Starting phenix.real_space_refine on Mon Feb 19 23:58:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg7_28109/02_2024/8eg7_28109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg7_28109/02_2024/8eg7_28109.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/8eg7_28109/02_2024/8eg7_28109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg7_28109/02_2024/8eg7_28109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg7_28109/02_2024/8eg7_28109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eg7_28109/02_2024/8eg7_28109_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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 65 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16229 2.51 5 N 4622 2.21 5 O 5175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 349": "OE1" <-> "OE2" Residue "I TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 392": "OE1" <-> "OE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I ASP 423": "OD1" <-> "OD2" Residue "I PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 781": "OD1" <-> "OD2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 947": "OE1" <-> "OE2" Residue "I TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I GLU 1174": "OE1" <-> "OE2" Residue "I ASP 1188": "OD1" <-> "OD2" Residue "I GLU 1194": "OE1" <-> "OE2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 67": "OD1" <-> "OD2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J GLU 195": "OE1" <-> "OE2" Residue "J GLU 207": "OE1" <-> "OE2" Residue "J PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 375": "OE1" <-> "OE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 404": "OE1" <-> "OE2" Residue "J PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J GLU 666": "OE1" <-> "OE2" Residue "J ASP 684": "OD1" <-> "OD2" Residue "J ASP 691": "OD1" <-> "OD2" Residue "J GLU 827": "OE1" <-> "OE2" Residue "J ASP 889": "OD1" <-> "OD2" Residue "J ASP 902": "OD1" <-> "OD2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J PHE 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1143": "OD1" <-> "OD2" Residue "J GLU 1146": "OE1" <-> "OE2" Residue "J PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1188": "OE1" <-> "OE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1343": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 74": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26200 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 487 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 216 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1262} Chain breaks: 1 Chain: "J" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15553 SG CYS J 70 53.029 119.153 59.080 1.00 86.99 S ATOM 15567 SG CYS J 72 54.601 122.596 59.656 1.00 88.75 S ATOM 15675 SG CYS J 85 52.546 121.989 56.573 1.00 89.70 S ATOM 15699 SG CYS J 88 55.890 120.173 56.949 1.00 87.25 S ATOM 21387 SG CYS J 814 47.420 53.415 48.194 1.00 45.00 S ATOM 21952 SG CYS J 888 49.889 56.203 49.052 1.00 39.19 S ATOM 22003 SG CYS J 895 47.509 54.773 51.686 1.00 35.31 S ATOM 22024 SG CYS J 898 50.362 52.689 50.469 1.00 37.07 S Time building chain proxies: 14.45, per 1000 atoms: 0.55 Number of scatterers: 26200 At special positions: 0 Unit cell: (148.2, 136.5, 145.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 65 15.00 Mg 1 11.99 O 5175 8.00 N 4622 7.00 C 16229 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: 9.63 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5858 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 29 sheets defined 31.9% alpha, 11.5% beta 29 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 13.38 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 231 removed outlier: 3.534A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 228 removed outlier: 3.648A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 39 removed outlier: 3.600A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.664A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 292 through 294 No H-bonds generated for 'chain 'I' and resid 292 through 294' Processing helix chain 'I' and resid 319 through 328 removed outlier: 3.791A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 4.224A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 481 removed outlier: 3.743A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 486 No H-bonds generated for 'chain 'I' and resid 484 through 486' Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 608 through 612 Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 4.206A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 859 through 862 No H-bonds generated for 'chain 'I' and resid 859 through 862' Processing helix chain 'I' and resid 943 through 980 Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1105 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1109 through 1133 removed outlier: 3.834A pdb=" N LYS I1133 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1168 through 1176 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 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 1310 Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 181 through 190 removed outlier: 3.591A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 266 through 284 removed outlier: 3.790A pdb=" N VAL J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 338 through 341 No H-bonds generated for 'chain 'J' and resid 338 through 341' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 408 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: 3.836A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 589 through 592 Processing helix chain 'J' and resid 598 through 611 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 741 Processing helix chain 'J' and resid 769 through 803 removed outlier: 4.112A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 866 through 874 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 927 Proline residue: J 926 - end of helix 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 1243 removed outlier: 4.031A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1347 through 1353 Processing helix chain 'J' and resid 1361 through 1371 removed outlier: 4.283A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 83 Processing sheet with id= A, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.865A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.783A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'H' and resid 12 through 18 removed outlier: 3.733A pdb=" N ARG H 12 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU H 29 " --> pdb=" O ARG H 12 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE H 16 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS H 25 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN H 18 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N HIS H 23 " --> pdb=" O GLN H 18 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 170 through 172 removed outlier: 3.640A pdb=" N GLY H 53 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.548A pdb=" N GLY H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU H 133 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'I' and resid 117 through 123 removed outlier: 3.703A pdb=" N LYS I 118 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= K, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.614A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= M, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= N, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= O, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.629A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.163A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.737A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.576A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= T, first strand: chain 'J' and resid 145 through 147 Processing sheet with id= U, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= V, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= W, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= X, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= Y, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= Z, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id= AA, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.650A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL J1061 " --> pdb=" O ALA J1105 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AC, first strand: chain 'J' and resid 1279 through 1281 826 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 10.78 Time building geometry restraints manager: 10.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8683 1.34 - 1.46: 5427 1.46 - 1.58: 12293 1.58 - 1.71: 134 1.71 - 1.83: 188 Bond restraints: 26725 Sorted by residual: bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.829 -0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.737 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.726 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.706 -0.164 2.00e-02 2.50e+03 6.71e+01 ... (remaining 26720 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.55: 782 105.55 - 112.66: 14348 112.66 - 119.78: 9052 119.78 - 126.89: 11838 126.89 - 134.00: 368 Bond angle restraints: 36388 Sorted by residual: angle pdb=" N TYR J 269 " pdb=" CA TYR J 269 " pdb=" C TYR J 269 " ideal model delta sigma weight residual 112.90 106.34 6.56 1.31e+00 5.83e-01 2.51e+01 angle pdb=" N ILE G 168 " pdb=" CA ILE G 168 " pdb=" C ILE G 168 " ideal model delta sigma weight residual 112.29 109.19 3.10 9.40e-01 1.13e+00 1.08e+01 angle pdb=" CA GLY H 106 " pdb=" C GLY H 106 " pdb=" N ILE H 107 " ideal model delta sigma weight residual 114.23 117.09 -2.86 8.80e-01 1.29e+00 1.06e+01 angle pdb=" N LYS I 161 " pdb=" CA LYS I 161 " pdb=" C LYS I 161 " ideal model delta sigma weight residual 110.97 114.38 -3.41 1.09e+00 8.42e-01 9.76e+00 angle pdb=" N GLY J 613 " pdb=" CA GLY J 613 " pdb=" C GLY J 613 " ideal model delta sigma weight residual 111.56 114.61 -3.05 1.01e+00 9.80e-01 9.10e+00 ... (remaining 36383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 15829 31.09 - 62.18: 533 62.18 - 93.27: 50 93.27 - 124.37: 0 124.37 - 155.46: 1 Dihedral angle restraints: 16413 sinusoidal: 7306 harmonic: 9107 Sorted by residual: dihedral pdb=" CA ASP I 696 " pdb=" C ASP I 696 " pdb=" N LYS I 697 " pdb=" CA LYS I 697 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA SER H 20 " pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ALA I1263 " pdb=" C ALA I1263 " pdb=" N GLN I1264 " pdb=" CA GLN I1264 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 16410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3939 0.091 - 0.182: 227 0.182 - 0.273: 6 0.273 - 0.364: 2 0.364 - 0.455: 2 Chirality restraints: 4176 Sorted by residual: 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 -2.99 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C15 1N7 I1401 " pdb=" C14 1N7 I1401 " pdb=" C16 1N7 I1401 " pdb=" C2 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.47 -2.77 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 4173 not shown) Planarity restraints: 4525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO I 698 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO I 590 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 551 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO I 552 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 552 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 552 " -0.022 5.00e-02 4.00e+02 ... (remaining 4522 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 233 2.58 - 3.16: 21370 3.16 - 3.74: 40574 3.74 - 4.32: 56787 4.32 - 4.90: 94762 Nonbonded interactions: 213726 Sorted by model distance: nonbonded pdb=" O3' G R 16 " pdb="MG MG J1501 " model vdw 2.006 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.021 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.043 2.170 nonbonded pdb=" OH TYR J 795 " pdb=" OE1 GLN J1326 " model vdw 2.161 2.440 nonbonded pdb=" OG SER J 977 " pdb=" OG1 THR J 980 " model vdw 2.191 2.440 ... (remaining 213721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 5.290 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 80.110 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.006 0.297 26725 Z= 0.380 Angle : 0.603 8.746 36388 Z= 0.340 Chirality : 0.045 0.455 4176 Planarity : 0.004 0.053 4525 Dihedral : 14.545 155.456 10555 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.52 % Allowed : 7.97 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3154 helix: 0.87 (0.16), residues: 1102 sheet: -0.87 (0.26), residues: 393 loop : -1.62 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 580 HIS 0.004 0.001 HIS I 447 PHE 0.014 0.001 PHE I1221 TYR 0.018 0.001 TYR G 177 ARG 0.003 0.000 ARG I1223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 393 time to evaluate : 2.963 Fit side-chains REVERT: I 223 LEU cc_start: 0.8427 (tt) cc_final: 0.8160 (tp) REVERT: I 228 VAL cc_start: 0.7399 (t) cc_final: 0.7107 (t) REVERT: I 359 ARG cc_start: 0.6644 (ttt-90) cc_final: 0.6147 (ttt-90) REVERT: I 430 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8292 (mttp) REVERT: I 580 GLN cc_start: 0.7816 (mt0) cc_final: 0.7610 (mt0) REVERT: I 825 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7414 (mt-10) REVERT: I 842 ASP cc_start: 0.6772 (t70) cc_final: 0.6403 (t70) REVERT: I 930 ASP cc_start: 0.8229 (t70) cc_final: 0.7958 (t0) REVERT: I 1033 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6390 (mtm180) REVERT: I 1085 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8469 (mmp) REVERT: I 1180 MET cc_start: 0.8532 (ttm) cc_final: 0.8130 (ttm) REVERT: I 1232 MET cc_start: 0.8752 (mmm) cc_final: 0.8495 (mmm) REVERT: J 267 ASP cc_start: 0.7968 (t0) cc_final: 0.7763 (m-30) REVERT: J 291 ILE cc_start: 0.8609 (mm) cc_final: 0.8170 (tt) REVERT: J 556 GLU cc_start: 0.7298 (tt0) cc_final: 0.7022 (tt0) REVERT: J 665 GLN cc_start: 0.7282 (tp40) cc_final: 0.6898 (tm-30) REVERT: J 667 GLN cc_start: 0.6967 (tt0) cc_final: 0.6592 (tt0) REVERT: J 827 GLU cc_start: 0.7259 (tp30) cc_final: 0.6744 (pm20) REVERT: J 913 GLU cc_start: 0.7787 (tt0) cc_final: 0.7552 (tt0) REVERT: J 1219 ASP cc_start: 0.7919 (m-30) cc_final: 0.7626 (m-30) REVERT: J 1275 LEU cc_start: 0.7835 (mm) cc_final: 0.7609 (mm) REVERT: J 1344 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8696 (pp) REVERT: K 42 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7504 (mt-10) REVERT: K 74 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7172 (mm-30) outliers start: 68 outliers final: 37 residues processed: 451 average time/residue: 0.3794 time to fit residues: 271.3747 Evaluate side-chains 351 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 311 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 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 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 290 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN G 186 ASN I 214 ASN I 490 GLN I 618 GLN I1116 HIS J 777 HIS J1108 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26725 Z= 0.240 Angle : 0.535 8.396 36388 Z= 0.277 Chirality : 0.042 0.209 4176 Planarity : 0.004 0.045 4525 Dihedral : 13.508 156.122 4428 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.19 % Allowed : 10.90 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3154 helix: 0.98 (0.16), residues: 1098 sheet: -0.92 (0.25), residues: 407 loop : -1.52 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.004 0.001 HIS I 447 PHE 0.025 0.001 PHE I1025 TYR 0.017 0.001 TYR G 177 ARG 0.006 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 328 time to evaluate : 2.714 Fit side-chains revert: symmetry clash REVERT: G 127 GLN cc_start: 0.8409 (mp10) cc_final: 0.8194 (mp10) REVERT: I 18 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7539 (mtm-85) REVERT: I 39 ILE cc_start: 0.8584 (pt) cc_final: 0.8317 (pt) REVERT: I 130 MET cc_start: 0.9326 (ttm) cc_final: 0.9124 (ttp) REVERT: I 239 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.4705 (ttm) REVERT: I 785 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8017 (p0) REVERT: I 805 MET cc_start: 0.8898 (ptm) cc_final: 0.8624 (ptp) REVERT: I 842 ASP cc_start: 0.6716 (t70) cc_final: 0.6392 (t70) REVERT: I 930 ASP cc_start: 0.8315 (t70) cc_final: 0.8070 (t0) REVERT: I 962 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6861 (mt-10) REVERT: I 1033 ARG cc_start: 0.7111 (ttm110) cc_final: 0.6363 (mtm180) REVERT: I 1085 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8632 (mmp) REVERT: I 1180 MET cc_start: 0.8540 (ttm) cc_final: 0.8164 (ttm) REVERT: I 1188 ASP cc_start: 0.7946 (t0) cc_final: 0.7550 (t0) REVERT: I 1243 MET cc_start: 0.8593 (ttp) cc_final: 0.8374 (tmm) REVERT: J 227 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: J 291 ILE cc_start: 0.8614 (mm) cc_final: 0.8316 (tp) REVERT: J 556 GLU cc_start: 0.7288 (tt0) cc_final: 0.7037 (tt0) REVERT: J 665 GLN cc_start: 0.7334 (tp40) cc_final: 0.6930 (tm-30) REVERT: J 827 GLU cc_start: 0.7285 (tp30) cc_final: 0.6807 (pm20) REVERT: J 913 GLU cc_start: 0.7770 (tt0) cc_final: 0.7551 (tt0) REVERT: J 1040 MET cc_start: 0.4222 (ttp) cc_final: 0.3150 (tpp) REVERT: J 1143 ASP cc_start: 0.7453 (m-30) cc_final: 0.7244 (m-30) REVERT: J 1275 LEU cc_start: 0.7836 (mm) cc_final: 0.7592 (mm) REVERT: J 1344 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8639 (pp) REVERT: K 76 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6062 (mt-10) outliers start: 86 outliers final: 55 residues processed: 393 average time/residue: 0.3891 time to fit residues: 245.2930 Evaluate side-chains 366 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 305 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 291 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 214 ASN I 330 HIS I 513 GLN J 777 HIS J1197 ASN K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26725 Z= 0.289 Angle : 0.546 9.034 36388 Z= 0.284 Chirality : 0.043 0.168 4176 Planarity : 0.004 0.048 4525 Dihedral : 13.516 156.544 4423 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.48 % Allowed : 12.34 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3154 helix: 0.85 (0.16), residues: 1104 sheet: -1.07 (0.25), residues: 418 loop : -1.52 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J1193 HIS 0.004 0.001 HIS I 447 PHE 0.015 0.001 PHE J 176 TYR 0.018 0.001 TYR G 177 ARG 0.006 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 320 time to evaluate : 2.921 Fit side-chains REVERT: G 33 ARG cc_start: 0.6572 (ttm-80) cc_final: 0.6278 (ttm-80) REVERT: G 197 ASP cc_start: 0.4695 (t70) cc_final: 0.4094 (t0) REVERT: I 18 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7424 (mtm-85) REVERT: I 430 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8236 (mttp) REVERT: I 487 LEU cc_start: 0.4082 (OUTLIER) cc_final: 0.3817 (pp) REVERT: I 638 SER cc_start: 0.8727 (t) cc_final: 0.8387 (p) REVERT: I 805 MET cc_start: 0.8919 (ptm) cc_final: 0.8663 (ptp) REVERT: I 842 ASP cc_start: 0.6831 (t70) cc_final: 0.6531 (t70) REVERT: I 930 ASP cc_start: 0.8295 (t70) cc_final: 0.8037 (t0) REVERT: I 962 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6861 (mt-10) REVERT: I 1033 ARG cc_start: 0.7139 (ttm110) cc_final: 0.6340 (mtm180) REVERT: I 1085 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8526 (mmp) REVERT: I 1180 MET cc_start: 0.8574 (ttm) cc_final: 0.8183 (ttm) REVERT: I 1188 ASP cc_start: 0.7964 (t0) cc_final: 0.7457 (t0) REVERT: J 215 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7758 (mmtm) REVERT: J 227 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: J 291 ILE cc_start: 0.8619 (mm) cc_final: 0.8321 (tp) REVERT: J 556 GLU cc_start: 0.7251 (tt0) cc_final: 0.7024 (tt0) REVERT: J 665 GLN cc_start: 0.7354 (tp40) cc_final: 0.6956 (tm-30) REVERT: J 802 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: J 805 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: J 807 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8647 (tt) REVERT: J 827 GLU cc_start: 0.7315 (tp30) cc_final: 0.6835 (pm20) REVERT: J 1143 ASP cc_start: 0.7464 (m-30) cc_final: 0.7247 (m-30) REVERT: J 1275 LEU cc_start: 0.7842 (mm) cc_final: 0.7572 (mm) REVERT: J 1344 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8677 (pp) REVERT: K 76 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6055 (mt-10) outliers start: 94 outliers final: 65 residues processed: 396 average time/residue: 0.3729 time to fit residues: 236.6320 Evaluate side-chains 377 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 303 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 292 optimal weight: 20.0000 chunk 309 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 276 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN G 132 HIS G 137 ASN H 37 HIS I 214 ASN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26725 Z= 0.311 Angle : 0.551 8.509 36388 Z= 0.287 Chirality : 0.043 0.170 4176 Planarity : 0.004 0.049 4525 Dihedral : 13.558 156.406 4423 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.08 % Allowed : 13.38 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3154 helix: 0.80 (0.16), residues: 1103 sheet: -1.03 (0.24), residues: 419 loop : -1.51 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J1193 HIS 0.004 0.001 HIS I 447 PHE 0.016 0.001 PHE I 645 TYR 0.018 0.001 TYR G 177 ARG 0.006 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 300 time to evaluate : 3.173 Fit side-chains REVERT: G 33 ARG cc_start: 0.6634 (ttm-80) cc_final: 0.6379 (ttm-80) REVERT: G 197 ASP cc_start: 0.4749 (t70) cc_final: 0.3964 (t0) REVERT: I 18 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7378 (mtm-85) REVERT: I 85 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7529 (m) REVERT: I 430 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8190 (mttp) REVERT: I 638 SER cc_start: 0.8700 (t) cc_final: 0.8364 (p) REVERT: I 805 MET cc_start: 0.8929 (ptm) cc_final: 0.8666 (ptp) REVERT: I 842 ASP cc_start: 0.6894 (t70) cc_final: 0.6606 (t70) REVERT: I 930 ASP cc_start: 0.8303 (t70) cc_final: 0.8037 (t0) REVERT: I 962 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6914 (mt-10) REVERT: I 1033 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6323 (mtm180) REVERT: I 1085 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8508 (mmp) REVERT: I 1180 MET cc_start: 0.8603 (ttm) cc_final: 0.8200 (ttm) REVERT: I 1188 ASP cc_start: 0.7988 (t0) cc_final: 0.7378 (t0) REVERT: J 66 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7729 (tppt) REVERT: J 215 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7789 (mmtm) REVERT: J 227 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: J 291 ILE cc_start: 0.8625 (mm) cc_final: 0.8322 (tp) REVERT: J 556 GLU cc_start: 0.7204 (tt0) cc_final: 0.6957 (tt0) REVERT: J 665 GLN cc_start: 0.7357 (tp40) cc_final: 0.6944 (tm-30) REVERT: J 740 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8372 (mp) REVERT: J 802 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: J 805 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: J 807 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8641 (tt) REVERT: J 827 GLU cc_start: 0.7334 (tp30) cc_final: 0.6855 (pm20) REVERT: J 891 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: J 1344 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8719 (pp) REVERT: K 76 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6046 (mt-10) outliers start: 110 outliers final: 72 residues processed: 389 average time/residue: 0.3787 time to fit residues: 236.2877 Evaluate side-chains 371 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 287 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 277 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 214 ASN I 513 GLN I 618 GLN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J1195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26725 Z= 0.150 Angle : 0.489 7.860 36388 Z= 0.254 Chirality : 0.041 0.169 4176 Planarity : 0.003 0.041 4525 Dihedral : 13.283 154.179 4421 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.41 % Allowed : 14.53 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3154 helix: 1.10 (0.16), residues: 1093 sheet: -0.95 (0.25), residues: 415 loop : -1.38 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J1193 HIS 0.004 0.001 HIS I 628 PHE 0.010 0.001 PHE I 645 TYR 0.015 0.001 TYR G 177 ARG 0.007 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 339 time to evaluate : 2.998 Fit side-chains REVERT: G 33 ARG cc_start: 0.6655 (ttm-80) cc_final: 0.6411 (ttm-80) REVERT: G 197 ASP cc_start: 0.4436 (t70) cc_final: 0.3617 (t0) REVERT: G 206 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: H 38 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8490 (t) REVERT: I 18 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7299 (mtm-85) REVERT: I 85 CYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7450 (m) REVERT: I 239 MET cc_start: 0.5016 (ttp) cc_final: 0.4603 (ttm) REVERT: I 386 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7863 (tm-30) REVERT: I 387 ASN cc_start: 0.8388 (m-40) cc_final: 0.7996 (m-40) REVERT: I 430 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8326 (mttp) REVERT: I 638 SER cc_start: 0.8538 (t) cc_final: 0.8205 (p) REVERT: I 805 MET cc_start: 0.8890 (ptm) cc_final: 0.8670 (ptp) REVERT: I 842 ASP cc_start: 0.6831 (t70) cc_final: 0.6549 (t70) REVERT: I 930 ASP cc_start: 0.8233 (t70) cc_final: 0.8024 (t0) REVERT: I 962 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6879 (mt-10) REVERT: I 1033 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6407 (mtm180) REVERT: I 1085 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8596 (mmp) REVERT: I 1180 MET cc_start: 0.8614 (ttm) cc_final: 0.8183 (ttm) REVERT: I 1188 ASP cc_start: 0.7771 (t0) cc_final: 0.7130 (t0) REVERT: J 164 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: J 227 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: J 291 ILE cc_start: 0.8611 (mm) cc_final: 0.8294 (tp) REVERT: J 556 GLU cc_start: 0.7070 (tt0) cc_final: 0.6842 (tt0) REVERT: J 807 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8703 (tt) REVERT: J 827 GLU cc_start: 0.7406 (tp30) cc_final: 0.6786 (pm20) REVERT: J 993 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6988 (mm-30) REVERT: J 1040 MET cc_start: 0.4113 (ttp) cc_final: 0.3218 (tpp) REVERT: J 1275 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7563 (mm) REVERT: J 1344 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8440 (pp) REVERT: K 76 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6118 (mt-10) outliers start: 92 outliers final: 51 residues processed: 412 average time/residue: 0.3711 time to fit residues: 244.6565 Evaluate side-chains 364 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 302 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 8 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 3.9990 chunk 278 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 309 optimal weight: 6.9990 chunk 257 optimal weight: 0.4980 chunk 143 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 ASN I 513 GLN J 232 ASN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26725 Z= 0.172 Angle : 0.493 8.609 36388 Z= 0.255 Chirality : 0.041 0.184 4176 Planarity : 0.003 0.041 4525 Dihedral : 13.191 154.648 4414 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.56 % Allowed : 14.42 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3154 helix: 1.19 (0.16), residues: 1096 sheet: -0.99 (0.25), residues: 405 loop : -1.32 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J1193 HIS 0.006 0.001 HIS H 66 PHE 0.012 0.001 PHE I 645 TYR 0.015 0.001 TYR G 177 ARG 0.007 0.000 ARG J1174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 320 time to evaluate : 3.125 Fit side-chains REVERT: G 33 ARG cc_start: 0.6694 (ttm-80) cc_final: 0.6441 (ttm-80) REVERT: G 197 ASP cc_start: 0.4420 (t70) cc_final: 0.3657 (t0) REVERT: G 206 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: H 38 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8510 (t) REVERT: I 18 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7408 (mtm-85) REVERT: I 85 CYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7470 (m) REVERT: I 490 GLN cc_start: 0.7299 (tp40) cc_final: 0.7003 (tp40) REVERT: I 638 SER cc_start: 0.8490 (t) cc_final: 0.8280 (p) REVERT: I 842 ASP cc_start: 0.6824 (t70) cc_final: 0.6549 (t70) REVERT: I 962 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6969 (mt-10) REVERT: I 1033 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6376 (mtm180) REVERT: I 1085 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8540 (mmp) REVERT: I 1180 MET cc_start: 0.8609 (ttm) cc_final: 0.8203 (ttm) REVERT: I 1188 ASP cc_start: 0.7881 (t0) cc_final: 0.7292 (t0) REVERT: J 164 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8356 (mp10) REVERT: J 202 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.8125 (ttm110) REVERT: J 227 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: J 291 ILE cc_start: 0.8600 (mm) cc_final: 0.8298 (tp) REVERT: J 556 GLU cc_start: 0.7041 (tt0) cc_final: 0.6812 (tt0) REVERT: J 740 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8342 (mp) REVERT: J 747 MET cc_start: 0.7629 (mmm) cc_final: 0.6518 (mmm) REVERT: J 802 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6696 (m-30) REVERT: J 805 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: J 807 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8664 (tt) REVERT: J 827 GLU cc_start: 0.7455 (tp30) cc_final: 0.6795 (pm20) REVERT: J 1040 MET cc_start: 0.4154 (ttp) cc_final: 0.3229 (tpp) REVERT: J 1181 ASP cc_start: 0.5297 (OUTLIER) cc_final: 0.4600 (t0) REVERT: J 1275 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7551 (mm) REVERT: J 1344 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8513 (pp) REVERT: K 76 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6113 (mt-10) outliers start: 96 outliers final: 66 residues processed: 397 average time/residue: 0.3817 time to fit residues: 243.4444 Evaluate side-chains 386 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 306 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 12 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 175 optimal weight: 0.0270 chunk 260 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 ASN J 232 ASN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 777 HIS K 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26725 Z= 0.174 Angle : 0.490 9.203 36388 Z= 0.254 Chirality : 0.041 0.195 4176 Planarity : 0.003 0.041 4525 Dihedral : 13.113 153.159 4408 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.67 % Allowed : 14.83 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3154 helix: 1.26 (0.16), residues: 1093 sheet: -0.89 (0.25), residues: 393 loop : -1.31 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 PHE 0.010 0.001 PHE I1221 TYR 0.016 0.001 TYR G 177 ARG 0.008 0.000 ARG J1174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 314 time to evaluate : 2.738 Fit side-chains REVERT: G 206 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: H 38 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8502 (t) REVERT: I 18 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7457 (mtm-85) REVERT: I 85 CYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7476 (m) REVERT: I 239 MET cc_start: 0.5027 (ttp) cc_final: 0.4647 (ttm) REVERT: I 386 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7871 (tm-30) REVERT: I 387 ASN cc_start: 0.8407 (m-40) cc_final: 0.8031 (m-40) REVERT: I 638 SER cc_start: 0.8527 (t) cc_final: 0.8243 (p) REVERT: I 842 ASP cc_start: 0.6817 (t70) cc_final: 0.6565 (t70) REVERT: I 962 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6859 (mt-10) REVERT: I 1033 ARG cc_start: 0.7219 (ttm110) cc_final: 0.6413 (mtm180) REVERT: I 1085 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8546 (mmp) REVERT: I 1180 MET cc_start: 0.8602 (ttm) cc_final: 0.8193 (ttm) REVERT: I 1188 ASP cc_start: 0.7877 (t0) cc_final: 0.7278 (t0) REVERT: J 164 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8300 (mp10) REVERT: J 202 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.8142 (ttm110) REVERT: J 227 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: J 291 ILE cc_start: 0.8604 (mm) cc_final: 0.8299 (tp) REVERT: J 556 GLU cc_start: 0.7026 (tt0) cc_final: 0.6814 (tt0) REVERT: J 740 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8338 (mp) REVERT: J 747 MET cc_start: 0.7635 (mmm) cc_final: 0.6543 (mmm) REVERT: J 802 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: J 805 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: J 807 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8663 (tt) REVERT: J 827 GLU cc_start: 0.7499 (tp30) cc_final: 0.6822 (pm20) REVERT: J 891 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: J 993 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7027 (mm-30) REVERT: J 1181 ASP cc_start: 0.5297 (OUTLIER) cc_final: 0.4603 (t0) REVERT: J 1275 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7553 (mm) REVERT: J 1344 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8530 (pp) REVERT: J 1357 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8230 (tt) REVERT: K 76 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6116 (mt-10) outliers start: 99 outliers final: 66 residues processed: 392 average time/residue: 0.3632 time to fit residues: 229.0029 Evaluate side-chains 386 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 304 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 677 ASN Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 12 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 242 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 ASN I 513 GLN J 232 ASN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26725 Z= 0.157 Angle : 0.483 9.844 36388 Z= 0.250 Chirality : 0.040 0.198 4176 Planarity : 0.003 0.040 4525 Dihedral : 13.031 152.049 4403 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.48 % Allowed : 14.75 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3154 helix: 1.32 (0.16), residues: 1096 sheet: -0.88 (0.25), residues: 415 loop : -1.25 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.004 0.001 HIS H 66 PHE 0.011 0.001 PHE J 176 TYR 0.015 0.001 TYR G 177 ARG 0.008 0.000 ARG J1174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 321 time to evaluate : 2.926 Fit side-chains REVERT: G 206 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: H 38 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8470 (t) REVERT: I 18 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7335 (mtm-85) REVERT: I 85 CYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7445 (m) REVERT: I 239 MET cc_start: 0.4849 (ttp) cc_final: 0.4390 (ttm) REVERT: I 386 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7858 (tm-30) REVERT: I 387 ASN cc_start: 0.8360 (m-40) cc_final: 0.7981 (m-40) REVERT: I 638 SER cc_start: 0.8568 (t) cc_final: 0.8215 (p) REVERT: I 842 ASP cc_start: 0.6809 (t70) cc_final: 0.6560 (t70) REVERT: I 962 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6878 (mt-10) REVERT: I 1033 ARG cc_start: 0.7255 (ttm110) cc_final: 0.6363 (mtm110) REVERT: I 1085 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8525 (mmp) REVERT: I 1180 MET cc_start: 0.8605 (ttm) cc_final: 0.8186 (ttm) REVERT: I 1188 ASP cc_start: 0.7858 (t0) cc_final: 0.7215 (t0) REVERT: J 164 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: J 202 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8150 (ttm110) REVERT: J 227 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: J 556 GLU cc_start: 0.6979 (tt0) cc_final: 0.6752 (tt0) REVERT: J 697 MET cc_start: 0.9016 (ttp) cc_final: 0.8766 (tmm) REVERT: J 740 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8319 (mp) REVERT: J 802 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6788 (m-30) REVERT: J 805 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: J 807 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8715 (tt) REVERT: J 891 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: J 993 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6961 (mm-30) REVERT: J 1181 ASP cc_start: 0.5287 (OUTLIER) cc_final: 0.4603 (t0) REVERT: J 1275 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7546 (mm) REVERT: J 1344 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8532 (pp) REVERT: J 1357 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8187 (tt) REVERT: K 74 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7435 (mm-30) REVERT: K 76 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6115 (mt-10) outliers start: 94 outliers final: 65 residues processed: 393 average time/residue: 0.3724 time to fit residues: 232.5665 Evaluate side-chains 386 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 305 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 12 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 ASN I 513 GLN J 232 ASN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 777 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26725 Z= 0.287 Angle : 0.543 10.110 36388 Z= 0.281 Chirality : 0.043 0.189 4176 Planarity : 0.004 0.044 4525 Dihedral : 13.181 152.623 4401 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.34 % Allowed : 15.31 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3154 helix: 1.10 (0.16), residues: 1114 sheet: -0.93 (0.25), residues: 410 loop : -1.32 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 PHE 0.014 0.001 PHE J 176 TYR 0.018 0.001 TYR G 177 ARG 0.008 0.000 ARG J1174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 307 time to evaluate : 2.889 Fit side-chains REVERT: G 206 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: H 38 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8619 (t) REVERT: I 7 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6476 (pm20) REVERT: I 18 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7589 (mtm-85) REVERT: I 85 CYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7503 (m) REVERT: I 386 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7860 (tm-30) REVERT: I 387 ASN cc_start: 0.8348 (m-40) cc_final: 0.7988 (m-40) REVERT: I 638 SER cc_start: 0.8575 (t) cc_final: 0.8218 (p) REVERT: I 842 ASP cc_start: 0.6886 (t70) cc_final: 0.6655 (t70) REVERT: I 962 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6972 (mt-10) REVERT: I 1033 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6372 (mtm110) REVERT: I 1085 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8545 (mmp) REVERT: I 1180 MET cc_start: 0.8591 (ttm) cc_final: 0.8147 (ttm) REVERT: I 1188 ASP cc_start: 0.7892 (t0) cc_final: 0.7265 (t0) REVERT: J 66 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7892 (tppt) REVERT: J 202 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8091 (ttm110) REVERT: J 291 ILE cc_start: 0.8625 (mm) cc_final: 0.8316 (tp) REVERT: J 556 GLU cc_start: 0.7088 (tt0) cc_final: 0.6850 (tt0) REVERT: J 740 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8396 (mp) REVERT: J 802 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: J 805 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: J 807 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8628 (tt) REVERT: J 827 GLU cc_start: 0.7484 (tp30) cc_final: 0.6803 (pm20) REVERT: J 891 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: J 993 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7054 (mm-30) REVERT: J 1040 MET cc_start: 0.5094 (mtm) cc_final: 0.4411 (mtp) REVERT: J 1275 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7563 (mm) REVERT: J 1344 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8657 (pp) REVERT: J 1357 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8238 (tt) REVERT: K 74 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7416 (mm-30) REVERT: K 76 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6112 (mt-10) outliers start: 90 outliers final: 66 residues processed: 380 average time/residue: 0.3680 time to fit residues: 224.9439 Evaluate side-chains 382 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 302 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 12 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 144 optimal weight: 0.0870 chunk 211 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 293 optimal weight: 0.5980 chunk 253 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 ASN I 513 GLN J 232 ASN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26725 Z= 0.148 Angle : 0.496 8.759 36388 Z= 0.258 Chirality : 0.040 0.200 4176 Planarity : 0.003 0.039 4525 Dihedral : 13.018 152.597 4399 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.00 % Allowed : 15.64 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3154 helix: 1.31 (0.16), residues: 1095 sheet: -0.78 (0.25), residues: 392 loop : -1.26 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 PHE 0.011 0.001 PHE I1025 TYR 0.014 0.001 TYR G 177 ARG 0.009 0.000 ARG J1174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 305 time to evaluate : 3.069 Fit side-chains REVERT: G 206 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: H 38 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8535 (t) REVERT: H 86 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7737 (tttp) REVERT: I 7 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6446 (pm20) REVERT: I 18 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7532 (mtm-85) REVERT: I 85 CYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7430 (m) REVERT: I 239 MET cc_start: 0.4840 (ttp) cc_final: 0.4562 (ttm) REVERT: I 386 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7820 (tm-30) REVERT: I 387 ASN cc_start: 0.8359 (m-40) cc_final: 0.7960 (m-40) REVERT: I 638 SER cc_start: 0.8622 (t) cc_final: 0.8291 (p) REVERT: I 842 ASP cc_start: 0.6705 (t70) cc_final: 0.6487 (t70) REVERT: I 962 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6888 (mt-10) REVERT: I 1033 ARG cc_start: 0.7218 (ttm110) cc_final: 0.6321 (mtm110) REVERT: I 1085 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8585 (mmp) REVERT: I 1180 MET cc_start: 0.8600 (ttm) cc_final: 0.8162 (ttm) REVERT: I 1188 ASP cc_start: 0.7925 (t0) cc_final: 0.7323 (t70) REVERT: J 66 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7797 (tppt) REVERT: J 202 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8162 (ttm110) REVERT: J 291 ILE cc_start: 0.8609 (mm) cc_final: 0.8163 (tt) REVERT: J 556 GLU cc_start: 0.6951 (tt0) cc_final: 0.6713 (tt0) REVERT: J 697 MET cc_start: 0.9049 (ttp) cc_final: 0.8782 (tmm) REVERT: J 740 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8336 (mp) REVERT: J 807 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8714 (tt) REVERT: J 993 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6911 (mm-30) REVERT: J 1181 ASP cc_start: 0.5303 (OUTLIER) cc_final: 0.4632 (t0) REVERT: J 1258 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8453 (ttt180) REVERT: J 1275 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7563 (mm) REVERT: J 1344 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8551 (pp) REVERT: J 1357 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8201 (tt) REVERT: K 74 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7422 (mm-30) REVERT: K 76 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6103 (mt-10) outliers start: 81 outliers final: 65 residues processed: 366 average time/residue: 0.3850 time to fit residues: 228.0593 Evaluate side-chains 377 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 299 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 12 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 ASN I 513 GLN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120093 restraints weight = 30954.319| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.19 r_work: 0.2980 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26725 Z= 0.305 Angle : 0.557 9.443 36388 Z= 0.287 Chirality : 0.043 0.228 4176 Planarity : 0.004 0.045 4525 Dihedral : 13.151 152.331 4399 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.22 % Allowed : 15.60 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3154 helix: 1.09 (0.16), residues: 1114 sheet: -0.93 (0.25), residues: 406 loop : -1.31 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 997 HIS 0.005 0.001 HIS H 66 PHE 0.013 0.001 PHE J 176 TYR 0.017 0.001 TYR G 177 ARG 0.010 0.000 ARG J1174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5933.25 seconds wall clock time: 112 minutes 15.74 seconds (6735.74 seconds total)