Starting phenix.real_space_refine on Wed Mar 20 06:01:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg8_28110/03_2024/8eg8_28110_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg8_28110/03_2024/8eg8_28110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg8_28110/03_2024/8eg8_28110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg8_28110/03_2024/8eg8_28110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg8_28110/03_2024/8eg8_28110_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg8_28110/03_2024/8eg8_28110_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 67 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16436 2.51 5 N 4686 2.21 5 O 5255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H ASP 77": "OD1" <-> "OD2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "I ASP 81": "OD1" <-> "OD2" Residue "I PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 222": "OD1" <-> "OD2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 254": "OD1" <-> "OD2" Residue "I TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 349": "OE1" <-> "OE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 648": "OD1" <-> "OD2" Residue "I ASP 651": "OD1" <-> "OD2" Residue "I TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 785": "OD1" <-> "OD2" Residue "I ASP 790": "OD1" <-> "OD2" Residue "I GLU 949": "OE1" <-> "OE2" Residue "I GLU 962": "OE1" <-> "OE2" Residue "I TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1274": "OE1" <-> "OE2" Residue "I GLU 1340": "OE1" <-> "OE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 195": "OE1" <-> "OE2" Residue "J PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 267": "OD1" <-> "OD2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "J ASP 642": "OD1" <-> "OD2" Residue "J ASP 684": "OD1" <-> "OD2" Residue "J ASP 837": "OD1" <-> "OD2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1030": "OE1" <-> "OE2" Residue "J GLU 1052": "OE1" <-> "OE2" Residue "J PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1200": "OE1" <-> "OE2" Residue "J GLU 1215": "OE1" <-> "OE2" Residue "J GLU 1291": "OE1" <-> "OE2" Residue "J GLU 1293": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "J GLU 1349": "OE1" <-> "OE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26553 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "B" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 615 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10559 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15745 SG CYS J 70 108.229 58.756 75.171 1.00 64.91 S ATOM 15759 SG CYS J 72 108.325 55.103 74.188 1.00 70.75 S ATOM 15867 SG CYS J 85 110.889 57.557 72.820 1.00 69.62 S ATOM 15891 SG CYS J 88 107.130 57.961 71.819 1.00 67.78 S ATOM 21579 SG CYS J 814 82.273 120.049 81.500 1.00 36.78 S ATOM 22144 SG CYS J 888 81.065 116.446 80.973 1.00 35.14 S ATOM 22195 SG CYS J 895 81.894 117.715 84.407 1.00 32.95 S ATOM 22216 SG CYS J 898 78.829 118.916 82.928 1.00 32.65 S Time building chain proxies: 13.94, per 1000 atoms: 0.52 Number of scatterers: 26553 At special positions: 0 Unit cell: (137.8, 150.8, 167.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 67 15.00 Mg 1 11.99 O 5255 8.00 N 4686 7.00 C 16436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 33 sheets defined 32.7% alpha, 12.0% beta 30 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 13.70 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 87 removed outlier: 3.523A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 231 removed outlier: 4.235A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 227 Processing helix chain 'I' and resid 29 through 39 removed outlier: 3.531A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.605A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 291 through 294 removed outlier: 3.599A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 291 through 294' Processing helix chain 'I' and resid 319 through 327 removed outlier: 3.847A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.996A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 481 removed outlier: 3.759A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 486 No H-bonds generated for 'chain 'I' and resid 484 through 486' Processing helix chain 'I' and resid 496 through 506 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.913A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 665 through 667 No H-bonds generated for 'chain 'I' and resid 665 through 667' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 3.732A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 897 through 905 Processing helix chain 'I' and resid 943 through 980 Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1105 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1109 through 1133 Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1176 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1298 through 1310 Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 97 through 99 No H-bonds generated for 'chain 'J' and resid 97 through 99' Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 212 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 247 through 250 Processing helix chain 'J' and resid 264 through 270 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 319 through 321 No H-bonds generated for 'chain 'J' and resid 319 through 321' Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 416 removed outlier: 4.224A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 4.550A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.552A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 592 No H-bonds generated for 'chain 'J' and resid 590 through 592' Processing helix chain 'J' and resid 598 through 611 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 741 Processing helix chain 'J' and resid 771 through 787 removed outlier: 4.237A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 803 Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 937 Proline residue: J 926 - end of helix removed outlier: 5.190A pdb=" N PHE J 935 " --> pdb=" O THR J 931 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS J 936 " --> pdb=" O MET J 932 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE J 937 " --> pdb=" O ARG J 933 " (cutoff:3.500A) Processing helix chain 'J' and resid 1134 through 1146 Proline residue: J1139 - end of helix Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1243 Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1347 through 1353 Processing helix chain 'J' and resid 1361 through 1371 removed outlier: 3.697A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 83 Processing sheet with id= A, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.699A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.712A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'G' and resid 108 through 111 Processing sheet with id= F, first strand: chain 'H' and resid 12 through 18 removed outlier: 3.692A pdb=" N ARG H 12 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE H 16 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS H 25 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLN H 18 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N HIS H 23 " --> pdb=" O GLN H 18 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 98 through 105 removed outlier: 6.336A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.765A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 188 through 190 removed outlier: 3.770A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= K, first strand: chain 'I' and resid 117 through 123 removed outlier: 3.764A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= M, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.706A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 332 through 336 removed outlier: 4.367A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= P, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= Q, first strand: chain 'I' and resid 749 through 751 removed outlier: 3.604A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.440A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.447A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.722A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= V, first strand: chain 'J' and resid 145 through 147 removed outlier: 3.837A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= X, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= Y, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= Z, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.027A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AB, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id= AC, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id= AD, first strand: chain 'J' and resid 1046 through 1050 Processing sheet with id= AE, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AF, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.641A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 949 through 952 removed outlier: 3.921A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 11.82 Time building geometry restraints manager: 11.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8829 1.34 - 1.46: 5285 1.46 - 1.58: 12648 1.58 - 1.70: 136 1.70 - 1.82: 190 Bond restraints: 27088 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.731 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.728 -0.196 2.00e-02 2.50e+03 9.62e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.707 -0.165 2.00e-02 2.50e+03 6.78e+01 ... (remaining 27083 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 887 105.94 - 112.97: 14812 112.97 - 120.00: 9401 120.00 - 127.02: 11438 127.02 - 134.05: 353 Bond angle restraints: 36891 Sorted by residual: angle pdb=" N VAL J 272 " pdb=" CA VAL J 272 " pdb=" C VAL J 272 " ideal model delta sigma weight residual 111.81 107.13 4.68 8.60e-01 1.35e+00 2.96e+01 angle pdb=" N HIS I 165 " pdb=" CA HIS I 165 " pdb=" CB HIS I 165 " ideal model delta sigma weight residual 114.17 110.62 3.55 1.14e+00 7.69e-01 9.69e+00 angle pdb=" C ALA I 746 " pdb=" N GLY I 747 " pdb=" CA GLY I 747 " ideal model delta sigma weight residual 121.70 127.30 -5.60 1.80e+00 3.09e-01 9.66e+00 angle pdb=" C4 1N7 I1402 " pdb=" C5 1N7 I1402 " pdb=" C9 1N7 I1402 " ideal model delta sigma weight residual 117.60 108.47 9.13 3.00e+00 1.11e-01 9.26e+00 angle pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 114.93 105.88 9.05 3.00e+00 1.11e-01 9.09e+00 ... (remaining 36886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 16057 32.51 - 65.02: 529 65.02 - 97.53: 48 97.53 - 130.03: 4 130.03 - 162.54: 1 Dihedral angle restraints: 16639 sinusoidal: 7406 harmonic: 9233 Sorted by residual: dihedral pdb=" CA GLY J 766 " pdb=" C GLY J 766 " pdb=" N LEU J 767 " pdb=" CA LEU J 767 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA PHE J1199 " pdb=" C PHE J1199 " pdb=" N GLU J1200 " pdb=" CA GLU J1200 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER H 20 " pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 16636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3908 0.083 - 0.166: 317 0.166 - 0.250: 4 0.250 - 0.333: 3 0.333 - 0.416: 3 Chirality restraints: 4235 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.95 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C15 1N7 I1402 " pdb=" C14 1N7 I1402 " pdb=" C16 1N7 I1402 " pdb=" C2 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.47 -2.88 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C15 1N7 I1401 " pdb=" C14 1N7 I1401 " pdb=" C16 1N7 I1401 " pdb=" C2 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.47 -2.83 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 4232 not shown) Planarity restraints: 4588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 344 " -0.055 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO I 345 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO I 345 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO I 345 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 742 " 0.050 5.00e-02 4.00e+02 7.44e-02 8.84e+00 pdb=" N PRO I 743 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 743 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 743 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 559 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO I 560 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 560 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 560 " -0.038 5.00e-02 4.00e+02 ... (remaining 4585 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 250 2.57 - 3.16: 22252 3.16 - 3.74: 40977 3.74 - 4.32: 58268 4.32 - 4.90: 96852 Nonbonded interactions: 218599 Sorted by model distance: nonbonded pdb=" OG1 THR I 91 " pdb=" O ILE I 138 " model vdw 1.992 2.440 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.060 2.170 nonbonded pdb=" OP1 C R 17 " pdb="MG MG J1501 " model vdw 2.072 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.080 2.170 ... (remaining 218594 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 'G' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.020 Extract box with map and model: 5.310 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 84.580 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.293 27088 Z= 0.320 Angle : 0.599 9.129 36891 Z= 0.324 Chirality : 0.044 0.416 4235 Planarity : 0.004 0.085 4588 Dihedral : 15.483 162.544 10703 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3205 helix: 1.27 (0.16), residues: 1135 sheet: -0.92 (0.24), residues: 446 loop : -1.03 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.006 0.001 HIS J 430 PHE 0.010 0.001 PHE I 337 TYR 0.014 0.001 TYR I1018 ARG 0.012 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 3.042 Fit side-chains REVERT: G 10 LYS cc_start: 0.8371 (mptt) cc_final: 0.8150 (mptt) REVERT: G 103 ASN cc_start: 0.7863 (m-40) cc_final: 0.7588 (m-40) REVERT: G 141 SER cc_start: 0.7660 (t) cc_final: 0.7311 (t) REVERT: H 142 MET cc_start: 0.7984 (ptm) cc_final: 0.7659 (ptp) REVERT: I 600 THR cc_start: 0.8369 (m) cc_final: 0.8151 (p) REVERT: I 1158 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7205 (tppt) REVERT: J 158 GLN cc_start: 0.7610 (tt0) cc_final: 0.7146 (tp40) REVERT: J 725 MET cc_start: 0.8196 (mtm) cc_final: 0.7979 (mtp) REVERT: J 873 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6895 (mt-10) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.4307 time to fit residues: 206.5294 Evaluate side-chains 269 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 189 optimal weight: 0.0670 chunk 295 optimal weight: 7.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS I 526 HIS I 686 GLN I 965 GLN J 708 ASN J 720 ASN J 875 ASN ** J 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27088 Z= 0.354 Angle : 0.592 9.406 36891 Z= 0.304 Chirality : 0.044 0.272 4235 Planarity : 0.004 0.054 4588 Dihedral : 13.919 154.887 4446 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.14 % Allowed : 5.58 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3205 helix: 1.20 (0.16), residues: 1124 sheet: -0.83 (0.24), residues: 455 loop : -1.11 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J1193 HIS 0.012 0.001 HIS G 23 PHE 0.013 0.002 PHE I1221 TYR 0.017 0.002 TYR J 589 ARG 0.005 0.001 ARG I1142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 2.984 Fit side-chains revert: symmetry clash REVERT: G 141 SER cc_start: 0.8303 (t) cc_final: 0.7908 (t) REVERT: H 142 MET cc_start: 0.8002 (ptm) cc_final: 0.7624 (ptp) REVERT: I 23 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7706 (t0) REVERT: I 83 GLN cc_start: 0.8084 (mp10) cc_final: 0.7844 (mp10) REVERT: I 488 MET cc_start: 0.5723 (mmp) cc_final: 0.5473 (mmp) REVERT: I 1158 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7295 (tppt) REVERT: J 158 GLN cc_start: 0.7700 (tt0) cc_final: 0.7421 (tp40) REVERT: J 873 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6958 (mt-10) REVERT: J 981 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7013 (mm-30) REVERT: J 1167 LYS cc_start: 0.7489 (mmmm) cc_final: 0.6895 (mmtp) REVERT: J 1370 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6281 (mmt) outliers start: 31 outliers final: 22 residues processed: 290 average time/residue: 0.4165 time to fit residues: 187.2749 Evaluate side-chains 277 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 979 ASN Chi-restraints excluded: chain J residue 1063 ASP Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 295 optimal weight: 0.2980 chunk 319 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 293 optimal weight: 0.9990 chunk 100 optimal weight: 0.0870 chunk 237 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN J 708 ASN J 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27088 Z= 0.150 Angle : 0.500 9.508 36891 Z= 0.258 Chirality : 0.041 0.190 4235 Planarity : 0.004 0.053 4588 Dihedral : 13.578 157.139 4446 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.14 % Allowed : 8.22 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3205 helix: 1.33 (0.16), residues: 1133 sheet: -0.70 (0.24), residues: 448 loop : -1.06 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 PHE 0.008 0.001 PHE I 405 TYR 0.012 0.001 TYR J 589 ARG 0.004 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 273 time to evaluate : 3.215 Fit side-chains revert: symmetry clash REVERT: H 142 MET cc_start: 0.7947 (ptm) cc_final: 0.7687 (ptp) REVERT: I 83 GLN cc_start: 0.8053 (mp10) cc_final: 0.7784 (mp10) REVERT: I 488 MET cc_start: 0.5860 (mmp) cc_final: 0.5636 (mmp) REVERT: I 519 ASN cc_start: 0.8188 (m-40) cc_final: 0.7856 (m110) REVERT: I 1158 LYS cc_start: 0.7909 (mmtp) cc_final: 0.7096 (tppt) REVERT: I 1319 MET cc_start: 0.7627 (ttp) cc_final: 0.7319 (ttp) REVERT: J 158 GLN cc_start: 0.7637 (tt0) cc_final: 0.7201 (tp40) REVERT: J 644 MET cc_start: 0.8225 (mpp) cc_final: 0.7850 (mtm) REVERT: J 981 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6965 (mm-30) REVERT: J 1370 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6032 (mmt) outliers start: 31 outliers final: 19 residues processed: 295 average time/residue: 0.4133 time to fit residues: 189.8898 Evaluate side-chains 271 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1063 ASP Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1370 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 292 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 314 optimal weight: 0.0770 chunk 155 optimal weight: 3.9990 chunk 281 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN J 708 ASN J 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27088 Z= 0.279 Angle : 0.541 9.624 36891 Z= 0.278 Chirality : 0.042 0.181 4235 Planarity : 0.004 0.053 4588 Dihedral : 13.649 156.590 4446 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.02 % Allowed : 9.76 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3205 helix: 1.27 (0.16), residues: 1127 sheet: -0.68 (0.24), residues: 451 loop : -1.12 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 PHE 0.010 0.001 PHE J 437 TYR 0.016 0.001 TYR J 589 ARG 0.004 0.000 ARG J1258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 257 time to evaluate : 3.041 Fit side-chains revert: symmetry clash REVERT: H 142 MET cc_start: 0.7976 (ptm) cc_final: 0.7700 (ptp) REVERT: I 519 ASN cc_start: 0.8272 (m-40) cc_final: 0.8057 (m-40) REVERT: I 1072 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8730 (p0) REVERT: I 1158 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7261 (tppt) REVERT: J 158 GLN cc_start: 0.7701 (tt0) cc_final: 0.7323 (tp40) REVERT: J 981 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6925 (mm-30) REVERT: J 1370 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6266 (mmt) outliers start: 55 outliers final: 37 residues processed: 300 average time/residue: 0.4170 time to fit residues: 195.0132 Evaluate side-chains 285 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 246 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1063 ASP Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 261 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 281 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS J 708 ASN J 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27088 Z= 0.174 Angle : 0.498 10.222 36891 Z= 0.256 Chirality : 0.041 0.153 4235 Planarity : 0.004 0.053 4588 Dihedral : 13.571 157.857 4446 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.61 % Allowed : 12.00 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3205 helix: 1.41 (0.16), residues: 1125 sheet: -0.72 (0.24), residues: 462 loop : -1.09 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 PHE 0.008 0.001 PHE J 437 TYR 0.012 0.001 TYR J 589 ARG 0.005 0.000 ARG J 709 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 3.052 Fit side-chains revert: symmetry clash REVERT: I 519 ASN cc_start: 0.8193 (m-40) cc_final: 0.7796 (m-40) REVERT: I 1158 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7132 (tppt) REVERT: J 158 GLN cc_start: 0.7732 (tt0) cc_final: 0.7361 (tp40) REVERT: J 267 ASP cc_start: 0.7926 (m-30) cc_final: 0.7572 (m-30) REVERT: J 873 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6392 (mt-10) REVERT: J 981 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6971 (mm-30) REVERT: J 1167 LYS cc_start: 0.7855 (mmmm) cc_final: 0.7380 (mmtt) REVERT: J 1370 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6271 (mmt) REVERT: K 55 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6707 (mt-10) outliers start: 44 outliers final: 29 residues processed: 294 average time/residue: 0.4226 time to fit residues: 193.7690 Evaluate side-chains 276 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 246 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 5.9990 chunk 282 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 314 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN J 708 ASN J 875 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27088 Z= 0.194 Angle : 0.504 10.449 36891 Z= 0.258 Chirality : 0.041 0.182 4235 Planarity : 0.004 0.053 4588 Dihedral : 13.536 157.905 4446 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.61 % Allowed : 12.95 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3205 helix: 1.46 (0.16), residues: 1122 sheet: -0.71 (0.24), residues: 466 loop : -1.08 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 PHE 0.008 0.001 PHE I 514 TYR 0.013 0.001 TYR J 589 ARG 0.004 0.000 ARG I 478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 2.973 Fit side-chains revert: symmetry clash REVERT: I 519 ASN cc_start: 0.8196 (m-40) cc_final: 0.7785 (m-40) REVERT: I 685 MET cc_start: 0.8707 (mtm) cc_final: 0.8483 (mtp) REVERT: I 1158 LYS cc_start: 0.7948 (mmtp) cc_final: 0.7172 (tppt) REVERT: J 158 GLN cc_start: 0.7761 (tt0) cc_final: 0.7381 (tp40) REVERT: J 267 ASP cc_start: 0.7886 (m-30) cc_final: 0.7528 (m-30) REVERT: J 873 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6393 (mt-10) REVERT: J 981 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6955 (mm-30) REVERT: J 1370 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6391 (mmt) REVERT: K 55 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6790 (mt-10) outliers start: 44 outliers final: 35 residues processed: 297 average time/residue: 0.4061 time to fit residues: 189.7512 Evaluate side-chains 283 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 247 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 264 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 196 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN J 708 ASN J 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27088 Z= 0.159 Angle : 0.495 10.784 36891 Z= 0.253 Chirality : 0.040 0.171 4235 Planarity : 0.004 0.053 4588 Dihedral : 13.480 158.393 4446 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.87 % Allowed : 13.54 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3205 helix: 1.47 (0.16), residues: 1134 sheet: -0.76 (0.23), residues: 471 loop : -1.02 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 PHE 0.008 0.001 PHE J 437 TYR 0.011 0.001 TYR J 589 ARG 0.004 0.000 ARG I 478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 267 time to evaluate : 4.084 Fit side-chains REVERT: I 407 ARG cc_start: 0.7391 (ttm170) cc_final: 0.6805 (ttm-80) REVERT: I 519 ASN cc_start: 0.8147 (m-40) cc_final: 0.7702 (m-40) REVERT: I 685 MET cc_start: 0.8684 (mtm) cc_final: 0.8477 (mtp) REVERT: I 1158 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7369 (tppt) REVERT: I 1319 MET cc_start: 0.7616 (ttp) cc_final: 0.7318 (ttp) REVERT: J 158 GLN cc_start: 0.7759 (tt0) cc_final: 0.7368 (tp40) REVERT: J 267 ASP cc_start: 0.7874 (m-30) cc_final: 0.7544 (m-30) REVERT: J 330 MET cc_start: 0.7361 (mtm) cc_final: 0.7146 (mtp) REVERT: J 873 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6517 (tt0) REVERT: J 981 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6946 (mm-30) REVERT: J 1167 LYS cc_start: 0.7877 (mmmm) cc_final: 0.7574 (mmtt) REVERT: J 1370 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6342 (mmt) REVERT: K 55 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6790 (mt-10) outliers start: 51 outliers final: 39 residues processed: 308 average time/residue: 0.4094 time to fit residues: 197.4296 Evaluate side-chains 290 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 250 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1199 PHE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 0.0070 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 0.0000 chunk 199 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 overall best weight: 1.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN H 66 HIS J 458 ASN J 708 ASN J 875 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27088 Z= 0.186 Angle : 0.506 11.121 36891 Z= 0.257 Chirality : 0.041 0.175 4235 Planarity : 0.004 0.053 4588 Dihedral : 13.336 158.073 4446 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.02 % Allowed : 14.01 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3205 helix: 1.50 (0.16), residues: 1128 sheet: -0.73 (0.23), residues: 468 loop : -1.03 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 PHE 0.010 0.001 PHE J 116 TYR 0.012 0.001 TYR J 589 ARG 0.004 0.000 ARG I 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 2.823 Fit side-chains REVERT: I 332 ARG cc_start: 0.6250 (ttt180) cc_final: 0.5972 (ttt180) REVERT: I 407 ARG cc_start: 0.7395 (ttm170) cc_final: 0.6815 (ttm-80) REVERT: I 519 ASN cc_start: 0.8127 (m-40) cc_final: 0.7690 (m-40) REVERT: I 685 MET cc_start: 0.8677 (mtm) cc_final: 0.8462 (mtp) REVERT: I 1158 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7389 (tppt) REVERT: J 158 GLN cc_start: 0.7769 (tt0) cc_final: 0.7382 (tp40) REVERT: J 267 ASP cc_start: 0.7879 (m-30) cc_final: 0.7534 (m-30) REVERT: J 330 MET cc_start: 0.7349 (mtm) cc_final: 0.7099 (mtp) REVERT: J 873 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6482 (tt0) REVERT: J 981 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6940 (mm-30) REVERT: J 1167 LYS cc_start: 0.7851 (mmmm) cc_final: 0.7553 (mmtt) REVERT: J 1370 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6310 (mmt) outliers start: 55 outliers final: 47 residues processed: 299 average time/residue: 0.3965 time to fit residues: 185.9746 Evaluate side-chains 301 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1199 PHE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 284 optimal weight: 2.9990 chunk 300 optimal weight: 0.0060 chunk 273 optimal weight: 0.6980 chunk 291 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 263 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS H 66 HIS J 458 ASN J 708 ASN J 875 ASN J1126 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27088 Z= 0.131 Angle : 0.488 12.098 36891 Z= 0.249 Chirality : 0.040 0.164 4235 Planarity : 0.004 0.053 4588 Dihedral : 13.237 158.857 4446 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.80 % Allowed : 14.20 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3205 helix: 1.55 (0.16), residues: 1136 sheet: -0.75 (0.24), residues: 441 loop : -0.96 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 PHE 0.008 0.001 PHE J 116 TYR 0.009 0.001 TYR J 631 ARG 0.004 0.000 ARG I 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 279 time to evaluate : 3.006 Fit side-chains REVERT: I 332 ARG cc_start: 0.6239 (ttt180) cc_final: 0.5964 (ttt180) REVERT: I 407 ARG cc_start: 0.7374 (ttm170) cc_final: 0.6849 (ttm-80) REVERT: I 519 ASN cc_start: 0.7978 (m-40) cc_final: 0.7517 (m-40) REVERT: I 936 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7502 (ttp80) REVERT: I 1158 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7261 (tppt) REVERT: I 1319 MET cc_start: 0.7591 (ttp) cc_final: 0.7275 (ttp) REVERT: J 158 GLN cc_start: 0.7752 (tt0) cc_final: 0.7380 (tp40) REVERT: J 267 ASP cc_start: 0.7854 (m-30) cc_final: 0.7567 (m-30) REVERT: J 873 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6432 (tt0) REVERT: J 981 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6946 (mm-30) REVERT: J 1167 LYS cc_start: 0.7807 (mmmm) cc_final: 0.7542 (mmtt) REVERT: J 1370 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6292 (mmt) outliers start: 49 outliers final: 39 residues processed: 316 average time/residue: 0.4237 time to fit residues: 209.4223 Evaluate side-chains 307 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 267 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1063 ASP Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1199 PHE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 0.8980 chunk 308 optimal weight: 0.0040 chunk 188 optimal weight: 7.9990 chunk 146 optimal weight: 30.0000 chunk 214 optimal weight: 0.3980 chunk 323 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 chunk 257 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS J 365 GLN J 708 ASN J 875 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27088 Z= 0.139 Angle : 0.483 11.207 36891 Z= 0.247 Chirality : 0.040 0.153 4235 Planarity : 0.004 0.052 4588 Dihedral : 13.198 158.901 4446 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.61 % Allowed : 14.60 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3205 helix: 1.57 (0.16), residues: 1136 sheet: -0.71 (0.24), residues: 449 loop : -0.92 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.009 0.001 HIS G 23 PHE 0.007 0.001 PHE I 514 TYR 0.010 0.001 TYR J 631 ARG 0.006 0.000 ARG J 709 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 3.073 Fit side-chains REVERT: I 124 MET cc_start: 0.8668 (mtp) cc_final: 0.8271 (ttm) REVERT: I 332 ARG cc_start: 0.6243 (ttt180) cc_final: 0.5979 (ttt180) REVERT: I 407 ARG cc_start: 0.7365 (ttm170) cc_final: 0.6849 (ttm-80) REVERT: I 519 ASN cc_start: 0.7962 (m-40) cc_final: 0.7525 (m-40) REVERT: I 936 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7496 (ttp80) REVERT: I 1319 MET cc_start: 0.7602 (ttp) cc_final: 0.7284 (ttp) REVERT: J 151 MET cc_start: 0.4438 (mmt) cc_final: 0.4047 (ppp) REVERT: J 158 GLN cc_start: 0.7741 (tt0) cc_final: 0.7373 (tp40) REVERT: J 267 ASP cc_start: 0.7869 (m-30) cc_final: 0.7552 (m-30) REVERT: J 981 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6937 (mm-30) REVERT: J 1165 PHE cc_start: 0.7493 (m-10) cc_final: 0.7170 (m-80) REVERT: J 1167 LYS cc_start: 0.7807 (mmmm) cc_final: 0.7537 (mmtt) REVERT: J 1370 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6294 (mmt) REVERT: K 55 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6596 (mm-30) REVERT: K 70 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7249 (tm-30) outliers start: 44 outliers final: 40 residues processed: 309 average time/residue: 0.4056 time to fit residues: 197.6667 Evaluate side-chains 309 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 268 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1063 ASP Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1199 PHE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 237 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 258 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 365 GLN J 458 ASN J 708 ASN J 875 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097937 restraints weight = 36414.074| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.84 r_work: 0.2886 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 27088 Z= 0.421 Angle : 0.618 10.803 36891 Z= 0.316 Chirality : 0.045 0.180 4235 Planarity : 0.005 0.053 4588 Dihedral : 13.435 154.253 4446 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.76 % Allowed : 14.64 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3205 helix: 1.19 (0.16), residues: 1139 sheet: -0.63 (0.24), residues: 454 loop : -1.13 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 686 HIS 0.020 0.002 HIS H 66 PHE 0.019 0.002 PHE J 49 TYR 0.021 0.002 TYR J 631 ARG 0.007 0.001 ARG J 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5679.16 seconds wall clock time: 103 minutes 19.48 seconds (6199.48 seconds total)