Starting phenix.real_space_refine on Fri Mar 22 04:53:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/03_2024/7mkd_23892_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/03_2024/7mkd_23892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/03_2024/7mkd_23892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/03_2024/7mkd_23892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/03_2024/7mkd_23892_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/03_2024/7mkd_23892_updated.pdb" } resolution = 3.2 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= 0.014 sd= 0.111 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 136 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19906 2.51 5 N 5727 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 67": "OE1" <-> "OE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 365": "OE1" <-> "OE2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 393": "OD1" <-> "OD2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 601": "OD1" <-> "OD2" Residue "I ASP 624": "OD1" <-> "OD2" Residue "I GLU 625": "OE1" <-> "OE2" Residue "I PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 654": "OD1" <-> "OD2" Residue "I TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 1024": "OE1" <-> "OE2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I ARG 1147": "NH1" <-> "NH2" Residue "I GLU 1192": "OE1" <-> "OE2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1289": "OE1" <-> "OE2" Residue "I ASP 1296": "OD1" <-> "OD2" Residue "I TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 267": "OD1" <-> "OD2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 925": "OE1" <-> "OE2" Residue "J GLU 1236": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "L TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 247": "OE1" <-> "OE2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 310": "OE1" <-> "OE2" Residue "L GLU 336": "OE1" <-> "OE2" Residue "L TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 477": "OE1" <-> "OE2" Residue "L GLU 508": "OE1" <-> "OE2" Residue "L GLU 515": "OE1" <-> "OE2" Residue "L PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32393 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10386 Classifications: {'peptide': 1336} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3847 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1402 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "Q" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1386 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "R" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} 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} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14538 SG CYS J 70 101.623 65.647 72.592 1.00101.34 S ATOM 14552 SG CYS J 72 99.864 64.175 69.772 1.00105.00 S ATOM 14660 SG CYS J 85 103.554 65.828 69.277 1.00104.39 S ATOM 14684 SG CYS J 88 100.156 66.070 70.354 1.00102.11 S ATOM 20372 SG CYS J 814 126.393 119.526 106.314 1.00 97.75 S ATOM 20937 SG CYS J 888 123.108 118.015 105.077 1.00 94.17 S ATOM 20988 SG CYS J 895 124.740 116.913 108.396 1.00 87.63 S ATOM 21009 SG CYS J 898 123.059 120.149 108.148 1.00 86.42 S Time building chain proxies: 16.29, per 1000 atoms: 0.50 Number of scatterers: 32393 At special positions: 0 Unit cell: (154.76, 193.98, 191.86, 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 130 16.00 P 136 15.00 Mg 1 11.99 O 6491 8.00 N 5727 7.00 C 19906 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: 12.48 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 37 sheets defined 36.6% alpha, 9.0% beta 53 base pairs and 105 stacking pairs defined. Time for finding SS restraints: 16.10 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 85 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 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 232 removed outlier: 4.075A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL G 232 " --> pdb=" O LEU G 228 " (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 228 Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 207 through 212 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 279 Processing helix chain 'I' and resid 289 through 292 Processing helix chain 'I' and resid 319 through 326 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 388 removed outlier: 3.761A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.609A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 520 through 526 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 610 through 613 No H-bonds generated for 'chain 'I' and resid 610 through 613' 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 677 through 685 Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' Processing helix chain 'I' and resid 821 through 824 No H-bonds generated for 'chain 'I' and resid 821 through 824' Processing helix chain 'I' and resid 861 through 864 removed outlier: 3.953A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 861 through 864' Processing helix chain 'I' and resid 897 through 906 Processing helix chain 'I' and resid 943 through 980 Processing helix chain 'I' and resid 994 through 996 No H-bonds generated for 'chain 'I' and resid 994 through 996' Processing helix chain 'I' and resid 1008 through 1037 removed outlier: 4.831A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN I1013 " --> pdb=" O ASN I1009 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) 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 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 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 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' 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 1309 removed outlier: 4.235A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) 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 95 through 99 removed outlier: 3.646A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 removed outlier: 3.790A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.529A pdb=" N SER J 191 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 265 through 285 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 333 through 335 No H-bonds generated for 'chain 'J' and resid 333 through 335' 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 387 Processing helix chain 'J' and resid 395 through 402 Processing helix chain 'J' and resid 409 through 415 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: 3.668A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR J 457 " --> pdb=" O CYS J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.787A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 599 through 612 removed outlier: 3.900A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) 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 769 through 803 removed outlier: 3.888A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) 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 929 Proline residue: J 926 - end of helix removed outlier: 5.587A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1072 No H-bonds generated for 'chain 'J' and resid 1069 through 1072' Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.234A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.649A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1309 through 1313 Processing helix chain 'J' and resid 1320 through 1323 No H-bonds generated for 'chain 'J' and resid 1320 through 1323' Processing helix chain 'J' and resid 1329 through 1338 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1362 through 1372 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 55 Processing helix chain 'K' and resid 61 through 77 Processing helix chain 'L' and resid 99 through 107 removed outlier: 4.258A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 136 removed outlier: 3.966A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'L' and resid 215 through 233 removed outlier: 5.626A pdb=" N ALA L 222 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU L 223 " --> pdb=" O ARG L 218 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU L 224 " --> pdb=" O GLU L 219 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG L 225 " --> pdb=" O LYS L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 258 Processing helix chain 'L' and resid 263 through 289 Processing helix chain 'L' and resid 299 through 306 Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 325 through 332 removed outlier: 4.726A pdb=" N HIS L 331 " --> pdb=" O SER L 327 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP L 332 " --> pdb=" O GLU L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 355 through 393 removed outlier: 6.005A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 446 Processing helix chain 'L' and resid 454 through 474 removed outlier: 3.919A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET L 474 " --> pdb=" O MET L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 removed outlier: 3.668A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 493 through 498 Processing helix chain 'L' and resid 519 through 521 No H-bonds generated for 'chain 'L' and resid 519 through 521' Processing helix chain 'L' and resid 531 through 550 removed outlier: 3.586A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 604 through 610 removed outlier: 4.121A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 260 Processing helix chain 'R' and resid 264 through 272 Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 286 through 290 Processing helix chain 'R' and resid 297 through 309 Processing sheet with id= A, first strand: chain 'G' and resid 13 through 17 removed outlier: 3.903A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (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 99 Processing sheet with id= D, first strand: chain 'G' and resid 102 through 105 Processing sheet with id= E, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.731A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 13 through 17 removed outlier: 3.624A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= H, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.644A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 109 through 111 removed outlier: 3.872A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 180 through 183 removed outlier: 6.546A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= L, first strand: chain 'I' and resid 116 through 123 removed outlier: 3.850A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= N, first strand: chain 'I' and resid 173 through 175 Processing sheet with id= O, first strand: chain 'I' and resid 227 through 231 removed outlier: 3.532A pdb=" N ILE I 333 " --> pdb=" O PHE I 230 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= Q, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= R, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= S, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.765A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.615A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= V, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id= W, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.801A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.278A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 816 through 818 removed outlier: 7.177A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.704A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.749A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.966A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AD, first strand: chain 'J' and resid 548 through 556 Processing sheet with id= AE, first strand: chain 'J' and resid 706 through 708 Processing sheet with id= AF, first strand: chain 'J' and resid 821 through 823 Processing sheet with id= AG, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.933A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AI, first strand: chain 'J' and resid 1046 through 1051 removed outlier: 4.014A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AK, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.882A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 105 stacking parallelities Total time for adding SS restraints: 14.97 Time building geometry restraints manager: 13.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 5315 1.26 - 1.41: 7725 1.41 - 1.55: 19569 1.55 - 1.69: 318 1.69 - 1.83: 237 Bond restraints: 33164 Sorted by residual: bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.826 -0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.817 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C19 1N7 Q 101 " pdb=" C3 1N7 Q 101 " ideal model delta sigma weight residual 1.532 1.816 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.735 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3 1N7 Q 101 " pdb=" C4 1N7 Q 101 " ideal model delta sigma weight residual 1.532 1.723 -0.191 2.00e-02 2.50e+03 9.11e+01 ... (remaining 33159 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.97: 1063 104.97 - 112.23: 17167 112.23 - 119.50: 11157 119.50 - 126.76: 15339 126.76 - 134.03: 658 Bond angle restraints: 45384 Sorted by residual: angle pdb=" N GLU J 86 " pdb=" CA GLU J 86 " pdb=" C GLU J 86 " ideal model delta sigma weight residual 111.14 121.92 -10.78 1.08e+00 8.57e-01 9.96e+01 angle pdb=" N GLU J 713 " pdb=" CA GLU J 713 " pdb=" C GLU J 713 " ideal model delta sigma weight residual 110.53 122.51 -11.98 1.32e+00 5.74e-01 8.24e+01 angle pdb=" C GLU L 503 " pdb=" N PRO L 504 " pdb=" CA PRO L 504 " ideal model delta sigma weight residual 119.84 130.10 -10.26 1.25e+00 6.40e-01 6.74e+01 angle pdb=" C VAL J 90 " pdb=" CA VAL J 90 " pdb=" CB VAL J 90 " ideal model delta sigma weight residual 110.96 101.31 9.65 1.21e+00 6.83e-01 6.36e+01 angle pdb=" C ILE I1210 " pdb=" CA ILE I1210 " pdb=" CB ILE I1210 " ideal model delta sigma weight residual 111.29 98.50 12.79 1.64e+00 3.72e-01 6.08e+01 ... (remaining 45379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 19178 34.45 - 68.90: 1029 68.90 - 103.36: 40 103.36 - 137.81: 0 137.81 - 172.26: 1 Dihedral angle restraints: 20248 sinusoidal: 9430 harmonic: 10818 Sorted by residual: dihedral pdb=" CA PHE J1325 " pdb=" C PHE J1325 " pdb=" N GLN J1326 " pdb=" CA GLN J1326 " ideal model delta harmonic sigma weight residual 180.00 136.30 43.70 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -143.95 -36.05 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA SER J 119 " pdb=" C SER J 119 " pdb=" N LEU J 120 " pdb=" CA LEU J 120 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 20245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4894 0.100 - 0.201: 280 0.201 - 0.301: 15 0.301 - 0.401: 5 0.401 - 0.501: 4 Chirality restraints: 5198 Sorted by residual: chirality pdb=" CA SER L 89 " pdb=" N SER L 89 " pdb=" C SER L 89 " pdb=" CB SER L 89 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -3.02 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C19 1N7 Q 101 " pdb=" C18 1N7 Q 101 " pdb=" C2 1N7 Q 101 " pdb=" C3 1N7 Q 101 " both_signs ideal model delta sigma weight residual False -2.53 -2.99 0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 5195 not shown) Planarity restraints: 5427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE J1325 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C PHE J1325 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE J1325 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN J1326 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 235 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ARG G 235 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG G 235 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP G 236 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 705 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C THR J 705 " -0.048 2.00e-02 2.50e+03 pdb=" O THR J 705 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL J 706 " 0.016 2.00e-02 2.50e+03 ... (remaining 5424 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 33 2.30 - 2.95: 14796 2.95 - 3.60: 45751 3.60 - 4.25: 72581 4.25 - 4.90: 122733 Nonbonded interactions: 255894 Sorted by model distance: nonbonded pdb=" NZ LYS J 74 " pdb=" NZ LYS J 87 " model vdw 1.653 3.200 nonbonded pdb=" O ASP I 516 " pdb=" OD1 ASP I 516 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR J 844 " pdb=" O ARG J 860 " model vdw 2.163 2.440 nonbonded pdb=" N ASP J 751 " pdb=" OD1 ASP J 751 " model vdw 2.165 2.520 nonbonded pdb=" O SER J 775 " pdb=" OG SER J 775 " model vdw 2.174 2.440 ... (remaining 255889 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 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } 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: 0.770 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: 5.410 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 97.570 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.010 0.294 33164 Z= 0.628 Angle : 0.832 12.791 45384 Z= 0.490 Chirality : 0.054 0.501 5198 Planarity : 0.005 0.092 5427 Dihedral : 17.856 172.262 13272 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 6.15 % Allowed : 10.85 % Favored : 83.00 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3732 helix: 0.30 (0.14), residues: 1450 sheet: -2.02 (0.24), residues: 444 loop : -1.93 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I1276 HIS 0.006 0.001 HIS J 80 PHE 0.017 0.002 PHE I 186 TYR 0.021 0.002 TYR G 177 ARG 0.005 0.001 ARG J1290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 238 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8597 (mp) REVERT: I 315 MET cc_start: 0.8352 (ttp) cc_final: 0.7715 (ptm) REVERT: I 332 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7804 (mtp85) REVERT: I 538 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8880 (pp) REVERT: I 768 MET cc_start: 0.7699 (mtm) cc_final: 0.7414 (mtm) REVERT: I 979 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7663 (mp) REVERT: I 1157 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8393 (pp30) REVERT: I 1161 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8038 (mp) REVERT: I 1327 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8052 (mp) REVERT: J 81 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8501 (tmm-80) REVERT: J 196 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8250 (tm-30) REVERT: J 267 ASP cc_start: 0.8140 (t70) cc_final: 0.7834 (t0) REVERT: J 342 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9083 (mt) REVERT: J 497 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8182 (mt-10) REVERT: J 789 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7142 (ptmt) REVERT: J 802 ASP cc_start: 0.7797 (m-30) cc_final: 0.7544 (m-30) REVERT: J 849 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7772 (pp) REVERT: J 903 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7780 (mp) REVERT: K 43 ASN cc_start: 0.8600 (t0) cc_final: 0.8270 (t0) REVERT: K 70 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7644 (tm-30) REVERT: L 89 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7186 (p) REVERT: L 93 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7816 (mtp-110) REVERT: L 100 MET cc_start: 0.8858 (mtt) cc_final: 0.8568 (mtm) REVERT: L 216 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7845 (pp) REVERT: L 277 MET cc_start: 0.8091 (tpt) cc_final: 0.7412 (tpp) REVERT: L 567 MET cc_start: 0.8483 (mtm) cc_final: 0.8101 (mtm) outliers start: 198 outliers final: 105 residues processed: 426 average time/residue: 0.4119 time to fit residues: 286.6638 Evaluate side-chains 328 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 209 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1088 ASP Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 85 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 789 LYS Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 30.0000 chunk 291 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.0370 chunk 196 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 301 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 349 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 761 GLN I 798 GLN I 856 ASN J 157 GLN J 777 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 437 GLN L 464 ASN L 472 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33164 Z= 0.153 Angle : 0.542 11.615 45384 Z= 0.288 Chirality : 0.040 0.162 5198 Planarity : 0.004 0.047 5427 Dihedral : 18.034 171.894 6039 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 4.10 % Allowed : 13.83 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3732 helix: 0.91 (0.14), residues: 1456 sheet: -1.87 (0.24), residues: 436 loop : -1.71 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.003 0.000 HIS J1252 PHE 0.017 0.001 PHE I 337 TYR 0.015 0.001 TYR J1186 ARG 0.007 0.000 ARG J 709 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 252 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 205 MET cc_start: 0.8871 (ptm) cc_final: 0.8536 (ptm) REVERT: I 315 MET cc_start: 0.8242 (ttp) cc_final: 0.7521 (ptp) REVERT: I 337 PHE cc_start: 0.8892 (t80) cc_final: 0.8611 (t80) REVERT: I 414 ILE cc_start: 0.9489 (pt) cc_final: 0.9284 (pt) REVERT: I 538 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8804 (pp) REVERT: I 768 MET cc_start: 0.7687 (mtm) cc_final: 0.7401 (mtm) REVERT: I 1157 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8364 (pp30) REVERT: I 1161 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7952 (mp) REVERT: I 1327 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8109 (mp) REVERT: J 196 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8246 (tm-30) REVERT: J 304 ASP cc_start: 0.8100 (m-30) cc_final: 0.7843 (m-30) REVERT: J 457 TYR cc_start: 0.8903 (m-80) cc_final: 0.8424 (m-80) REVERT: J 497 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8161 (mt-10) REVERT: J 789 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7166 (ptmt) REVERT: J 802 ASP cc_start: 0.7580 (m-30) cc_final: 0.7331 (m-30) REVERT: J 849 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7835 (pp) REVERT: J 903 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7702 (mp) REVERT: J 1189 MET cc_start: 0.8341 (mmp) cc_final: 0.8031 (mmp) REVERT: J 1193 TRP cc_start: 0.8654 (p90) cc_final: 0.8278 (p90) REVERT: K 43 ASN cc_start: 0.8615 (t0) cc_final: 0.8261 (t0) REVERT: K 70 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7619 (tm-30) REVERT: L 89 SER cc_start: 0.7013 (OUTLIER) cc_final: 0.6509 (p) REVERT: L 93 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7735 (mtp-110) REVERT: L 259 PHE cc_start: 0.7544 (m-80) cc_final: 0.7021 (m-80) REVERT: L 277 MET cc_start: 0.8079 (tpt) cc_final: 0.7428 (tpp) REVERT: L 474 MET cc_start: 0.8559 (ptm) cc_final: 0.8225 (ptm) REVERT: L 476 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8121 (pmt-80) REVERT: L 567 MET cc_start: 0.8390 (mtm) cc_final: 0.8032 (mtm) outliers start: 132 outliers final: 75 residues processed: 370 average time/residue: 0.4348 time to fit residues: 261.7398 Evaluate side-chains 310 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 225 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 789 LYS Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 290 optimal weight: 0.3980 chunk 238 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 chunk 378 optimal weight: 8.9990 chunk 311 optimal weight: 2.9990 chunk 347 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 798 GLN J 157 GLN J 186 GLN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 33164 Z= 0.387 Angle : 0.603 10.380 45384 Z= 0.318 Chirality : 0.043 0.179 5198 Planarity : 0.004 0.053 5427 Dihedral : 17.951 171.565 5945 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.53 % Favored : 92.42 % Rotamer: Outliers : 4.79 % Allowed : 14.98 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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: -0.93 (0.14), residues: 3732 helix: 0.99 (0.14), residues: 1461 sheet: -1.73 (0.24), residues: 432 loop : -1.70 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 326 HIS 0.005 0.001 HIS J 545 PHE 0.015 0.002 PHE I 186 TYR 0.021 0.002 TYR J 144 ARG 0.003 0.000 ARG L 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 223 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 205 MET cc_start: 0.8964 (ptm) cc_final: 0.8654 (ptm) REVERT: I 47 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7024 (p90) REVERT: I 315 MET cc_start: 0.8278 (ttp) cc_final: 0.7808 (ttp) REVERT: I 337 PHE cc_start: 0.8903 (t80) cc_final: 0.8668 (t80) REVERT: I 538 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8845 (pp) REVERT: I 768 MET cc_start: 0.7770 (mtm) cc_final: 0.7485 (mtm) REVERT: I 1157 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (pp30) REVERT: I 1327 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8066 (mp) REVERT: J 180 MET cc_start: 0.8768 (ttm) cc_final: 0.8469 (ttm) REVERT: J 196 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8266 (tm-30) REVERT: J 304 ASP cc_start: 0.8082 (m-30) cc_final: 0.7818 (m-30) REVERT: J 324 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8129 (pp) REVERT: J 497 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8172 (mt-10) REVERT: J 789 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7025 (ptmt) REVERT: J 802 ASP cc_start: 0.7649 (m-30) cc_final: 0.7373 (m-30) REVERT: J 849 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7826 (pp) REVERT: J 903 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7871 (mp) REVERT: J 1193 TRP cc_start: 0.8664 (p90) cc_final: 0.8289 (p90) REVERT: K 43 ASN cc_start: 0.8749 (t0) cc_final: 0.8371 (t0) REVERT: K 70 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7636 (tm-30) REVERT: L 89 SER cc_start: 0.7149 (OUTLIER) cc_final: 0.6659 (p) REVERT: L 93 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8049 (mtt-85) REVERT: L 277 MET cc_start: 0.8033 (tpt) cc_final: 0.7412 (tpp) REVERT: L 474 MET cc_start: 0.8539 (ptm) cc_final: 0.8179 (ptm) REVERT: L 476 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8119 (pmt-80) REVERT: L 567 MET cc_start: 0.8391 (mtm) cc_final: 0.8056 (mtm) outliers start: 154 outliers final: 108 residues processed: 366 average time/residue: 0.4194 time to fit residues: 251.8893 Evaluate side-chains 336 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 217 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1088 ASP Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 789 LYS Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 235 optimal weight: 0.2980 chunk 351 optimal weight: 6.9990 chunk 372 optimal weight: 20.0000 chunk 183 optimal weight: 0.6980 chunk 333 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN J 365 GLN J 720 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33164 Z= 0.171 Angle : 0.518 9.424 45384 Z= 0.274 Chirality : 0.040 0.158 5198 Planarity : 0.004 0.054 5427 Dihedral : 17.619 171.584 5943 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 4.13 % Allowed : 16.35 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.57 (0.14), residues: 3732 helix: 1.37 (0.14), residues: 1445 sheet: -1.65 (0.25), residues: 435 loop : -1.52 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 326 HIS 0.002 0.000 HIS J 865 PHE 0.013 0.001 PHE L 259 TYR 0.018 0.001 TYR J 144 ARG 0.004 0.000 ARG I 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 238 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 188 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: G 205 MET cc_start: 0.8886 (ptm) cc_final: 0.8560 (ptm) REVERT: G 228 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7425 (mp) REVERT: I 262 TYR cc_start: 0.7294 (m-10) cc_final: 0.7047 (m-10) REVERT: I 332 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7297 (mtp85) REVERT: I 414 ILE cc_start: 0.9480 (pt) cc_final: 0.9261 (pt) REVERT: I 524 ILE cc_start: 0.8678 (tt) cc_final: 0.8470 (tt) REVERT: I 538 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8810 (pp) REVERT: I 768 MET cc_start: 0.7673 (mtm) cc_final: 0.7410 (mtm) REVERT: I 781 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: I 1157 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8433 (pp30) REVERT: I 1327 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8144 (mp) REVERT: J 196 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8208 (tm-30) REVERT: J 227 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7099 (t80) REVERT: J 304 ASP cc_start: 0.8117 (m-30) cc_final: 0.7817 (m-30) REVERT: J 324 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8048 (pp) REVERT: J 365 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8455 (pt0) REVERT: J 497 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8182 (mt-10) REVERT: J 789 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6881 (ptmt) REVERT: J 802 ASP cc_start: 0.7365 (m-30) cc_final: 0.7027 (m-30) REVERT: J 849 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7804 (pp) REVERT: J 903 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7744 (mp) REVERT: J 1193 TRP cc_start: 0.8622 (p90) cc_final: 0.8318 (p90) REVERT: K 25 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7059 (ttt-90) REVERT: K 43 ASN cc_start: 0.8689 (t0) cc_final: 0.8282 (t0) REVERT: L 89 SER cc_start: 0.7209 (OUTLIER) cc_final: 0.6741 (p) REVERT: L 277 MET cc_start: 0.7969 (tpt) cc_final: 0.7400 (tpp) REVERT: L 288 MET cc_start: 0.7012 (tmm) cc_final: 0.6631 (tmm) REVERT: L 389 SER cc_start: 0.6825 (OUTLIER) cc_final: 0.6529 (p) REVERT: L 474 MET cc_start: 0.8525 (ptm) cc_final: 0.8081 (ptm) REVERT: L 476 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7973 (pmt-80) REVERT: L 567 MET cc_start: 0.8365 (mtm) cc_final: 0.8053 (mtm) outliers start: 133 outliers final: 92 residues processed: 356 average time/residue: 0.4214 time to fit residues: 246.3048 Evaluate side-chains 333 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 225 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 789 LYS Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 0.0030 chunk 211 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 277 optimal weight: 0.5980 chunk 153 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 334 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN J 157 GLN J1098 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33164 Z= 0.169 Angle : 0.505 10.935 45384 Z= 0.267 Chirality : 0.039 0.149 5198 Planarity : 0.003 0.048 5427 Dihedral : 17.465 171.622 5928 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 94.00 % Rotamer: Outliers : 4.07 % Allowed : 16.66 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.40 (0.14), residues: 3732 helix: 1.47 (0.14), residues: 1473 sheet: -1.45 (0.25), residues: 428 loop : -1.46 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1020 HIS 0.007 0.001 HIS J 364 PHE 0.009 0.001 PHE J 437 TYR 0.015 0.001 TYR J 165 ARG 0.004 0.000 ARG I 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 240 time to evaluate : 3.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 205 MET cc_start: 0.8886 (ptm) cc_final: 0.8563 (ptm) REVERT: G 228 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7379 (mp) REVERT: H 75 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: I 262 TYR cc_start: 0.7350 (m-10) cc_final: 0.7009 (m-10) REVERT: I 315 MET cc_start: 0.8041 (ttp) cc_final: 0.7568 (ptm) REVERT: I 524 ILE cc_start: 0.8661 (tt) cc_final: 0.8453 (tt) REVERT: I 529 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7688 (mmm-85) REVERT: I 538 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8816 (pp) REVERT: I 997 TRP cc_start: 0.6789 (m-10) cc_final: 0.6524 (m-10) REVERT: I 1327 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8208 (mp) REVERT: J 144 TYR cc_start: 0.8448 (m-10) cc_final: 0.8231 (m-10) REVERT: J 196 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7990 (tm-30) REVERT: J 304 ASP cc_start: 0.8129 (m-30) cc_final: 0.7801 (m-30) REVERT: J 324 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7883 (pp) REVERT: J 497 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8189 (mt-10) REVERT: J 802 ASP cc_start: 0.7345 (m-30) cc_final: 0.7136 (m-30) REVERT: J 849 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7731 (pp) REVERT: J 1193 TRP cc_start: 0.8618 (p90) cc_final: 0.8281 (p90) REVERT: J 1326 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.5151 (tp40) REVERT: K 25 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7187 (ttt-90) REVERT: K 43 ASN cc_start: 0.8658 (t0) cc_final: 0.8237 (t0) REVERT: L 277 MET cc_start: 0.7919 (tpt) cc_final: 0.7381 (tpp) REVERT: L 389 SER cc_start: 0.6806 (OUTLIER) cc_final: 0.6496 (p) REVERT: L 474 MET cc_start: 0.8539 (ptm) cc_final: 0.8165 (ptm) REVERT: L 476 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7904 (pmt-80) REVERT: L 507 MET cc_start: 0.9050 (ttm) cc_final: 0.8817 (ttm) REVERT: L 567 MET cc_start: 0.8374 (mtm) cc_final: 0.8065 (mtm) outliers start: 131 outliers final: 97 residues processed: 357 average time/residue: 0.4104 time to fit residues: 240.3759 Evaluate side-chains 335 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 227 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 4.9990 chunk 335 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 372 optimal weight: 30.0000 chunk 309 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN J 157 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 33164 Z= 0.370 Angle : 0.578 10.084 45384 Z= 0.303 Chirality : 0.042 0.156 5198 Planarity : 0.004 0.047 5427 Dihedral : 17.576 171.314 5911 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.95 % Rotamer: Outliers : 4.82 % Allowed : 17.03 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.48 (0.14), residues: 3732 helix: 1.36 (0.14), residues: 1469 sheet: -1.48 (0.25), residues: 431 loop : -1.46 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 326 HIS 0.004 0.001 HIS J 545 PHE 0.013 0.001 PHE I 186 TYR 0.035 0.002 TYR J 144 ARG 0.003 0.000 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 219 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 205 MET cc_start: 0.8956 (ptm) cc_final: 0.8644 (ptm) REVERT: G 228 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7381 (mp) REVERT: H 75 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: H 145 LYS cc_start: 0.8507 (tttt) cc_final: 0.8133 (tttt) REVERT: I 229 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7361 (mm) REVERT: I 262 TYR cc_start: 0.7432 (m-10) cc_final: 0.7069 (m-10) REVERT: I 315 MET cc_start: 0.8185 (ttp) cc_final: 0.7640 (ptm) REVERT: I 524 ILE cc_start: 0.8748 (tt) cc_final: 0.8537 (tt) REVERT: I 529 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7753 (mtt-85) REVERT: I 538 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8854 (pp) REVERT: I 768 MET cc_start: 0.7761 (mtm) cc_final: 0.7520 (mtm) REVERT: I 1327 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8120 (mp) REVERT: J 196 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8012 (tm-30) REVERT: J 304 ASP cc_start: 0.8084 (m-30) cc_final: 0.7794 (m-30) REVERT: J 324 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8014 (pp) REVERT: J 497 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8186 (mt-10) REVERT: J 802 ASP cc_start: 0.7506 (m-30) cc_final: 0.7223 (m-30) REVERT: J 849 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7807 (pp) REVERT: J 1193 TRP cc_start: 0.8670 (p90) cc_final: 0.8304 (p90) REVERT: K 25 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6751 (ttt-90) REVERT: K 43 ASN cc_start: 0.8780 (t0) cc_final: 0.8329 (t0) REVERT: L 277 MET cc_start: 0.7941 (tpt) cc_final: 0.7391 (tpp) REVERT: L 288 MET cc_start: 0.7007 (tmm) cc_final: 0.6536 (tmm) REVERT: L 389 SER cc_start: 0.7038 (OUTLIER) cc_final: 0.6754 (p) REVERT: L 474 MET cc_start: 0.8510 (ptm) cc_final: 0.8150 (ptm) REVERT: L 476 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7922 (pmt-80) REVERT: L 507 MET cc_start: 0.9041 (ttm) cc_final: 0.8805 (ttm) REVERT: L 567 MET cc_start: 0.8376 (mtm) cc_final: 0.8061 (mtm) outliers start: 155 outliers final: 122 residues processed: 360 average time/residue: 0.4229 time to fit residues: 251.0771 Evaluate side-chains 347 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 214 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1088 ASP Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 283 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 212 optimal weight: 0.8980 chunk 272 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 313 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN J 157 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33164 Z= 0.280 Angle : 0.545 9.808 45384 Z= 0.287 Chirality : 0.041 0.152 5198 Planarity : 0.004 0.043 5427 Dihedral : 17.526 171.166 5909 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 4.75 % Allowed : 17.22 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3732 helix: 1.37 (0.14), residues: 1475 sheet: -1.46 (0.25), residues: 431 loop : -1.44 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 326 HIS 0.004 0.001 HIS J 545 PHE 0.011 0.001 PHE J 437 TYR 0.022 0.001 TYR J 144 ARG 0.006 0.000 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 223 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 205 MET cc_start: 0.8933 (ptm) cc_final: 0.8614 (ptm) REVERT: G 228 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7400 (mp) REVERT: H 66 HIS cc_start: 0.7793 (t-170) cc_final: 0.7524 (t-90) REVERT: H 75 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: I 47 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7032 (p90) REVERT: I 239 MET cc_start: 0.6194 (tmm) cc_final: 0.5969 (tmm) REVERT: I 262 TYR cc_start: 0.7497 (m-10) cc_final: 0.7106 (m-10) REVERT: I 315 MET cc_start: 0.8183 (ttp) cc_final: 0.7642 (ptm) REVERT: I 332 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7319 (mtp85) REVERT: I 524 ILE cc_start: 0.8730 (tt) cc_final: 0.8515 (tt) REVERT: I 529 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7738 (mtt-85) REVERT: I 538 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8844 (pp) REVERT: I 768 MET cc_start: 0.7757 (mtm) cc_final: 0.7513 (mtm) REVERT: I 781 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: I 1327 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8099 (mp) REVERT: J 180 MET cc_start: 0.8662 (ttp) cc_final: 0.8377 (ttp) REVERT: J 196 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8008 (tm-30) REVERT: J 304 ASP cc_start: 0.8086 (m-30) cc_final: 0.7774 (m-30) REVERT: J 324 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8059 (pp) REVERT: J 497 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8193 (mt-10) REVERT: J 802 ASP cc_start: 0.7388 (m-30) cc_final: 0.7037 (m-30) REVERT: J 849 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7805 (pp) REVERT: J 1193 TRP cc_start: 0.8606 (p90) cc_final: 0.8315 (p90) REVERT: K 25 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7016 (ttt-90) REVERT: K 43 ASN cc_start: 0.8780 (t0) cc_final: 0.8312 (t0) REVERT: L 277 MET cc_start: 0.7921 (tpt) cc_final: 0.7382 (tpp) REVERT: L 288 MET cc_start: 0.6986 (tmm) cc_final: 0.6549 (tmm) REVERT: L 389 SER cc_start: 0.7009 (OUTLIER) cc_final: 0.6721 (p) REVERT: L 474 MET cc_start: 0.8468 (ptm) cc_final: 0.8228 (ptm) REVERT: L 476 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7904 (pmt-80) REVERT: L 507 MET cc_start: 0.8956 (ttm) cc_final: 0.8755 (ttm) REVERT: L 567 MET cc_start: 0.8374 (mtm) cc_final: 0.8042 (mtm) outliers start: 153 outliers final: 121 residues processed: 363 average time/residue: 0.4282 time to fit residues: 255.5472 Evaluate side-chains 348 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 215 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1088 ASP Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 283 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 235 optimal weight: 0.9980 chunk 252 optimal weight: 0.0010 chunk 183 optimal weight: 3.9990 chunk 34 optimal weight: 0.0000 chunk 291 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN I1157 GLN J 157 GLN J1249 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33164 Z= 0.188 Angle : 0.517 9.316 45384 Z= 0.273 Chirality : 0.040 0.168 5198 Planarity : 0.003 0.042 5427 Dihedral : 17.388 171.250 5909 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.94 % Rotamer: Outliers : 4.44 % Allowed : 17.78 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3732 helix: 1.46 (0.14), residues: 1485 sheet: -1.36 (0.25), residues: 427 loop : -1.38 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 326 HIS 0.002 0.001 HIS J 865 PHE 0.009 0.001 PHE I 186 TYR 0.015 0.001 TYR J 679 ARG 0.006 0.000 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 229 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 205 MET cc_start: 0.8906 (ptm) cc_final: 0.8582 (ptm) REVERT: G 228 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7349 (mp) REVERT: H 66 HIS cc_start: 0.7834 (t-170) cc_final: 0.7531 (t-90) REVERT: H 75 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: H 145 LYS cc_start: 0.8375 (tttp) cc_final: 0.8007 (tttt) REVERT: I 47 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.6977 (p90) REVERT: I 239 MET cc_start: 0.6151 (tmm) cc_final: 0.5907 (tmm) REVERT: I 262 TYR cc_start: 0.7531 (m-10) cc_final: 0.7115 (m-10) REVERT: I 315 MET cc_start: 0.8143 (ttp) cc_final: 0.7623 (ptm) REVERT: I 332 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7452 (mtp85) REVERT: I 524 ILE cc_start: 0.8670 (tt) cc_final: 0.8455 (tt) REVERT: I 529 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7669 (mtt-85) REVERT: I 538 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8828 (pp) REVERT: I 781 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: I 1327 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8152 (mp) REVERT: J 196 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7997 (tm-30) REVERT: J 227 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7102 (t80) REVERT: J 304 ASP cc_start: 0.8116 (m-30) cc_final: 0.7760 (m-30) REVERT: J 324 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8022 (pp) REVERT: J 497 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8207 (mt-10) REVERT: J 802 ASP cc_start: 0.7299 (m-30) cc_final: 0.7000 (m-30) REVERT: J 849 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7817 (pp) REVERT: J 1189 MET cc_start: 0.8226 (mmp) cc_final: 0.7925 (mmp) REVERT: J 1193 TRP cc_start: 0.8586 (p90) cc_final: 0.8304 (p90) REVERT: J 1326 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.4975 (tp40) REVERT: K 25 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7038 (ttt-90) REVERT: K 43 ASN cc_start: 0.8720 (t0) cc_final: 0.8308 (t0) REVERT: L 277 MET cc_start: 0.7887 (tpt) cc_final: 0.7393 (tpp) REVERT: L 288 MET cc_start: 0.6949 (tmm) cc_final: 0.6535 (tmm) REVERT: L 297 MET cc_start: 0.2551 (ptt) cc_final: 0.2225 (ptm) REVERT: L 389 SER cc_start: 0.6874 (OUTLIER) cc_final: 0.6566 (p) REVERT: L 567 MET cc_start: 0.8369 (mtm) cc_final: 0.7979 (mtm) outliers start: 143 outliers final: 125 residues processed: 357 average time/residue: 0.4175 time to fit residues: 246.9596 Evaluate side-chains 362 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 224 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 283 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 40.0000 chunk 355 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 chunk 345 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 chunk 344 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 33164 Z= 0.401 Angle : 0.596 9.970 45384 Z= 0.313 Chirality : 0.043 0.159 5198 Planarity : 0.004 0.045 5427 Dihedral : 17.542 171.148 5905 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.23 % Favored : 92.71 % Rotamer: Outliers : 4.51 % Allowed : 17.81 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.44 (0.14), residues: 3732 helix: 1.37 (0.14), residues: 1474 sheet: -1.49 (0.25), residues: 443 loop : -1.41 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 326 HIS 0.005 0.001 HIS J 545 PHE 0.013 0.001 PHE I1144 TYR 0.023 0.002 TYR J 144 ARG 0.005 0.000 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 213 time to evaluate : 3.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 205 MET cc_start: 0.8964 (ptm) cc_final: 0.8639 (ptm) REVERT: G 228 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7379 (mp) REVERT: H 66 HIS cc_start: 0.7850 (t-170) cc_final: 0.7546 (t-90) REVERT: H 75 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: I 47 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7121 (p90) REVERT: I 262 TYR cc_start: 0.7563 (m-10) cc_final: 0.7158 (m-10) REVERT: I 315 MET cc_start: 0.8219 (ttp) cc_final: 0.7629 (ptm) REVERT: I 332 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7627 (mtp85) REVERT: I 524 ILE cc_start: 0.8764 (tt) cc_final: 0.8540 (tt) REVERT: I 529 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7812 (mtt-85) REVERT: I 538 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8852 (pp) REVERT: I 1327 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8129 (mp) REVERT: J 196 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8017 (tm-30) REVERT: J 304 ASP cc_start: 0.8061 (m-30) cc_final: 0.7793 (m-30) REVERT: J 324 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8249 (pp) REVERT: J 497 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8195 (mt-10) REVERT: J 802 ASP cc_start: 0.7555 (m-30) cc_final: 0.7282 (m-30) REVERT: J 849 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7800 (pp) REVERT: J 1189 MET cc_start: 0.8216 (mmp) cc_final: 0.7909 (mmp) REVERT: J 1193 TRP cc_start: 0.8629 (p90) cc_final: 0.8301 (p90) REVERT: K 25 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6802 (ttt-90) REVERT: K 43 ASN cc_start: 0.8810 (t0) cc_final: 0.8376 (t0) REVERT: L 277 MET cc_start: 0.7922 (tpt) cc_final: 0.7395 (tpp) REVERT: L 288 MET cc_start: 0.7016 (tmm) cc_final: 0.6587 (tmm) REVERT: L 297 MET cc_start: 0.2589 (ptt) cc_final: 0.2222 (ptm) REVERT: L 389 SER cc_start: 0.7178 (OUTLIER) cc_final: 0.6898 (p) REVERT: L 476 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8310 (pmt-80) REVERT: L 507 MET cc_start: 0.8900 (ttm) cc_final: 0.8544 (tpp) REVERT: L 567 MET cc_start: 0.8373 (mtm) cc_final: 0.7943 (mtm) outliers start: 145 outliers final: 127 residues processed: 347 average time/residue: 0.4257 time to fit residues: 243.3464 Evaluate side-chains 350 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 212 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 283 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.9990 chunk 365 optimal weight: 9.9990 chunk 223 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 383 optimal weight: 30.0000 chunk 353 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1157 GLN J 157 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33164 Z= 0.176 Angle : 0.520 9.402 45384 Z= 0.274 Chirality : 0.040 0.171 5198 Planarity : 0.003 0.041 5427 Dihedral : 17.358 171.164 5903 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 4.16 % Allowed : 18.33 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.27 (0.14), residues: 3732 helix: 1.51 (0.14), residues: 1479 sheet: -1.30 (0.25), residues: 427 loop : -1.34 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 326 HIS 0.003 0.001 HIS J 430 PHE 0.008 0.001 PHE L 302 TYR 0.017 0.001 TYR J 144 ARG 0.007 0.000 ARG J 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 234 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 205 MET cc_start: 0.8899 (ptm) cc_final: 0.8571 (ptm) REVERT: G 228 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7349 (mp) REVERT: H 66 HIS cc_start: 0.7826 (t-170) cc_final: 0.7485 (t-90) REVERT: H 75 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: I 47 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7039 (p90) REVERT: I 239 MET cc_start: 0.6007 (tmm) cc_final: 0.5792 (tmm) REVERT: I 262 TYR cc_start: 0.7543 (m-10) cc_final: 0.7140 (m-10) REVERT: I 315 MET cc_start: 0.8141 (ttp) cc_final: 0.7611 (ptm) REVERT: I 332 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7612 (mtp85) REVERT: I 370 MET cc_start: 0.8980 (mmm) cc_final: 0.8772 (mmm) REVERT: I 445 ILE cc_start: 0.8966 (pt) cc_final: 0.8748 (mm) REVERT: I 524 ILE cc_start: 0.8662 (tt) cc_final: 0.8443 (tt) REVERT: I 529 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7683 (mtt-85) REVERT: I 538 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8823 (pp) REVERT: I 959 ASP cc_start: 0.7807 (t70) cc_final: 0.7514 (t0) REVERT: I 1327 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8110 (mp) REVERT: J 196 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8002 (tm-30) REVERT: J 304 ASP cc_start: 0.8125 (m-30) cc_final: 0.7816 (m-30) REVERT: J 324 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8072 (pp) REVERT: J 330 MET cc_start: 0.7770 (mtp) cc_final: 0.7497 (ttm) REVERT: J 497 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8214 (mt-10) REVERT: J 802 ASP cc_start: 0.7324 (m-30) cc_final: 0.7049 (m-30) REVERT: J 849 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7831 (pp) REVERT: J 1189 MET cc_start: 0.8256 (mmp) cc_final: 0.7978 (mmp) REVERT: J 1193 TRP cc_start: 0.8585 (p90) cc_final: 0.8315 (p90) REVERT: K 25 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7042 (ttt-90) REVERT: K 43 ASN cc_start: 0.8763 (t0) cc_final: 0.8429 (t0) REVERT: L 277 MET cc_start: 0.7824 (tpt) cc_final: 0.7383 (tpp) REVERT: L 288 MET cc_start: 0.6990 (tmm) cc_final: 0.6626 (tmm) REVERT: L 297 MET cc_start: 0.2705 (ptt) cc_final: 0.2364 (ptm) REVERT: L 389 SER cc_start: 0.6856 (OUTLIER) cc_final: 0.6558 (p) REVERT: L 507 MET cc_start: 0.8788 (ttm) cc_final: 0.8539 (tpp) REVERT: L 567 MET cc_start: 0.8369 (mtm) cc_final: 0.7977 (mtm) outliers start: 134 outliers final: 122 residues processed: 353 average time/residue: 0.4132 time to fit residues: 238.3895 Evaluate side-chains 356 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 224 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1088 ASP Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 283 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 281 optimal weight: 50.0000 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 0.2980 chunk 305 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 314 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1157 GLN J 157 GLN K 31 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.132048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.075865 restraints weight = 50750.676| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.75 r_work: 0.2827 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 33164 Z= 0.272 Angle : 0.663 59.200 45384 Z= 0.370 Chirality : 0.044 0.933 5198 Planarity : 0.003 0.040 5427 Dihedral : 17.355 171.155 5903 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.19 % Rotamer: Outliers : 4.32 % Allowed : 18.27 % Favored : 77.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.14), residues: 3732 helix: 1.48 (0.14), residues: 1479 sheet: -1.29 (0.25), residues: 427 loop : -1.35 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 326 HIS 0.003 0.001 HIS J 430 PHE 0.008 0.001 PHE L 302 TYR 0.015 0.001 TYR J 679 ARG 0.021 0.000 ARG L 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6957.66 seconds wall clock time: 125 minutes 44.97 seconds (7544.97 seconds total)