Starting phenix.real_space_refine (version: dev) on Fri Mar 17 12:36:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2023/7awt_11930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2023/7awt_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_2023/7awt_11930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2023/7awt_11930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2023/7awt_11930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awt_11930/03_2023/7awt_11930_updated.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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: 10.64, 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: 7.52 Conformation dependent library (CDL) restraints added in 3.0 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: 2.22 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: 6.25 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 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. 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 6.250 Check model and map are aligned: 0.290 Process input model: 53.330 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 % 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 *********************** 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 : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 361 average time/residue: 1.6319 time to fit residues: 649.0205 Evaluate side-chains 218 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 2.270 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.7219 time to fit residues: 4.8566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 315 HIS ** D 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 196 ASN F 386 GLN 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: 0.7393 moved from start: 0.1690 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= 0.930 Angle : 2.817 50.876 26113 Z= 1.860 Chirality : 0.589 6.559 2808 Planarity : 0.005 0.099 3416 Dihedral : 6.127 168.533 2622 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 2.85 % 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: -2.39 (0.16), residues: 2359 helix: -0.76 (0.17), residues: 857 sheet: -1.74 (0.33), residues: 228 loop : -2.19 (0.16), residues: 1274 *********************** 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 283 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 28 residues processed: 262 average time/residue: 1.5916 time to fit residues: 463.8478 Evaluate side-chains 221 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 8 average time/residue: 0.4173 time to fit residues: 7.6955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 566 GLN E 103 GLN E 142 ASN F 224 ASN F 386 GLN G 325 ASN G 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2050 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= 0.919 Angle : 2.811 50.582 26113 Z= 1.859 Chirality : 0.584 6.391 2808 Planarity : 0.004 0.053 3416 Dihedral : 5.863 167.435 2622 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 3.30 % 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: -1.89 (0.17), residues: 2359 helix: -0.31 (0.18), residues: 857 sheet: -1.41 (0.32), residues: 239 loop : -1.92 (0.16), residues: 1263 *********************** 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 274 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 209 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 30 residues processed: 254 average time/residue: 1.5617 time to fit residues: 442.4312 Evaluate side-chains 223 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 21 residues processed: 12 average time/residue: 0.3999 time to fit residues: 9.6494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 5.9990 chunk 160 optimal weight: 0.0870 chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 HIS F 386 GLN G 804 GLN G 881 GLN G 908 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 0.246 19227 Z= 0.926 Angle : 2.812 50.542 26113 Z= 1.859 Chirality : 0.586 6.443 2808 Planarity : 0.005 0.055 3416 Dihedral : 5.841 165.662 2622 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 3.76 % 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: -1.67 (0.17), residues: 2359 helix: -0.14 (0.18), residues: 852 sheet: -1.27 (0.32), residues: 251 loop : -1.78 (0.17), residues: 1256 *********************** 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 280 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 206 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 40 residues processed: 258 average time/residue: 1.4570 time to fit residues: 421.8377 Evaluate side-chains 229 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 11 average time/residue: 0.3810 time to fit residues: 8.9616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 chunk 193 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 47 GLN G 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2417 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= 0.934 Angle : 2.817 50.593 26113 Z= 1.861 Chirality : 0.586 6.463 2808 Planarity : 0.005 0.056 3416 Dihedral : 5.900 165.374 2622 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 3.61 % 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: -1.61 (0.17), residues: 2359 helix: -0.15 (0.18), residues: 856 sheet: -1.13 (0.32), residues: 250 loop : -1.73 (0.17), residues: 1253 *********************** 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 272 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 201 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 40 residues processed: 254 average time/residue: 1.5204 time to fit residues: 431.4015 Evaluate side-chains 228 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 2.155 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 33 residues processed: 10 average time/residue: 0.2503 time to fit residues: 7.3814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 44 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 226 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN F 386 GLN G 47 GLN G 726 GLN G 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2624 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= 0.915 Angle : 2.807 50.527 26113 Z= 1.856 Chirality : 0.585 6.412 2808 Planarity : 0.004 0.054 3416 Dihedral : 5.703 165.996 2622 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 3.15 % 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: -1.42 (0.17), residues: 2359 helix: 0.05 (0.19), residues: 859 sheet: -1.06 (0.32), residues: 258 loop : -1.65 (0.17), residues: 1242 *********************** 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 263 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 201 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 36 residues processed: 247 average time/residue: 1.4910 time to fit residues: 420.2587 Evaluate side-chains 222 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 9 average time/residue: 0.2680 time to fit residues: 7.0621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7391 moved from start: 0.2687 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= 0.920 Angle : 2.810 50.593 26113 Z= 1.858 Chirality : 0.584 6.394 2808 Planarity : 0.004 0.055 3416 Dihedral : 5.680 165.630 2622 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 2.90 % 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: -1.32 (0.17), residues: 2359 helix: 0.13 (0.19), residues: 858 sheet: -0.98 (0.32), residues: 258 loop : -1.59 (0.17), residues: 1243 *********************** 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 251 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 194 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 37 residues processed: 239 average time/residue: 1.4159 time to fit residues: 379.8434 Evaluate side-chains 228 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.626 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 31 residues processed: 8 average time/residue: 0.1910 time to fit residues: 4.8211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 chunk 205 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: