc_start: 0.7899 (t70) cc_final: 0.7603 (t0) REVERT: D 103 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6795 (pmm-80) REVERT: D 272 GLU cc_start: 0.7731 (tm-30) cc_final: 0.6767 (tm-30) REVERT: D 383 MET cc_start: 0.8186 (mmt) cc_final: 0.7642 (mmm) REVERT: D 449 GLU cc_start: 0.7850 (pt0) cc_final: 0.7224 (mm-30) REVERT: D 471 ARG cc_start: 0.6430 (mmm-85) cc_final: 0.6178 (mmm-85) REVERT: D 575 SER cc_start: 0.7580 (m) cc_final: 0.7178 (t) REVERT: F 28 GLU cc_start: 0.7991 (tt0) cc_final: 0.7503 (tt0) REVERT: F 31 SER cc_start: 0.9014 (t) cc_final: 0.8752 (p) REVERT: F 152 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7866 (tm-30) REVERT: F 158 LYS cc_start: 0.8439 (mmpt) cc_final: 0.7910 (mmpt) REVERT: F 183 GLU cc_start: 0.8413 (tt0) cc_final: 0.8113 (tt0) REVERT: F 241 LYS cc_start: 0.9217 (mmpt) cc_final: 0.8986 (mppt) REVERT: F 257 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7481 (mttt) REVERT: F 275 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7612 (mm-30) REVERT: F 286 LYS cc_start: 0.8297 (mtpp) cc_final: 0.7818 (mtmt) REVERT: F 386 GLN cc_start: 0.6851 (tt0) cc_final: 0.6545 (tt0) REVERT: F 424 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8353 (mtpp) REVERT: G 57 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: G 62 ARG cc_start: 0.7149 (ptt-90) cc_final: 0.6716 (ptt-90) REVERT: G 80 ASP cc_start: 0.8133 (m-30) cc_final: 0.7891 (m-30) REVERT: G 185 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6238 (pp20) REVERT: G 199 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: G 209 LYS cc_start: 0.7560 (mttt) cc_final: 0.7015 (mttp) REVERT: G 277 ASP cc_start: 0.8186 (p0) cc_final: 0.7979 (p0) REVERT: G 335 GLU cc_start: 0.7435 (mp0) cc_final: 0.7221 (pm20) REVERT: G 467 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6961 (t0) REVERT: G 484 ASP cc_start: 0.7309 (m-30) cc_final: 0.6719 (m-30) REVERT: G 488 GLN cc_start: 0.7539 (tt0) cc_final: 0.7141 (mt0) REVERT: G 494 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7413 (mmtm) REVERT: G 531 MET cc_start: 0.8661 (mmt) cc_final: 0.8147 (mmt) REVERT: G 544 MET cc_start: 0.8262 (ttm) cc_final: 0.7864 (ttm) REVERT: G 589 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7455 (tp) REVERT: G 642 LYS cc_start: 0.8689 (pttp) cc_final: 0.8347 (ptpp) REVERT: G 712 ARG cc_start: 0.7572 (ttp-110) cc_final: 0.7190 (ttt90) REVERT: G 715 MET cc_start: 0.8686 (ptt) cc_final: 0.8390 (ptm) REVERT: G 787 GLU cc_start: 0.7658 (pm20) cc_final: 0.7420 (mp0) REVERT: G 849 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8302 (ttmt) REVERT: G 881 GLN cc_start: 0.7522 (mt0) cc_final: 0.7155 (mt0) REVERT: G 888 MET cc_start: 0.7642 (tpp) cc_final: 0.7023 (mmm) REVERT: I 83 LYS cc_start: 0.8070 (tppt) cc_final: 0.7823 (mptt) REVERT: I 122 MET cc_start: 0.5840 (mmp) cc_final: 0.5101 (ptm) REVERT: I 153 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.5806 (mmm) REVERT: I 171 LYS cc_start: 0.8366 (mttt) cc_final: 0.7792 (mptt) outliers start: 59 outliers final: 27 residues processed: 258 average time/residue: 1.5457 time to fit residues: 446.8212 Evaluate side-chains 246 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 382 TRP Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 177 optimal weight: 0.0570 chunk 205 optimal weight: 0.3980 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 308 GLN G 769 GLN G 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.248 19227 Z= 0.916 Angle : 2.807 50.553 26113 Z= 1.857 Chirality : 0.584 6.381 2808 Planarity : 0.004 0.053 3416 Dihedral : 5.887 165.631 2630 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.59 % Allowed : 19.92 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2359 helix: 0.30 (0.19), residues: 858 sheet: -0.91 (0.32), residues: 258 loop : -1.48 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 651 HIS 0.006 0.001 HIS G 176 PHE 0.012 0.001 PHE F 167 TYR 0.013 0.001 TYR I 44 ARG 0.009 0.000 ARG G 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6689 (pp20) REVERT: B 170 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5809 (mmt) REVERT: D 48 ILE cc_start: 0.8367 (mm) cc_final: 0.7956 (pt) REVERT: D 58 ASP cc_start: 0.7912 (t70) cc_final: 0.7613 (t0) REVERT: D 85 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: D 103 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6772 (pmm-80) REVERT: D 272 GLU cc_start: 0.7736 (tm-30) cc_final: 0.6800 (tm-30) REVERT: D 273 TYR cc_start: 0.7876 (p90) cc_final: 0.7509 (p90) REVERT: D 383 MET cc_start: 0.8151 (mmt) cc_final: 0.7626 (mmm) REVERT: D 449 GLU cc_start: 0.7872 (pt0) cc_final: 0.7243 (mm-30) REVERT: D 575 SER cc_start: 0.7585 (m) cc_final: 0.7140 (t) REVERT: D 579 ASP cc_start: 0.7888 (m-30) cc_final: 0.7658 (m-30) REVERT: F 28 GLU cc_start: 0.7972 (tt0) cc_final: 0.7457 (tt0) REVERT: F 31 SER cc_start: 0.9027 (t) cc_final: 0.8676 (p) REVERT: F 152 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7860 (tm-30) REVERT: F 158 LYS cc_start: 0.8455 (mmpt) cc_final: 0.7903 (mmpt) REVERT: F 183 GLU cc_start: 0.8415 (tt0) cc_final: 0.8118 (tt0) REVERT: F 241 LYS cc_start: 0.9236 (mmpt) cc_final: 0.9002 (mppt) REVERT: F 257 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7503 (mttt) REVERT: F 275 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7622 (mm-30) REVERT: F 286 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7843 (mtmt) REVERT: F 386 GLN cc_start: 0.6850 (tt0) cc_final: 0.6539 (tt0) REVERT: F 424 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8357 (mtpp) REVERT: G 57 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: G 62 ARG cc_start: 0.7133 (ptt-90) cc_final: 0.6602 (ptt-90) REVERT: G 80 ASP cc_start: 0.8150 (m-30) cc_final: 0.7927 (m-30) REVERT: G 185 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6215 (pp20) REVERT: G 190 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7779 (mp0) REVERT: G 199 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: G 209 LYS cc_start: 0.7598 (mttt) cc_final: 0.7030 (mttp) REVERT: G 277 ASP cc_start: 0.8152 (p0) cc_final: 0.7950 (p0) REVERT: G 305 ILE cc_start: 0.8363 (tp) cc_final: 0.8122 (tp) REVERT: G 335 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: G 467 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6973 (t0) REVERT: G 484 ASP cc_start: 0.7249 (m-30) cc_final: 0.6663 (m-30) REVERT: G 488 GLN cc_start: 0.7511 (tt0) cc_final: 0.7150 (mt0) REVERT: G 494 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7410 (mmtm) REVERT: G 531 MET cc_start: 0.8669 (mmt) cc_final: 0.8173 (mmt) REVERT: G 544 MET cc_start: 0.8259 (ttm) cc_final: 0.7867 (ttm) REVERT: G 589 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7272 (tp) REVERT: G 642 LYS cc_start: 0.8677 (pttp) cc_final: 0.8322 (ptpp) REVERT: G 715 MET cc_start: 0.8658 (ptt) cc_final: 0.8362 (ptm) REVERT: G 787 GLU cc_start: 0.7662 (pm20) cc_final: 0.7425 (mp0) REVERT: G 849 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8273 (ttmt) REVERT: G 881 GLN cc_start: 0.7539 (mt0) cc_final: 0.7150 (mt0) REVERT: G 888 MET cc_start: 0.7629 (tpp) cc_final: 0.7157 (mmm) REVERT: I 122 MET cc_start: 0.5839 (mmp) cc_final: 0.5070 (ptm) REVERT: I 153 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.5923 (mmm) REVERT: I 171 LYS cc_start: 0.8367 (mttt) cc_final: 0.7790 (mptt) outliers start: 51 outliers final: 27 residues processed: 249 average time/residue: 1.5125 time to fit residues: 418.1479 Evaluate side-chains 253 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 382 TRP Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 769 GLN Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 159 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.1980 chunk 197 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 91 optimal weight: 0.0570 chunk 165 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.247 19227 Z= 0.915 Angle : 2.804 50.539 26113 Z= 1.856 Chirality : 0.583 6.363 2808 Planarity : 0.004 0.055 3416 Dihedral : 5.769 165.612 2630 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.54 % Allowed : 20.33 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2359 helix: 0.49 (0.19), residues: 852 sheet: -0.85 (0.32), residues: 258 loop : -1.42 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 382 HIS 0.006 0.001 HIS G 176 PHE 0.012 0.001 PHE G 768 TYR 0.013 0.001 TYR I 44 ARG 0.014 0.000 ARG G 712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 224 time to evaluate : 2.185 Fit side-chains revert: symmetry clash REVERT: B 170 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5788 (mmt) REVERT: D 48 ILE cc_start: 0.8340 (mm) cc_final: 0.7961 (pt) REVERT: D 58 ASP cc_start: 0.7905 (t70) cc_final: 0.7605 (t0) REVERT: D 85 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: D 103 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6779 (pmm-80) REVERT: D 272 GLU cc_start: 0.7705 (tm-30) cc_final: 0.6776 (tm-30) REVERT: D 273 TYR cc_start: 0.7835 (p90) cc_final: 0.7477 (p90) REVERT: D 383 MET cc_start: 0.8059 (mmt) cc_final: 0.7531 (mmm) REVERT: D 449 GLU cc_start: 0.7835 (pt0) cc_final: 0.7196 (mm-30) REVERT: E 148 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7755 (p0) REVERT: F 28 GLU cc_start: 0.7979 (tt0) cc_final: 0.7469 (tt0) REVERT: F 31 SER cc_start: 0.9026 (t) cc_final: 0.8677 (p) REVERT: F 152 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7856 (tm-30) REVERT: F 158 LYS cc_start: 0.8539 (mmpt) cc_final: 0.8036 (mmpt) REVERT: F 183 GLU cc_start: 0.8394 (tt0) cc_final: 0.8118 (tt0) REVERT: F 241 LYS cc_start: 0.9240 (mmpt) cc_final: 0.8999 (mppt) REVERT: F 257 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7482 (mttt) REVERT: F 275 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7587 (mm-30) REVERT: F 286 LYS cc_start: 0.8350 (mtpp) cc_final: 0.7879 (mtmt) REVERT: F 386 GLN cc_start: 0.6872 (tt0) cc_final: 0.6556 (tt0) REVERT: F 424 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8370 (mtpp) REVERT: G 57 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: G 62 ARG cc_start: 0.7068 (ptt-90) cc_final: 0.6605 (ptt-90) REVERT: G 80 ASP cc_start: 0.8119 (m-30) cc_final: 0.7898 (m-30) REVERT: G 185 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6182 (pp20) REVERT: G 190 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7809 (mp0) REVERT: G 199 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: G 277 ASP cc_start: 0.8129 (p0) cc_final: 0.7925 (p0) REVERT: G 305 ILE cc_start: 0.8393 (tp) cc_final: 0.8151 (tp) REVERT: G 467 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.6975 (t0) REVERT: G 484 ASP cc_start: 0.7230 (m-30) cc_final: 0.6644 (m-30) REVERT: G 488 GLN cc_start: 0.7485 (tt0) cc_final: 0.7114 (mt0) REVERT: G 494 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7410 (mmtm) REVERT: G 531 MET cc_start: 0.8647 (mmt) cc_final: 0.8098 (mmt) REVERT: G 544 MET cc_start: 0.8333 (ttm) cc_final: 0.8054 (ttm) REVERT: G 642 LYS cc_start: 0.8659 (pttp) cc_final: 0.8297 (ptpp) REVERT: G 715 MET cc_start: 0.8581 (ptt) cc_final: 0.8265 (ptm) REVERT: G 787 GLU cc_start: 0.7687 (pm20) cc_final: 0.7407 (mp0) REVERT: G 849 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8248 (ttmt) REVERT: G 881 GLN cc_start: 0.7477 (mt0) cc_final: 0.7118 (mt0) REVERT: G 888 MET cc_start: 0.7664 (tpp) cc_final: 0.7189 (mmm) REVERT: G 901 GLU cc_start: 0.8351 (tp30) cc_final: 0.8148 (tp30) REVERT: I 122 MET cc_start: 0.5740 (mmp) cc_final: 0.5022 (ptm) REVERT: I 152 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7014 (mmp-170) REVERT: I 153 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6954 (mmt) REVERT: I 171 LYS cc_start: 0.8362 (mttt) cc_final: 0.7788 (mptt) outliers start: 50 outliers final: 26 residues processed: 253 average time/residue: 1.5315 time to fit residues: 429.9115 Evaluate side-chains 246 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 382 TRP Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 769 GLN Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 152 ARG Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 233 optimal weight: 0.9980 chunk 214 optimal weight: 0.2980 chunk 185 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN G 308 GLN G 769 GLN G 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.244 19227 Z= 0.915 Angle : 2.805 50.548 26113 Z= 1.856 Chirality : 0.584 6.394 2808 Planarity : 0.004 0.063 3416 Dihedral : 5.627 165.314 2628 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.98 % Allowed : 21.19 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2359 helix: 0.52 (0.19), residues: 852 sheet: -0.81 (0.32), residues: 256 loop : -1.38 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 382 HIS 0.006 0.001 HIS G 176 PHE 0.012 0.001 PHE F 167 TYR 0.012 0.001 TYR I 44 ARG 0.014 0.000 ARG G 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 2.475 Fit side-chains revert: symmetry clash REVERT: B 170 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5821 (mmt) REVERT: D 48 ILE cc_start: 0.8336 (mm) cc_final: 0.7943 (pt) REVERT: D 58 ASP cc_start: 0.7911 (t70) cc_final: 0.7606 (t0) REVERT: D 85 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: D 103 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6739 (pmm-80) REVERT: D 237 GLU cc_start: 0.7524 (pt0) cc_final: 0.7313 (pp20) REVERT: D 272 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6792 (tm-30) REVERT: D 383 MET cc_start: 0.8126 (mmt) cc_final: 0.7584 (mmm) REVERT: D 449 GLU cc_start: 0.7826 (pt0) cc_final: 0.7177 (mm-30) REVERT: E 148 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7749 (p0) REVERT: F 28 GLU cc_start: 0.8019 (tt0) cc_final: 0.7496 (tt0) REVERT: F 31 SER cc_start: 0.9029 (t) cc_final: 0.8678 (p) REVERT: F 152 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7907 (tm-30) REVERT: F 158 LYS cc_start: 0.8541 (mmpt) cc_final: 0.8005 (mmpt) REVERT: F 183 GLU cc_start: 0.8404 (tt0) cc_final: 0.8123 (tt0) REVERT: F 241 LYS cc_start: 0.9245 (mmpt) cc_final: 0.8962 (mppt) REVERT: F 250 MET cc_start: 0.8778 (mtt) cc_final: 0.8499 (mtt) REVERT: F 275 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7617 (mm-30) REVERT: F 286 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7890 (mtmt) REVERT: F 386 GLN cc_start: 0.6896 (tt0) cc_final: 0.6579 (tt0) REVERT: F 424 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8350 (mtpp) REVERT: G 57 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: G 62 ARG cc_start: 0.7084 (ptt-90) cc_final: 0.6608 (ptt-90) REVERT: G 80 ASP cc_start: 0.8118 (m-30) cc_final: 0.7895 (m-30) REVERT: G 185 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6112 (pp20) REVERT: G 190 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7811 (mp0) REVERT: G 199 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: G 277 ASP cc_start: 0.8122 (p0) cc_final: 0.7913 (p0) REVERT: G 289 ASP cc_start: 0.7811 (p0) cc_final: 0.7446 (p0) REVERT: G 467 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.6979 (t0) REVERT: G 484 ASP cc_start: 0.7228 (m-30) cc_final: 0.6638 (m-30) REVERT: G 488 GLN cc_start: 0.7482 (tt0) cc_final: 0.7108 (mt0) REVERT: G 494 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7413 (mmtm) REVERT: G 531 MET cc_start: 0.8655 (mmt) cc_final: 0.8121 (mmt) REVERT: G 544 MET cc_start: 0.8345 (ttm) cc_final: 0.7959 (ttm) REVERT: G 642 LYS cc_start: 0.8651 (pttp) cc_final: 0.8285 (ptpp) REVERT: G 715 MET cc_start: 0.8611 (ptt) cc_final: 0.8333 (ptm) REVERT: G 787 GLU cc_start: 0.7693 (pm20) cc_final: 0.7409 (mp0) REVERT: G 849 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8223 (ttpp) REVERT: G 881 GLN cc_start: 0.7520 (mt0) cc_final: 0.7153 (mt0) REVERT: G 888 MET cc_start: 0.7668 (tpp) cc_final: 0.7198 (mmm) REVERT: G 901 GLU cc_start: 0.8370 (tp30) cc_final: 0.8113 (tp30) REVERT: I 122 MET cc_start: 0.5755 (mmp) cc_final: 0.5020 (ptm) REVERT: I 153 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.5805 (mmm) REVERT: I 171 LYS cc_start: 0.8358 (mttt) cc_final: 0.7778 (mptt) outliers start: 39 outliers final: 23 residues processed: 237 average time/residue: 1.5174 time to fit residues: 400.7961 Evaluate side-chains 243 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 382 TRP Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain G residue 654 SER Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105613 restraints weight = 15857.405| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.69 r_work: 0.3274 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.249 19227 Z= 0.921 Angle : 2.809 50.592 26113 Z= 1.858 Chirality : 0.585 6.398 2808 Planarity : 0.004 0.065 3416 Dihedral : 5.694 165.388 2628 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.24 % Allowed : 21.04 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2359 helix: 0.47 (0.19), residues: 856 sheet: -0.81 (0.31), residues: 258 loop : -1.35 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 382 HIS 0.006 0.001 HIS G 176 PHE 0.013 0.001 PHE F 167 TYR 0.012 0.001 TYR F 178 ARG 0.014 0.000 ARG G 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7523.57 seconds wall clock time: 132 minutes 57.83 seconds (7977.83 seconds total)