Starting phenix.real_space_refine on Fri Jan 19 03:42:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6d_24875/01_2024/7s6d_24875_trim_updated.pdb" } resolution = 3.1 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= 0.002 sd= 1.170 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 16375 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 67 5.16 5 C 14606 2.51 5 N 4164 2.21 5 O 4507 1.98 5 H 22846 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 1151": "OD1" <-> "OD2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 151": "OD1" <-> "OD2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 127": "OD1" <-> "OD2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G GLU 217": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "F TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 46193 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 7005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 7005 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 29, 'TRANS': 448} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 13231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 13231 Classifications: {'peptide': 895} Link IDs: {'PTRANS': 55, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 13217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 13217 Classifications: {'peptide': 893} Link IDs: {'PTRANS': 53, 'TRANS': 839} Chain breaks: 2 Chain: "E" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3081 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Chain: "G" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3249 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 199} Chain breaks: 1 Chain: "D" Number of atoms: 3092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3092 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "F" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3287 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLN G 66 " occ=0.90 ... (15 atoms not shown) pdb="HE22 GLN G 66 " occ=0.90 residue: pdb=" N GLN F 66 " occ=0.90 ... (15 atoms not shown) pdb="HE22 GLN F 66 " occ=0.90 Time building chain proxies: 15.48, per 1000 atoms: 0.34 Number of scatterers: 46193 At special positions: 0 Unit cell: (115.776, 170.448, 200.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 67 16.00 P 3 15.00 O 4507 8.00 N 4164 7.00 C 14606 6.00 H 22846 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.04 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 109 " distance=2.04 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.04 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 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: 31.45 Conformation dependent library (CDL) restraints added in 3.8 seconds 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 29 sheets defined 30.7% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.18 Creating SS restraints... Processing helix chain 'C' and resid 967 through 979 removed outlier: 3.595A pdb=" N LEU C 979 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1023 Processing helix chain 'C' and resid 1041 through 1052 Processing helix chain 'C' and resid 1065 through 1067 No H-bonds generated for 'chain 'C' and resid 1065 through 1067' Processing helix chain 'C' and resid 1080 through 1095 Processing helix chain 'C' and resid 1120 through 1135 removed outlier: 3.974A pdb=" N LEU C1134 " --> pdb=" O ARG C1130 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C1135 " --> pdb=" O VAL C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1152 through 1162 Processing helix chain 'C' and resid 1211 through 1221 Processing helix chain 'C' and resid 1235 through 1237 No H-bonds generated for 'chain 'C' and resid 1235 through 1237' Processing helix chain 'C' and resid 1241 through 1250 Processing helix chain 'C' and resid 1265 through 1274 Processing helix chain 'C' and resid 1297 through 1299 No H-bonds generated for 'chain 'C' and resid 1297 through 1299' Processing helix chain 'C' and resid 1302 through 1322 removed outlier: 4.252A pdb=" N VAL C1311 " --> pdb=" O GLN C1307 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS C1312 " --> pdb=" O VAL C1308 " (cutoff:3.500A) Processing helix chain 'C' and resid 1337 through 1340 No H-bonds generated for 'chain 'C' and resid 1337 through 1340' Processing helix chain 'C' and resid 1347 through 1366 Proline residue: C1351 - end of helix removed outlier: 3.679A pdb=" N GLU C1357 " --> pdb=" O ASN C1353 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C1358 " --> pdb=" O ALA C1354 " (cutoff:3.500A) Processing helix chain 'C' and resid 1402 through 1414 Processing helix chain 'C' and resid 1427 through 1437 removed outlier: 4.557A pdb=" N VAL C1432 " --> pdb=" O GLU C1428 " (cutoff:3.500A) Processing helix chain 'C' and resid 1447 through 1455 Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.612A pdb=" N TYR A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 186 through 196 removed outlier: 3.788A pdb=" N SER A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG A 192 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 196 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 225 removed outlier: 4.790A pdb=" N SER A 213 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 214 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 215 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.603A pdb=" N THR A 247 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.866A pdb=" N GLN A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 350 through 363 Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.717A pdb=" N ILE A 383 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 404 removed outlier: 4.176A pdb=" N GLY A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA A 401 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.893A pdb=" N HIS A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 604 removed outlier: 4.643A pdb=" N ASP A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 625 through 645 removed outlier: 3.871A pdb=" N GLN A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Proline residue: A 630 - end of helix Processing helix chain 'A' and resid 657 through 667 Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.857A pdb=" N LEU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 733 through 746 removed outlier: 3.877A pdb=" N THR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 774 removed outlier: 5.676A pdb=" N ASP A 769 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 841 through 849 Processing helix chain 'A' and resid 868 through 881 Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'B' and resid 10 through 37 removed outlier: 4.166A pdb=" N ALA B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 146 through 149 Processing helix chain 'B' and resid 186 through 196 removed outlier: 3.632A pdb=" N SER B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG B 192 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 225 removed outlier: 5.050A pdb=" N SER B 213 " --> pdb=" O CYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 350 through 364 Proline residue: B 354 - end of helix Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.795A pdb=" N ILE B 383 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 404 removed outlier: 3.950A pdb=" N GLY B 391 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL B 392 " --> pdb=" O ALA B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 503 Processing helix chain 'B' and resid 510 through 519 Processing helix chain 'B' and resid 537 through 547 Processing helix chain 'B' and resid 581 through 585 removed outlier: 4.168A pdb=" N HIS B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 585' Processing helix chain 'B' and resid 588 through 600 removed outlier: 3.618A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 614 Processing helix chain 'B' and resid 625 through 645 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 659 through 666 Processing helix chain 'B' and resid 672 through 689 Proline residue: B 688 - end of helix Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.769A pdb=" N GLN B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Proline residue: B 711 - end of helix Processing helix chain 'B' and resid 733 through 745 removed outlier: 3.553A pdb=" N THR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP B 744 " --> pdb=" O HIS B 740 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 745 " --> pdb=" O THR B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 769 through 774 Processing helix chain 'B' and resid 798 through 800 No H-bonds generated for 'chain 'B' and resid 798 through 800' Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 841 through 851 Processing helix chain 'B' and resid 868 through 880 Processing helix chain 'B' and resid 887 through 891 Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'G' and resid 101 through 103 No H-bonds generated for 'chain 'G' and resid 101 through 103' Processing helix chain 'G' and resid 144 through 149 Processing helix chain 'G' and resid 205 through 210 removed outlier: 4.260A pdb=" N LYS G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 205 through 208 No H-bonds generated for 'chain 'F' and resid 205 through 208' Processing sheet with id= A, first strand: chain 'C' and resid 981 through 987 removed outlier: 5.974A pdb=" N GLN C1170 " --> pdb=" O ARG C1181 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL C1171 " --> pdb=" O ALA C1141 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU C1143 " --> pdb=" O VAL C1171 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU C1173 " --> pdb=" O LEU C1143 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP C1145 " --> pdb=" O LEU C1173 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU C1101 " --> pdb=" O ALA C1141 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU C1143 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS C1103 " --> pdb=" O LEU C1143 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP C1145 " --> pdb=" O CYS C1103 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N THR C1105 " --> pdb=" O ASP C1145 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C1060 " --> pdb=" O THR C 999 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG C1027 " --> pdb=" O TRP C1000 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C1002 " --> pdb=" O ARG C1027 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL C1029 " --> pdb=" O VAL C1002 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C1004 " --> pdb=" O VAL C1029 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU C1031 " --> pdb=" O VAL C1004 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 1227 through 1231 removed outlier: 7.170A pdb=" N LEU C1204 " --> pdb=" O THR C1283 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL C1285 " --> pdb=" O LEU C1204 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR C1206 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS C1287 " --> pdb=" O THR C1206 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA C1330 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N HIS C1287 " --> pdb=" O ALA C1330 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C1332 " --> pdb=" O HIS C1287 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 203 through 206 removed outlier: 8.431A pdb=" N VAL A 204 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 156 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 206 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL A 158 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 231 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE A 157 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU A 233 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY A 159 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY A 235 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU A 283 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE A 42 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 297 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 460 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR A 302 " --> pdb=" O HIS A 458 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS A 458 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 304 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 456 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.420A pdb=" N ARG A 375 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 481 through 485 Processing sheet with id= F, first strand: chain 'A' and resid 653 through 655 removed outlier: 8.222A pdb=" N ILE A 654 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 567 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 566 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE A 831 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 568 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU A 833 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG A 856 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU A 833 " --> pdb=" O ARG A 856 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR A 858 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 693 through 698 removed outlier: 6.057A pdb=" N SER A 730 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE A 718 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 203 through 206 removed outlier: 8.391A pdb=" N VAL B 204 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 156 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 206 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 158 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B 231 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE B 157 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU B 233 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY B 159 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY B 235 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU B 283 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE B 42 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 297 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 460 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 302 " --> pdb=" O HIS B 458 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 458 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE B 304 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN B 456 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA B 341 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER B 448 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU B 343 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE B 450 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG B 375 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 481 through 485 Processing sheet with id= J, first strand: chain 'B' and resid 652 through 655 removed outlier: 6.884A pdb=" N VAL B 566 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE B 831 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 568 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU B 833 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG B 856 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLU B 833 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 858 " --> pdb=" O GLU B 833 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 693 through 698 removed outlier: 6.054A pdb=" N SER B 730 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE B 718 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 5 through 9 Processing sheet with id= M, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.031A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.998A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA E 143 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.172A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 21 through 23 Processing sheet with id= Q, first strand: chain 'G' and resid 105 through 111 removed outlier: 6.138A pdb=" N LEU G 58 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU G 67 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 151 through 155 Processing sheet with id= S, first strand: chain 'G' and resid 167 through 171 Processing sheet with id= T, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.046A pdb=" N TYR G 195 " --> pdb=" O ASN G 160 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 5 through 9 Processing sheet with id= V, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.667A pdb=" N THR D 117 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG D 40 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TRP D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= X, first strand: chain 'D' and resid 170 through 172 removed outlier: 7.022A pdb=" N LEU D 185 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS D 150 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER D 187 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU D 148 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL D 189 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY D 146 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL D 191 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA D 144 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.585A pdb=" N ASP F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 26 through 29 removed outlier: 6.710A pdb=" N LYS F 125 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL F 29 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP F 127 " --> pdb=" O VAL F 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 105 through 111 removed outlier: 6.234A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 138 through 140 removed outlier: 3.763A pdb=" N VAL F 155 " --> pdb=" O PHE F 140 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 167 through 171 822 hydrogen bonds defined for protein. 2112 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: 16.49 Time building geometry restraints manager: 33.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 22824 1.04 - 1.24: 2243 1.24 - 1.44: 8046 1.44 - 1.63: 13499 1.63 - 1.83: 104 Bond restraints: 46716 Sorted by residual: bond pdb=" C2' ATR C1701 " pdb=" C3' ATR C1701 " ideal model delta sigma weight residual 1.245 1.539 -0.294 2.00e-02 2.50e+03 2.17e+02 bond pdb=" O3B ATR C1701 " pdb=" PB ATR C1701 " ideal model delta sigma weight residual 1.508 1.756 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C2' ATR C1701 " pdb=" O2' ATR C1701 " ideal model delta sigma weight residual 1.514 1.331 0.183 2.00e-02 2.50e+03 8.42e+01 bond pdb=" O2' ATR C1701 " pdb=" P2' ATR C1701 " ideal model delta sigma weight residual 1.671 1.834 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C3' ATR C1701 " pdb=" C4' ATR C1701 " ideal model delta sigma weight residual 1.663 1.518 0.145 2.00e-02 2.50e+03 5.26e+01 ... (remaining 46711 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.65: 479 104.65 - 112.01: 53383 112.01 - 119.38: 11612 119.38 - 126.74: 18392 126.74 - 134.10: 472 Bond angle restraints: 84338 Sorted by residual: angle pdb=" C1' ATR C1701 " pdb=" N9 ATR C1701 " pdb=" C8 ATR C1701 " ideal model delta sigma weight residual 102.81 128.41 -25.60 3.00e+00 1.11e-01 7.28e+01 angle pdb=" C1' ATR C1701 " pdb=" N9 ATR C1701 " pdb=" C4 ATR C1701 " ideal model delta sigma weight residual 149.16 124.99 24.17 3.00e+00 1.11e-01 6.49e+01 angle pdb=" C5 ATR C1701 " pdb=" C6 ATR C1701 " pdb=" N6 ATR C1701 " ideal model delta sigma weight residual 138.99 120.61 18.38 3.00e+00 1.11e-01 3.76e+01 angle pdb=" N1 ATR C1701 " pdb=" C6 ATR C1701 " pdb=" N6 ATR C1701 " ideal model delta sigma weight residual 100.02 117.67 -17.65 3.00e+00 1.11e-01 3.46e+01 angle pdb=" PA ATR C1701 " pdb=" O3A ATR C1701 " pdb=" PB ATR C1701 " ideal model delta sigma weight residual 123.61 108.73 14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 84333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 19699 18.01 - 36.02: 1517 36.02 - 54.03: 313 54.03 - 72.04: 37 72.04 - 90.05: 32 Dihedral angle restraints: 21598 sinusoidal: 11498 harmonic: 10100 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 203 " pdb=" CB CYS E 203 " ideal model delta sinusoidal sigma weight residual 93.00 141.22 -48.22 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CB CYS G 39 " pdb=" SG CYS G 39 " pdb=" SG CYS G 109 " pdb=" CB CYS G 109 " ideal model delta sinusoidal sigma weight residual 93.00 128.65 -35.65 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" CA LYS B 98 " pdb=" C LYS B 98 " pdb=" N GLU B 99 " pdb=" CA GLU B 99 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 21595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3081 0.051 - 0.103: 470 0.103 - 0.154: 160 0.154 - 0.206: 2 0.206 - 0.257: 1 Chirality restraints: 3714 Sorted by residual: chirality pdb=" CB ILE B 648 " pdb=" CA ILE B 648 " pdb=" CG1 ILE B 648 " pdb=" CG2 ILE B 648 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE A 785 " pdb=" N ILE A 785 " pdb=" C ILE A 785 " pdb=" CB ILE A 785 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE B 785 " pdb=" N ILE B 785 " pdb=" C ILE B 785 " pdb=" CB ILE B 785 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 3711 not shown) Planarity restraints: 7177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATR C1701 " -0.295 2.00e-02 2.50e+03 4.59e-01 4.74e+03 pdb=" C2' ATR C1701 " 0.247 2.00e-02 2.50e+03 pdb=" C3' ATR C1701 " 0.588 2.00e-02 2.50e+03 pdb=" C4' ATR C1701 " -0.417 2.00e-02 2.50e+03 pdb=" C5' ATR C1701 " 0.041 2.00e-02 2.50e+03 pdb=" N9 ATR C1701 " 0.659 2.00e-02 2.50e+03 pdb=" O2' ATR C1701 " -0.700 2.00e-02 2.50e+03 pdb=" O3' ATR C1701 " 0.322 2.00e-02 2.50e+03 pdb=" O4' ATR C1701 " -0.445 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 155 " -0.049 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO E 156 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 156 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 156 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 569 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 570 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.031 5.00e-02 4.00e+02 ... (remaining 7174 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 6481 2.26 - 2.85: 103776 2.85 - 3.43: 121879 3.43 - 4.02: 168773 4.02 - 4.60: 258491 Nonbonded interactions: 659400 Sorted by model distance: nonbonded pdb=" H HIS B 345 " pdb=" OE2 GLU B 356 " model vdw 1.679 1.850 nonbonded pdb=" HG SER G 143 " pdb=" OE1 GLU G 145 " model vdw 1.680 1.850 nonbonded pdb=" H GLY B 691 " pdb=" O ASP B 756 " model vdw 1.707 1.850 nonbonded pdb=" H HIS A 345 " pdb=" OE2 GLU A 356 " model vdw 1.708 1.850 nonbonded pdb=" O VAL F 29 " pdb=" H LYS F 129 " model vdw 1.714 1.850 ... (remaining 659395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 467 or (resid 473 and (name N or name CA or name \ C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resi \ d 474 through 913)) selection = (chain 'B' and (resid 8 through 506 or (resid 507 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 508 through 768 or (res \ id 769 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 770 through 913)) } ncs_group { reference = (chain 'D' and (resid 3 through 193 or resid 199 through 220)) selection = chain 'E' } ncs_group { reference = (chain 'F' and ((resid 18 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 19 through 172 or resid 1 \ 76 through 234)) selection = chain 'G' } 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=0.90 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.530 Extract box with map and model: 11.410 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 121.540 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.005 0.294 23870 Z= 0.349 Angle : 0.720 25.597 32574 Z= 0.337 Chirality : 0.043 0.257 3714 Planarity : 0.008 0.459 4269 Dihedral : 13.597 90.046 8501 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.10 (0.15), residues: 3076 helix: 1.51 (0.17), residues: 907 sheet: -1.07 (0.18), residues: 745 loop : -0.43 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 712 HIS 0.006 0.001 HIS F 211 PHE 0.019 0.001 PHE C1331 TYR 0.020 0.001 TYR A 757 ARG 0.010 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 HIS cc_start: 0.8602 (t70) cc_final: 0.8343 (t70) REVERT: A 884 ASP cc_start: 0.8299 (p0) cc_final: 0.7996 (p0) REVERT: B 207 ASP cc_start: 0.7831 (t0) cc_final: 0.7437 (t0) REVERT: B 318 ASP cc_start: 0.8306 (p0) cc_final: 0.7705 (t0) REVERT: E 48 GLU cc_start: 0.8441 (tt0) cc_final: 0.8037 (tt0) REVERT: G 145 GLU cc_start: 0.8540 (mp0) cc_final: 0.8177 (mp0) REVERT: G 189 ASP cc_start: 0.8492 (t0) cc_final: 0.8250 (t0) REVERT: G 191 LYS cc_start: 0.9343 (mppt) cc_final: 0.9140 (mmtm) REVERT: D 151 ASP cc_start: 0.8591 (m-30) cc_final: 0.8248 (m-30) REVERT: D 211 ASN cc_start: 0.9417 (m-40) cc_final: 0.9159 (m-40) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.7685 time to fit residues: 192.6265 Evaluate side-chains 133 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 0.9980 chunk 232 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1353 ASN E 204 ASN G 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23870 Z= 0.295 Angle : 0.545 19.596 32574 Z= 0.258 Chirality : 0.039 0.135 3714 Planarity : 0.004 0.056 4269 Dihedral : 4.929 85.739 3378 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.20 % Allowed : 2.86 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.16), residues: 3076 helix: 1.58 (0.18), residues: 917 sheet: -1.08 (0.19), residues: 747 loop : -0.34 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 161 HIS 0.005 0.001 HIS F 211 PHE 0.010 0.001 PHE G 231 TYR 0.014 0.001 TYR B 85 ARG 0.005 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 HIS cc_start: 0.8703 (t70) cc_final: 0.8481 (t70) REVERT: A 884 ASP cc_start: 0.8348 (p0) cc_final: 0.8025 (p0) REVERT: B 94 LYS cc_start: 0.9361 (mttp) cc_final: 0.9113 (mttp) REVERT: B 318 ASP cc_start: 0.8381 (p0) cc_final: 0.7713 (t0) REVERT: G 144 ASP cc_start: 0.8476 (p0) cc_final: 0.8235 (p0) REVERT: G 187 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8782 (mm-30) REVERT: G 191 LYS cc_start: 0.9336 (mppt) cc_final: 0.9033 (mmtm) REVERT: D 151 ASP cc_start: 0.8755 (m-30) cc_final: 0.8404 (m-30) REVERT: D 211 ASN cc_start: 0.9412 (m-40) cc_final: 0.9139 (m-40) outliers start: 5 outliers final: 5 residues processed: 132 average time/residue: 0.6868 time to fit residues: 142.0494 Evaluate side-chains 130 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 279 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1353 ASN B 382 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23870 Z= 0.282 Angle : 0.531 19.034 32574 Z= 0.252 Chirality : 0.039 0.147 3714 Planarity : 0.004 0.061 4269 Dihedral : 4.638 86.970 3378 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.33 % Allowed : 3.97 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.06 (0.16), residues: 3076 helix: 1.49 (0.18), residues: 926 sheet: -1.00 (0.19), residues: 744 loop : -0.22 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 161 HIS 0.004 0.001 HIS F 211 PHE 0.012 0.001 PHE E 153 TYR 0.014 0.001 TYR B 85 ARG 0.004 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 HIS cc_start: 0.8682 (t70) cc_final: 0.8430 (t70) REVERT: A 884 ASP cc_start: 0.8349 (p0) cc_final: 0.8024 (p0) REVERT: B 351 LEU cc_start: 0.9373 (mp) cc_final: 0.9165 (pp) REVERT: G 187 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8769 (mm-30) REVERT: G 191 LYS cc_start: 0.9355 (mppt) cc_final: 0.9071 (mmtm) REVERT: D 151 ASP cc_start: 0.8797 (m-30) cc_final: 0.8476 (m-30) REVERT: D 211 ASN cc_start: 0.9401 (m-40) cc_final: 0.9140 (m-40) outliers start: 8 outliers final: 8 residues processed: 134 average time/residue: 0.7775 time to fit residues: 164.9636 Evaluate side-chains 128 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 SER Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 133 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1353 ASN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23870 Z= 0.163 Angle : 0.496 17.496 32574 Z= 0.230 Chirality : 0.039 0.151 3714 Planarity : 0.004 0.057 4269 Dihedral : 4.466 88.512 3378 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.16 % Allowed : 4.95 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.23 (0.16), residues: 3076 helix: 1.63 (0.18), residues: 924 sheet: -0.91 (0.19), residues: 715 loop : -0.13 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 161 HIS 0.003 0.000 HIS F 211 PHE 0.007 0.001 PHE G 231 TYR 0.009 0.001 TYR B 85 ARG 0.002 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 HIS cc_start: 0.8665 (t70) cc_final: 0.8413 (t70) REVERT: A 884 ASP cc_start: 0.8352 (p0) cc_final: 0.7998 (p0) REVERT: B 94 LYS cc_start: 0.9366 (mttp) cc_final: 0.9124 (mttp) REVERT: B 351 LEU cc_start: 0.9370 (mp) cc_final: 0.9163 (pp) REVERT: G 187 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8778 (mm-30) REVERT: G 191 LYS cc_start: 0.9355 (mppt) cc_final: 0.9077 (mmtm) REVERT: D 151 ASP cc_start: 0.8837 (m-30) cc_final: 0.8550 (m-30) REVERT: D 211 ASN cc_start: 0.9400 (m-40) cc_final: 0.9149 (m-40) outliers start: 4 outliers final: 4 residues processed: 132 average time/residue: 0.7297 time to fit residues: 149.2915 Evaluate side-chains 125 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 SER Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 253 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23870 Z= 0.225 Angle : 0.505 17.795 32574 Z= 0.236 Chirality : 0.039 0.142 3714 Planarity : 0.004 0.054 4269 Dihedral : 4.304 87.536 3378 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.37 % Allowed : 5.48 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.23 (0.16), residues: 3076 helix: 1.60 (0.18), residues: 929 sheet: -0.90 (0.19), residues: 737 loop : -0.11 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 712 HIS 0.003 0.000 HIS F 211 PHE 0.009 0.001 PHE C1337 TYR 0.010 0.001 TYR E 183 ARG 0.005 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 HIS cc_start: 0.8663 (t70) cc_final: 0.8421 (t70) REVERT: A 884 ASP cc_start: 0.8350 (p0) cc_final: 0.7991 (p0) REVERT: B 351 LEU cc_start: 0.9378 (mp) cc_final: 0.9177 (pp) REVERT: G 187 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8795 (mm-30) REVERT: G 191 LYS cc_start: 0.9345 (mppt) cc_final: 0.9069 (mmtm) REVERT: D 151 ASP cc_start: 0.8824 (m-30) cc_final: 0.8543 (m-30) REVERT: D 211 ASN cc_start: 0.9398 (m-40) cc_final: 0.9157 (m-40) outliers start: 9 outliers final: 7 residues processed: 136 average time/residue: 0.7122 time to fit residues: 150.4100 Evaluate side-chains 132 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 SER Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 297 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23870 Z= 0.170 Angle : 0.491 17.707 32574 Z= 0.228 Chirality : 0.039 0.139 3714 Planarity : 0.004 0.053 4269 Dihedral : 4.266 87.749 3378 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.29 % Allowed : 6.01 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.32 (0.16), residues: 3076 helix: 1.69 (0.18), residues: 926 sheet: -0.83 (0.19), residues: 716 loop : -0.09 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 712 HIS 0.003 0.000 HIS F 211 PHE 0.009 0.001 PHE C1337 TYR 0.009 0.001 TYR C1349 ARG 0.006 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 HIS cc_start: 0.8670 (t70) cc_final: 0.8432 (t70) REVERT: A 884 ASP cc_start: 0.8336 (p0) cc_final: 0.7995 (p0) REVERT: B 351 LEU cc_start: 0.9376 (mp) cc_final: 0.9173 (pp) REVERT: G 187 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8792 (mm-30) REVERT: G 191 LYS cc_start: 0.9346 (mppt) cc_final: 0.9074 (mmtm) REVERT: D 63 GLU cc_start: 0.8455 (tp30) cc_final: 0.8255 (tp30) REVERT: D 151 ASP cc_start: 0.8820 (m-30) cc_final: 0.8538 (m-30) REVERT: D 211 ASN cc_start: 0.9389 (m-40) cc_final: 0.9149 (m-40) outliers start: 7 outliers final: 6 residues processed: 137 average time/residue: 0.6983 time to fit residues: 150.3693 Evaluate side-chains 130 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 SER Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 295 optimal weight: 0.0970 chunk 185 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23870 Z= 0.154 Angle : 0.487 17.676 32574 Z= 0.225 Chirality : 0.039 0.139 3714 Planarity : 0.004 0.052 4269 Dihedral : 4.207 87.016 3378 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.33 % Allowed : 6.30 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.37 (0.16), residues: 3076 helix: 1.73 (0.18), residues: 925 sheet: -0.77 (0.19), residues: 713 loop : -0.08 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 712 HIS 0.003 0.000 HIS B 345 PHE 0.011 0.001 PHE C1337 TYR 0.022 0.001 TYR D 183 ARG 0.006 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1340 THR cc_start: 0.9432 (m) cc_final: 0.9187 (p) REVERT: A 734 HIS cc_start: 0.8662 (t70) cc_final: 0.8423 (t70) REVERT: A 884 ASP cc_start: 0.8330 (p0) cc_final: 0.7985 (p0) REVERT: B 351 LEU cc_start: 0.9377 (mp) cc_final: 0.9173 (pp) REVERT: G 191 LYS cc_start: 0.9347 (mppt) cc_final: 0.9070 (mmtm) REVERT: D 63 GLU cc_start: 0.8453 (tp30) cc_final: 0.8242 (tp30) REVERT: D 151 ASP cc_start: 0.8799 (m-30) cc_final: 0.8478 (m-30) REVERT: D 211 ASN cc_start: 0.9390 (m-40) cc_final: 0.9155 (m-40) outliers start: 8 outliers final: 8 residues processed: 143 average time/residue: 0.7141 time to fit residues: 159.7778 Evaluate side-chains 140 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 SER Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 232 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23870 Z= 0.229 Angle : 0.505 17.709 32574 Z= 0.235 Chirality : 0.039 0.139 3714 Planarity : 0.004 0.051 4269 Dihedral : 4.194 85.613 3378 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.41 % Allowed : 6.38 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.31 (0.16), residues: 3076 helix: 1.66 (0.18), residues: 930 sheet: -0.83 (0.19), residues: 737 loop : -0.08 (0.18), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 712 HIS 0.003 0.000 HIS F 211 PHE 0.013 0.001 PHE C1337 TYR 0.010 0.001 TYR E 34 ARG 0.009 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 HIS cc_start: 0.8693 (t70) cc_final: 0.8452 (t70) REVERT: A 884 ASP cc_start: 0.8344 (p0) cc_final: 0.8002 (p0) REVERT: G 191 LYS cc_start: 0.9353 (mppt) cc_final: 0.9070 (mmtm) REVERT: D 151 ASP cc_start: 0.8795 (m-30) cc_final: 0.8475 (m-30) REVERT: D 211 ASN cc_start: 0.9390 (m-40) cc_final: 0.9156 (m-40) outliers start: 10 outliers final: 8 residues processed: 139 average time/residue: 0.7275 time to fit residues: 157.3352 Evaluate side-chains 134 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 SER Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 3.9990 chunk 283 optimal weight: 0.6980 chunk 258 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 0.4980 chunk 260 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23870 Z= 0.163 Angle : 0.492 17.654 32574 Z= 0.227 Chirality : 0.039 0.140 3714 Planarity : 0.004 0.051 4269 Dihedral : 4.167 85.828 3378 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.25 % Allowed : 6.70 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.39 (0.16), residues: 3076 helix: 1.74 (0.18), residues: 928 sheet: -0.75 (0.19), residues: 712 loop : -0.07 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 712 HIS 0.003 0.000 HIS B 345 PHE 0.012 0.001 PHE C1337 TYR 0.021 0.001 TYR E 34 ARG 0.004 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1340 THR cc_start: 0.9376 (m) cc_final: 0.9153 (p) REVERT: A 734 HIS cc_start: 0.8670 (t70) cc_final: 0.8428 (t70) REVERT: A 884 ASP cc_start: 0.8364 (p0) cc_final: 0.8008 (p0) REVERT: G 127 ASP cc_start: 0.8430 (p0) cc_final: 0.8068 (p0) REVERT: G 191 LYS cc_start: 0.9352 (mppt) cc_final: 0.9071 (mmtm) REVERT: D 63 GLU cc_start: 0.8412 (tp30) cc_final: 0.8203 (tp30) REVERT: D 151 ASP cc_start: 0.8786 (m-30) cc_final: 0.8467 (m-30) REVERT: D 211 ASN cc_start: 0.9389 (m-40) cc_final: 0.9145 (m-40) outliers start: 6 outliers final: 6 residues processed: 142 average time/residue: 0.7094 time to fit residues: 157.0235 Evaluate side-chains 138 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 SER Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 0.4980 chunk 291 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 281 optimal weight: 0.8980 chunk 243 optimal weight: 0.0270 chunk 25 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23870 Z= 0.199 Angle : 0.499 17.658 32574 Z= 0.232 Chirality : 0.039 0.139 3714 Planarity : 0.004 0.050 4269 Dihedral : 4.137 84.764 3378 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.29 % Allowed : 6.79 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.35 (0.16), residues: 3076 helix: 1.71 (0.18), residues: 930 sheet: -0.81 (0.19), residues: 737 loop : -0.06 (0.18), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 712 HIS 0.003 0.000 HIS F 211 PHE 0.011 0.001 PHE C1337 TYR 0.018 0.001 TYR E 34 ARG 0.006 0.000 ARG G 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 HIS cc_start: 0.8656 (t70) cc_final: 0.8405 (t70) REVERT: A 884 ASP cc_start: 0.8370 (p0) cc_final: 0.8011 (p0) REVERT: G 103 ASP cc_start: 0.8688 (m-30) cc_final: 0.8311 (m-30) REVERT: G 127 ASP cc_start: 0.8442 (p0) cc_final: 0.8073 (p0) REVERT: G 191 LYS cc_start: 0.9355 (mppt) cc_final: 0.9072 (mmtm) REVERT: D 63 GLU cc_start: 0.8443 (tp30) cc_final: 0.8228 (tp30) REVERT: D 151 ASP cc_start: 0.8791 (m-30) cc_final: 0.8511 (m-30) REVERT: D 211 ASN cc_start: 0.9388 (m-40) cc_final: 0.9142 (m-40) outliers start: 7 outliers final: 7 residues processed: 141 average time/residue: 0.7112 time to fit residues: 157.0138 Evaluate side-chains 139 residues out of total 2449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 SER Chi-restraints excluded: chain C residue 1202 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain F residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 250 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.0060 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.064799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.046679 restraints weight = 205002.676| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.41 r_work: 0.2532 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23870 Z= 0.132 Angle : 0.488 17.590 32574 Z= 0.225 Chirality : 0.039 0.149 3714 Planarity : 0.004 0.051 4269 Dihedral : 4.097 85.238 3378 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.16 % Allowed : 7.07 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.46 (0.16), residues: 3076 helix: 1.80 (0.18), residues: 927 sheet: -0.71 (0.19), residues: 715 loop : -0.03 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 712 HIS 0.003 0.000 HIS B 345 PHE 0.010 0.001 PHE C1337 TYR 0.016 0.001 TYR E 34 ARG 0.005 0.000 ARG G 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6391.67 seconds wall clock time: 112 minutes 24.58 seconds (6744.58 seconds total)