Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 13:20:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh8_22185/04_2023/6xh8_22185_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh8_22185/04_2023/6xh8_22185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh8_22185/04_2023/6xh8_22185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh8_22185/04_2023/6xh8_22185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh8_22185/04_2023/6xh8_22185_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xh8_22185/04_2023/6xh8_22185_trim_updated.pdb" } resolution = 4.1 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 Cu 2 5.60 5 P 113 5.49 5 S 143 5.16 5 C 20507 2.51 5 N 5926 2.21 5 O 6656 1.98 5 H 32621 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 65970 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21153 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 21011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21011 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 934 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "F" Number of atoms: 8105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 8105 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 15, 'TRANS': 481} Chain breaks: 1 Chain: "G" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2038 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "H" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2038 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "1" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1713 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "2" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1719 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "3" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 100 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'3*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29467 SG CYS D 85 101.936 126.010 115.068 1.00197.25 S ATOM 29515 SG CYS D 88 99.500 122.813 115.966 1.00186.19 S ATOM 41049 SG CYS D 814 103.767 58.400 88.971 1.00107.06 S ATOM 42186 SG CYS D 888 101.780 62.190 90.395 1.00103.54 S ATOM 42277 SG CYS D 895 102.950 61.530 86.869 1.00101.54 S ATOM 42314 SG CYS D 898 100.750 59.016 87.458 1.00102.21 S ATOM 60164 SG CYS G 112 73.612 176.834 99.115 1.00355.03 S ATOM 60252 SG CYS G 120 76.090 173.446 97.324 1.00356.49 S ATOM 62202 SG CYS H 112 89.231 173.990 146.538 1.00304.45 S ATOM 62290 SG CYS H 120 89.912 170.239 146.743 1.00308.12 S Residues with excluded nonbonded symmetry interactions: 43 residue: pdb=" P DA 1 41 " occ=0.50 ... (30 atoms not shown) pdb=" H2 DA 1 41 " occ=0.50 residue: pdb=" P DC 1 42 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 42 " occ=0.50 residue: pdb=" P DC 1 43 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 43 " occ=0.50 residue: pdb=" P DT 1 44 " occ=0.50 ... (30 atoms not shown) pdb=" H6 DT 1 44 " occ=0.50 residue: pdb=" P DT 1 45 " occ=0.50 ... (30 atoms not shown) pdb=" H6 DT 1 45 " occ=0.50 residue: pdb=" P DC 1 46 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 46 " occ=0.50 residue: pdb=" P DC 1 47 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 47 " occ=0.50 residue: pdb=" P DC 1 48 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 48 " occ=0.50 residue: pdb=" P DC 1 49 " occ=0.50 ... (28 atoms not shown) pdb=" H6 DC 1 49 " occ=0.50 residue: pdb=" P DT 1 50 " occ=0.50 ... (30 atoms not shown) pdb=" H6 DT 1 50 " occ=0.50 residue: pdb=" P DT 1 51 " occ=0.50 ... (30 atoms not shown) pdb=" H6 DT 1 51 " occ=0.50 residue: pdb=" P DG 1 52 " occ=0.50 ... (31 atoms not shown) pdb=" H22 DG 1 52 " occ=0.50 ... (remaining 31 not shown) Time building chain proxies: 21.10, per 1000 atoms: 0.32 Number of scatterers: 65970 At special positions: 0 Unit cell: (143.29, 189.57, 196.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Cu 2 28.99 S 143 16.00 P 113 15.00 O 6656 8.00 N 5926 7.00 C 20507 6.00 H 32621 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 44.46 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 31 sheets defined 37.5% alpha, 7.4% beta 40 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 22.14 Creating SS restraints... Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 213 through 233 removed outlier: 4.752A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 79 through 86 removed outlier: 4.070A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 213 through 231 removed outlier: 4.914A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 371 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.572A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 476 removed outlier: 4.427A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 492 removed outlier: 3.501A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 492' Processing helix chain 'C' and resid 496 through 508 removed outlier: 3.863A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 610 through 613 No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 685 Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 821 through 824 No H-bonds generated for 'chain 'C' and resid 821 through 824' Processing helix chain 'C' and resid 859 through 864 removed outlier: 3.733A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 905 Processing helix chain 'C' and resid 943 through 977 removed outlier: 4.422A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C 976 " --> pdb=" O PHE C 972 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 989 No H-bonds generated for 'chain 'C' and resid 986 through 989' Processing helix chain 'C' and resid 1006 through 1037 removed outlier: 4.179A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 Proline residue: C1104 - end of helix No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1110 through 1134 removed outlier: 3.820A pdb=" N GLU C1114 " --> pdb=" O GLY C1110 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1161 through 1163 No H-bonds generated for 'chain 'C' and resid 1161 through 1163' Processing helix chain 'C' and resid 1167 through 1178 removed outlier: 5.469A pdb=" N LYS C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1274 through 1281 Processing helix chain 'C' and resid 1285 through 1292 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1322 through 1333 removed outlier: 4.338A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.786A pdb=" N LYS D 118 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 206 removed outlier: 4.272A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 264 through 284 removed outlier: 4.681A pdb=" N ARG D 271 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU D 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 416 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 3.634A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 574 through 582 removed outlier: 4.076A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 615 through 635 Processing helix chain 'D' and resid 652 through 670 Processing helix chain 'D' and resid 675 through 699 Processing helix chain 'D' and resid 721 through 728 Processing helix chain 'D' and resid 734 through 740 Processing helix chain 'D' and resid 769 through 787 removed outlier: 4.334A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 803 Processing helix chain 'D' and resid 835 through 838 No H-bonds generated for 'chain 'D' and resid 835 through 838' Processing helix chain 'D' and resid 866 through 873 Processing helix chain 'D' and resid 916 through 928 Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 1069 through 1072 No H-bonds generated for 'chain 'D' and resid 1069 through 1072' Processing helix chain 'D' and resid 1139 through 1146 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1227 through 1244 removed outlier: 4.516A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1253 through 1259 Processing helix chain 'D' and resid 1280 through 1287 Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1322 through 1324 No H-bonds generated for 'chain 'D' and resid 1322 through 1324' Processing helix chain 'D' and resid 1328 through 1336 Processing helix chain 'D' and resid 1347 through 1352 Processing helix chain 'D' and resid 1362 through 1374 removed outlier: 4.450A pdb=" N GLN D1367 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D1374 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 13 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'F' and resid 81 through 90 removed outlier: 3.918A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 115 through 134 Processing helix chain 'F' and resid 144 through 151 Processing helix chain 'F' and resid 160 through 163 No H-bonds generated for 'chain 'F' and resid 160 through 163' Processing helix chain 'F' and resid 214 through 220 Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 264 through 291 removed outlier: 4.704A pdb=" N VAL F 275 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP F 278 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG F 281 " --> pdb=" O ASP F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 Processing helix chain 'F' and resid 315 through 322 removed outlier: 4.658A pdb=" N MET F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 351 removed outlier: 4.184A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 382 removed outlier: 3.770A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 393 Processing helix chain 'F' and resid 402 through 418 removed outlier: 3.893A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 445 removed outlier: 4.356A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 removed outlier: 4.204A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 487 Processing helix chain 'F' and resid 491 through 500 Processing helix chain 'F' and resid 519 through 522 Processing helix chain 'F' and resid 531 through 550 Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 573 through 580 Processing helix chain 'F' and resid 585 through 599 Processing helix chain 'F' and resid 604 through 606 No H-bonds generated for 'chain 'F' and resid 604 through 606' Processing helix chain 'G' and resid 3 through 9 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 41 through 56 removed outlier: 4.159A pdb=" N ARG G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN G 55 " --> pdb=" O ARG G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 71 Processing helix chain 'G' and resid 77 through 110 Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'H' and resid 3 through 10 Processing helix chain 'H' and resid 14 through 22 Processing helix chain 'H' and resid 41 through 54 Processing helix chain 'H' and resid 60 through 71 removed outlier: 3.501A pdb=" N ASN H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 111 Processing helix chain 'H' and resid 121 through 126 Processing sheet with id= A, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.587A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 26 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 203 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.787A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 103 through 105 Processing sheet with id= D, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.050A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 16 through 18 removed outlier: 4.332A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 188 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.915A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= H, first strand: chain 'C' and resid 116 through 123 removed outlier: 4.086A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= J, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= K, first strand: chain 'C' and resid 154 through 161 removed outlier: 5.377A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 230 through 232 removed outlier: 4.104A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 589 through 592 Processing sheet with id= N, first strand: chain 'C' and resid 634 through 638 Processing sheet with id= O, first strand: chain 'C' and resid 1227 through 1232 removed outlier: 3.593A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 817 through 819 removed outlier: 6.750A pdb=" N LYS C1078 " --> pdb=" O VAL C 818 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 848 through 850 Processing sheet with id= R, first strand: chain 'C' and resid 876 through 878 Processing sheet with id= S, first strand: chain 'C' and resid 722 through 727 removed outlier: 6.541A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.534A pdb=" N LEU C 836 " --> pdb=" O VAL C1052 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= V, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= W, first strand: chain 'D' and resid 351 through 354 Processing sheet with id= X, first strand: chain 'D' and resid 355 through 357 removed outlier: 5.845A pdb=" N ILE D 447 " --> pdb=" O THR D 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 548 through 556 Processing sheet with id= Z, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= AA, first strand: chain 'D' and resid 957 through 959 removed outlier: 3.523A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AC, first strand: chain 'D' and resid 1105 through 1107 Processing sheet with id= AD, first strand: chain 'D' and resid 1264 through 1266 Processing sheet with id= AE, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.475A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 21.51 Time building geometry restraints manager: 46.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 32592 1.03 - 1.22: 86 1.22 - 1.42: 13886 1.42 - 1.62: 19882 1.62 - 1.81: 248 Bond restraints: 66694 Sorted by residual: bond pdb=" C VAL D 808 " pdb=" N VAL D 809 " ideal model delta sigma weight residual 1.334 1.261 0.073 1.24e-02 6.50e+03 3.43e+01 bond pdb=" C ASP D 462 " pdb=" N GLY D 463 " ideal model delta sigma weight residual 1.331 1.248 0.082 1.46e-02 4.69e+03 3.18e+01 bond pdb=" C GLY D 819 " pdb=" N ILE D 820 " ideal model delta sigma weight residual 1.327 1.287 0.040 9.50e-03 1.11e+04 1.77e+01 bond pdb=" C VAL C1046 " pdb=" N LEU C1047 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.34e-02 5.57e+03 1.53e+01 bond pdb=" C ILE D1090 " pdb=" N PRO D1091 " ideal model delta sigma weight residual 1.331 1.374 -0.042 1.20e-02 6.94e+03 1.25e+01 ... (remaining 66689 not shown) Histogram of bond angle deviations from ideal: 96.67 - 104.99: 1115 104.99 - 113.30: 79975 113.30 - 121.62: 27011 121.62 - 129.94: 12637 129.94 - 138.26: 198 Bond angle restraints: 120936 Sorted by residual: angle pdb=" C GLU A 29 " pdb=" N PRO A 30 " pdb=" CD PRO A 30 " ideal model delta sigma weight residual 120.60 109.56 11.04 2.20e+00 2.07e-01 2.52e+01 angle pdb=" N VAL D 858 " pdb=" CA VAL D 858 " pdb=" C VAL D 858 " ideal model delta sigma weight residual 109.19 113.07 -3.88 8.20e-01 1.49e+00 2.24e+01 angle pdb=" C GLU A 29 " pdb=" N PRO A 30 " pdb=" CA PRO A 30 " ideal model delta sigma weight residual 127.00 138.26 -11.26 2.40e+00 1.74e-01 2.20e+01 angle pdb=" C3' DG 1 76 " pdb=" O3' DG 1 76 " pdb=" P DT 1 77 " ideal model delta sigma weight residual 120.20 126.88 -6.68 1.50e+00 4.44e-01 1.98e+01 angle pdb=" N ALA C 399 " pdb=" CA ALA C 399 " pdb=" C ALA C 399 " ideal model delta sigma weight residual 110.80 119.90 -9.10 2.13e+00 2.20e-01 1.83e+01 ... (remaining 120931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 25366 35.23 - 70.47: 732 70.47 - 105.70: 28 105.70 - 140.94: 2 140.94 - 176.17: 2 Dihedral angle restraints: 26130 sinusoidal: 13512 harmonic: 12618 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -122.92 -57.08 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA ASN F 396 " pdb=" C ASN F 396 " pdb=" N ARG F 397 " pdb=" CA ARG F 397 " ideal model delta harmonic sigma weight residual -180.00 -134.96 -45.04 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA ARG F 599 " pdb=" C ARG F 599 " pdb=" N HIS F 600 " pdb=" CA HIS F 600 " ideal model delta harmonic sigma weight residual 180.00 140.40 39.60 0 5.00e+00 4.00e-02 6.27e+01 ... (remaining 26127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3663 0.059 - 0.119: 1337 0.119 - 0.178: 261 0.178 - 0.237: 25 0.237 - 0.297: 2 Chirality restraints: 5288 Sorted by residual: chirality pdb=" CB ILE F 452 " pdb=" CA ILE F 452 " pdb=" CG1 ILE F 452 " pdb=" CG2 ILE F 452 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" P DT 1 77 " pdb=" OP1 DT 1 77 " pdb=" OP2 DT 1 77 " pdb=" O5' DT 1 77 " both_signs ideal model delta sigma weight residual True 2.35 -2.60 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU D 510 " pdb=" CB LEU D 510 " pdb=" CD1 LEU D 510 " pdb=" CD2 LEU D 510 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 5285 not shown) Planarity restraints: 9567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 465 " -0.082 2.00e-02 2.50e+03 8.67e-02 1.13e+02 pdb=" CD GLN D 465 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN D 465 " 0.078 2.00e-02 2.50e+03 pdb=" NE2 GLN D 465 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 465 " 0.126 2.00e-02 2.50e+03 pdb="HE22 GLN D 465 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 462 " -0.026 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" N GLY D 463 " 0.080 2.00e-02 2.50e+03 pdb=" CA GLY D 463 " -0.022 2.00e-02 2.50e+03 pdb=" H GLY D 463 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 465 " 0.018 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" N MET D 466 " -0.059 2.00e-02 2.50e+03 pdb=" CA MET D 466 " 0.016 2.00e-02 2.50e+03 pdb=" H MET D 466 " 0.025 2.00e-02 2.50e+03 ... (remaining 9564 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 4789 2.18 - 2.79: 140776 2.79 - 3.39: 181027 3.39 - 4.00: 234614 4.00 - 4.60: 359001 Nonbonded interactions: 920207 Sorted by model distance: nonbonded pdb=" H SER H 4 " pdb=" OP1 DC 1 43 " model vdw 1.580 1.850 nonbonded pdb="HG22 VAL D 354 " pdb=" HG3 GLN D 465 " model vdw 1.586 2.440 nonbonded pdb=" O THR D 161 " pdb=" H TYR D 165 " model vdw 1.595 1.850 nonbonded pdb=" O MET G 30 " pdb=" H THR G 38 " model vdw 1.605 1.850 nonbonded pdb=" O ILE C 138 " pdb=" HG1 THR C 141 " model vdw 1.610 1.850 ... (remaining 920202 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 6 through 233) selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.710 Extract box with map and model: 15.310 Check model and map are aligned: 0.720 Set scattering table: 0.430 Process input model: 188.160 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.180 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:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 0.121 34073 Z= 0.761 Angle : 1.124 11.699 46483 Z= 0.636 Chirality : 0.060 0.297 5288 Planarity : 0.007 0.077 5696 Dihedral : 14.732 176.171 13265 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.72 % Favored : 86.18 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.66 % 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: -4.93 (0.11), residues: 3929 helix: -2.81 (0.10), residues: 1570 sheet: -3.93 (0.21), residues: 352 loop : -3.59 (0.12), residues: 2007 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 497 time to evaluate : 3.859 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 outliers start: 9 outliers final: 4 residues processed: 504 average time/residue: 1.1232 time to fit residues: 833.8799 Evaluate side-chains 316 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 312 time to evaluate : 3.845 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6590 time to fit residues: 9.6120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 7.9990 chunk 304 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 315 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 365 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 103 ASN C 618 GLN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1157 GLN C1220 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN H 76 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 34073 Z= 0.188 Angle : 0.669 8.484 46483 Z= 0.364 Chirality : 0.042 0.176 5288 Planarity : 0.005 0.064 5696 Dihedral : 15.759 174.976 5443 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.22 % Favored : 91.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.11 % 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: -3.78 (0.12), residues: 3929 helix: -1.61 (0.12), residues: 1576 sheet: -3.54 (0.22), residues: 378 loop : -3.10 (0.13), residues: 1975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.907 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 1.0518 time to fit residues: 651.2566 Evaluate side-chains 306 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 303 optimal weight: 0.8980 chunk 248 optimal weight: 0.0770 chunk 100 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 395 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 362 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 340 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS H 76 HIS H 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 34073 Z= 0.178 Angle : 0.611 9.091 46483 Z= 0.333 Chirality : 0.041 0.155 5288 Planarity : 0.005 0.083 5696 Dihedral : 15.381 178.898 5443 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.93 % Favored : 91.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -3.20 (0.12), residues: 3929 helix: -1.10 (0.12), residues: 1591 sheet: -3.08 (0.22), residues: 403 loop : -2.83 (0.13), residues: 1935 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 3.884 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 1.0258 time to fit residues: 596.3011 Evaluate side-chains 294 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 367 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 347 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN D1350 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN G 125 ASN H 71 ASN H 74 GLN H 76 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 34073 Z= 0.304 Angle : 0.665 8.592 46483 Z= 0.367 Chirality : 0.043 0.157 5288 Planarity : 0.005 0.108 5696 Dihedral : 15.350 178.865 5443 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.08 % Favored : 89.87 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -3.22 (0.12), residues: 3929 helix: -1.11 (0.12), residues: 1603 sheet: -2.98 (0.22), residues: 398 loop : -2.89 (0.13), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 3.887 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: 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: 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: 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: 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: 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: 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: 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 outliers start: 1 outliers final: 0 residues processed: 354 average time/residue: 0.9841 time to fit residues: 532.1584 Evaluate side-chains 284 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 4.218 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 20.0000 chunk 220 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 331 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 348 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 34073 Z= 0.275 Angle : 0.650 8.782 46483 Z= 0.355 Chirality : 0.043 0.248 5288 Planarity : 0.005 0.086 5696 Dihedral : 15.266 175.175 5443 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.67 % Favored : 90.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % 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: -3.00 (0.12), residues: 3929 helix: -0.94 (0.12), residues: 1602 sheet: -2.97 (0.22), residues: 417 loop : -2.71 (0.13), residues: 1910 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 3.905 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: 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: 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: 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: 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: 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: 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 outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 1.0163 time to fit residues: 526.0043 Evaluate side-chains 277 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 322 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 34073 Z= 0.312 Angle : 0.651 8.727 46483 Z= 0.359 Chirality : 0.042 0.154 5288 Planarity : 0.005 0.076 5696 Dihedral : 15.309 178.869 5443 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.15 % Favored : 88.80 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % 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: -3.04 (0.12), residues: 3929 helix: -0.97 (0.12), residues: 1597 sheet: -2.94 (0.22), residues: 415 loop : -2.74 (0.13), residues: 1917 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 3.861 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.9906 time to fit residues: 493.3999 Evaluate side-chains 268 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 327 optimal weight: 20.0000 chunk 217 optimal weight: 7.9990 chunk 387 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 495 ASN ** D1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 34073 Z= 0.295 Angle : 0.646 8.768 46483 Z= 0.356 Chirality : 0.042 0.152 5288 Planarity : 0.005 0.078 5696 Dihedral : 15.310 177.269 5443 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.12 % Favored : 88.83 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -2.97 (0.12), residues: 3929 helix: -0.92 (0.12), residues: 1595 sheet: -2.88 (0.21), residues: 418 loop : -2.70 (0.13), residues: 1916 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.939 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: 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: 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: 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: 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: 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: 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: symmetry clash outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 1.0117 time to fit residues: 508.5603 Evaluate side-chains 272 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 3.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS C 447 HIS C 573 ASN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 495 ASN ** D1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 34073 Z= 0.190 Angle : 0.584 8.490 46483 Z= 0.319 Chirality : 0.041 0.148 5288 Planarity : 0.004 0.075 5696 Dihedral : 15.198 172.329 5443 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.88 % Favored : 91.07 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -2.54 (0.13), residues: 3929 helix: -0.53 (0.12), residues: 1601 sheet: -2.69 (0.22), residues: 405 loop : -2.49 (0.13), residues: 1923 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 time to evaluate : 3.853 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.9796 time to fit residues: 507.3375 Evaluate side-chains 274 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 3.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 361 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 283 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 326 optimal weight: 20.0000 chunk 341 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN C 573 ASN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 34073 Z= 0.356 Angle : 0.684 9.186 46483 Z= 0.378 Chirality : 0.043 0.163 5288 Planarity : 0.005 0.075 5696 Dihedral : 15.360 174.722 5443 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.52 % Favored : 87.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -2.96 (0.12), residues: 3929 helix: -0.91 (0.12), residues: 1598 sheet: -2.78 (0.22), residues: 422 loop : -2.73 (0.13), residues: 1909 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 3.879 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: 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: 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: 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: 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: 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: 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 outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 1.0162 time to fit residues: 482.6410 Evaluate side-chains 265 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 0.1980 chunk 381 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 400 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 246 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 34073 Z= 0.228 Angle : 0.606 8.772 46483 Z= 0.332 Chirality : 0.041 0.154 5288 Planarity : 0.004 0.075 5696 Dihedral : 15.271 169.263 5443 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.52 % Favored : 90.43 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -2.65 (0.13), residues: 3929 helix: -0.64 (0.12), residues: 1602 sheet: -2.62 (0.22), residues: 405 loop : -2.58 (0.13), residues: 1922 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 3.905 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: 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: 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: 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: 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: 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: 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 outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.9844 time to fit residues: 481.7834 Evaluate side-chains 268 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.863 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 1.9990 chunk 339 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 294 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 319 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 327 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.105457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082328 restraints weight = 438956.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.084888 restraints weight = 220878.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.086424 restraints weight = 142204.930| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 34073 Z= 0.159 Angle : 0.560 8.323 46483 Z= 0.304 Chirality : 0.041 0.150 5288 Planarity : 0.004 0.074 5696 Dihedral : 15.109 165.810 5443 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.96 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -2.13 (0.13), residues: 3929 helix: -0.23 (0.13), residues: 1611 sheet: -2.33 (0.23), residues: 385 loop : -2.29 (0.14), residues: 1933 =============================================================================== Job complete usr+sys time: 11278.88 seconds wall clock time: 196 minutes 47.80 seconds (11807.80 seconds total)