Starting phenix.real_space_refine on Thu Feb 15 07:18:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckl_30387/02_2024/7ckl_30387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckl_30387/02_2024/7ckl_30387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckl_30387/02_2024/7ckl_30387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckl_30387/02_2024/7ckl_30387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckl_30387/02_2024/7ckl_30387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckl_30387/02_2024/7ckl_30387.pdb" } resolution = 3.88 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 S 82 5.16 5 C 7343 2.51 5 N 1938 2.21 5 O 2155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 4": "OD1" <-> "OD2" Residue "A TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A ASP 436": "OD1" <-> "OD2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ASP 669": "OD1" <-> "OD2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 718": "NH1" <-> "NH2" Residue "A PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A ASP 754": "OD1" <-> "OD2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A TYR 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A ARG 1226": "NH1" <-> "NH2" Residue "A GLU 1242": "OE1" <-> "OE2" Residue "A PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1272": "OE1" <-> "OE2" Residue "A TYR 1276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1304": "OD1" <-> "OD2" Residue "A ARG 1312": "NH1" <-> "NH2" Residue "A ASP 1333": "OD1" <-> "OD2" Residue "A ASP 1334": "OD1" <-> "OD2" Residue "A GLU 1345": "OE1" <-> "OE2" Residue "A GLU 1353": "OE1" <-> "OE2" Residue "A PHE 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1355": "NH1" <-> "NH2" Residue "A GLU 1359": "OE1" <-> "OE2" Residue "A TYR 1362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1366": "OD1" <-> "OD2" Residue "A PHE 1381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1458": "OD1" <-> "OD2" Residue "A ASP 1467": "OD1" <-> "OD2" Residue "A ARG 1469": "NH1" <-> "NH2" Residue "A ASP 1470": "OD1" <-> "OD2" Residue "A ARG 1476": "NH1" <-> "NH2" Residue "A TYR 1503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1544": "OD1" <-> "OD2" Residue "A TYR 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1624": "NH1" <-> "NH2" Residue "A ARG 1632": "NH1" <-> "NH2" Residue "A TYR 1640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1667": "NH1" <-> "NH2" Residue "A PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1751": "NH1" <-> "NH2" Residue "A PHE 1764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11521 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1415, 11137 Classifications: {'peptide': 1415} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 43, 'TRANS': 1371} Chain breaks: 17 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11192 SG CYS B 31 16.943 55.949 31.813 1.00125.91 S ATOM 11213 SG CYS B 34 17.543 60.081 32.522 1.00113.55 S ATOM 11350 SG CYS B 50 15.013 58.009 29.830 1.00158.06 S ATOM 11372 SG CYS B 53 18.328 57.675 29.156 1.00152.26 S ATOM 11298 SG CYS B 44 17.566 45.961 30.824 1.00171.86 S ATOM 11451 SG CYS B 64 20.438 47.396 29.537 1.00165.66 S ATOM 11472 SG CYS B 67 20.599 45.550 32.419 1.00176.90 S Time building chain proxies: 8.14, per 1000 atoms: 0.71 Number of scatterers: 11521 At special positions: 0 Unit cell: (123.76, 114.24, 116.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 82 16.00 O 2155 8.00 N 1938 7.00 C 7343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1692 " - pdb=" SG CYS A1792 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.50 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 31 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 50 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 53 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 34 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 47 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 67 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 44 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 64 " Number of angles added : 9 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 58.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 4.021A pdb=" N ILE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 3.624A pdb=" N GLN A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 58 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 108 through 132 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 232 through 252 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.613A pdb=" N LYS A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 340 through 363 removed outlier: 3.790A pdb=" N ARG A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.054A pdb=" N VAL A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.590A pdb=" N ARG A 581 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 582 " --> pdb=" O PRO A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 589 through 603 removed outlier: 4.401A pdb=" N GLN A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 603 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 removed outlier: 4.645A pdb=" N ASN A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 612 through 630 Processing helix chain 'A' and resid 632 through 650 removed outlier: 4.048A pdb=" N VAL A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.723A pdb=" N LEU A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 707 removed outlier: 3.603A pdb=" N ARG A 697 " --> pdb=" O MET A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 717 through 737 removed outlier: 3.683A pdb=" N ASP A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.662A pdb=" N LEU A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 795 Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 873 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 902 through 910 removed outlier: 3.556A pdb=" N SER A 910 " --> pdb=" O ASP A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 1139 through 1159 Processing helix chain 'A' and resid 1167 through 1184 removed outlier: 3.629A pdb=" N MET A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.662A pdb=" N MET A1200 " --> pdb=" O TRP A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1211 removed outlier: 3.619A pdb=" N PHE A1205 " --> pdb=" O CYS A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1238 Processing helix chain 'A' and resid 1244 through 1261 removed outlier: 3.531A pdb=" N VAL A1248 " --> pdb=" O PRO A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1280 Processing helix chain 'A' and resid 1299 through 1323 Processing helix chain 'A' and resid 1340 through 1350 Processing helix chain 'A' and resid 1350 through 1368 removed outlier: 3.523A pdb=" N PHE A1354 " --> pdb=" O ASP A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1409 removed outlier: 3.590A pdb=" N PHE A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1433 Processing helix chain 'A' and resid 1435 through 1453 removed outlier: 3.766A pdb=" N CYS A1439 " --> pdb=" O PRO A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1490 through 1508 removed outlier: 3.750A pdb=" N LYS A1494 " --> pdb=" O ASP A1490 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A1508 " --> pdb=" O ASN A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1520 removed outlier: 3.560A pdb=" N THR A1516 " --> pdb=" O HIS A1512 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1536 removed outlier: 3.968A pdb=" N LYS A1529 " --> pdb=" O LEU A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1586 removed outlier: 4.177A pdb=" N ILE A1586 " --> pdb=" O ILE A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1626 Processing helix chain 'A' and resid 1640 through 1650 removed outlier: 3.528A pdb=" N ILE A1644 " --> pdb=" O TYR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1681 Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1703 through 1707 Processing helix chain 'A' and resid 1744 through 1753 Processing helix chain 'A' and resid 1753 through 1759 Processing helix chain 'A' and resid 1782 through 1791 removed outlier: 4.741A pdb=" N ASP A1789 " --> pdb=" O CYS A1785 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A1790 " --> pdb=" O VAL A1786 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A1791 " --> pdb=" O ALA A1787 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 58 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.690A pdb=" N GLY A 90 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 98 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 100 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 removed outlier: 6.096A pdb=" N LEU A 207 " --> pdb=" O TYR A1109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.837A pdb=" N ARG A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 537 through 542 removed outlier: 6.598A pdb=" N LYS A 560 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR A 576 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 562 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 574 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 564 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1133 through 1138 removed outlier: 7.231A pdb=" N PHE A1121 " --> pdb=" O GLU A1242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1326 through 1330 Processing sheet with id=AA8, first strand: chain 'A' and resid 1383 through 1385 Processing sheet with id=AA9, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AB1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.604A pdb=" N VAL A1631 " --> pdb=" O LEU A1639 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 41 through 43 613 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3724 1.35 - 1.46: 2639 1.46 - 1.58: 5241 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 11725 Sorted by residual: bond pdb=" N ASP A1467 " pdb=" CA ASP A1467 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.22e-02 6.72e+03 6.71e+00 bond pdb=" C PHE A 583 " pdb=" N PRO A 584 " ideal model delta sigma weight residual 1.337 1.351 -0.014 9.80e-03 1.04e+04 2.06e+00 bond pdb=" CA VAL A1434 " pdb=" CB VAL A1434 " ideal model delta sigma weight residual 1.537 1.524 0.014 1.29e-02 6.01e+03 1.12e+00 bond pdb=" C VAL A1468 " pdb=" O VAL A1468 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.19e-02 7.06e+03 1.06e+00 bond pdb=" C TRP A1392 " pdb=" O TRP A1392 " ideal model delta sigma weight residual 1.235 1.247 -0.011 1.12e-02 7.97e+03 1.03e+00 ... (remaining 11720 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.88: 275 106.88 - 113.73: 6611 113.73 - 120.58: 4889 120.58 - 127.43: 3962 127.43 - 134.28: 95 Bond angle restraints: 15832 Sorted by residual: angle pdb=" N ARG A1469 " pdb=" CA ARG A1469 " pdb=" C ARG A1469 " ideal model delta sigma weight residual 114.62 107.07 7.55 1.14e+00 7.69e-01 4.39e+01 angle pdb=" C ASP A1467 " pdb=" N VAL A1468 " pdb=" CA VAL A1468 " ideal model delta sigma weight residual 121.97 130.31 -8.34 1.80e+00 3.09e-01 2.15e+01 angle pdb=" CA GLU A 929 " pdb=" C GLU A 929 " pdb=" N PRO A 930 " ideal model delta sigma weight residual 120.81 117.23 3.58 8.60e-01 1.35e+00 1.73e+01 angle pdb=" N ASP A1467 " pdb=" CA ASP A1467 " pdb=" C ASP A1467 " ideal model delta sigma weight residual 111.56 106.02 5.54 1.38e+00 5.25e-01 1.61e+01 angle pdb=" O ASP A1467 " pdb=" C ASP A1467 " pdb=" N VAL A1468 " ideal model delta sigma weight residual 122.19 127.11 -4.92 1.34e+00 5.57e-01 1.35e+01 ... (remaining 15827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6530 17.74 - 35.47: 498 35.47 - 53.21: 73 53.21 - 70.95: 9 70.95 - 88.68: 15 Dihedral angle restraints: 7125 sinusoidal: 2824 harmonic: 4301 Sorted by residual: dihedral pdb=" CA VAL A1468 " pdb=" C VAL A1468 " pdb=" N ARG A1469 " pdb=" CA ARG A1469 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR A 746 " pdb=" C THR A 746 " pdb=" N ALA A 747 " pdb=" CA ALA A 747 " ideal model delta harmonic sigma weight residual -180.00 -162.16 -17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " pdb=" CD GLU A 41 " pdb=" OE1 GLU A 41 " ideal model delta sinusoidal sigma weight residual 0.00 -88.35 88.35 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1295 0.037 - 0.074: 407 0.074 - 0.111: 101 0.111 - 0.148: 14 0.148 - 0.185: 2 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CB ILE A 451 " pdb=" CA ILE A 451 " pdb=" CG1 ILE A 451 " pdb=" CG2 ILE A 451 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA ILE A 667 " pdb=" N ILE A 667 " pdb=" C ILE A 667 " pdb=" CB ILE A 667 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1816 not shown) Planarity restraints: 2001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1396 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A1397 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1397 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1397 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1414 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A1415 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1415 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1415 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1468 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C VAL A1468 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A1468 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A1469 " 0.008 2.00e-02 2.50e+03 ... (remaining 1998 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2450 2.78 - 3.31: 11760 3.31 - 3.84: 18557 3.84 - 4.37: 21087 4.37 - 4.90: 35793 Nonbonded interactions: 89647 Sorted by model distance: nonbonded pdb=" O ASP A 129 " pdb=" OG SER A 132 " model vdw 2.244 2.440 nonbonded pdb=" O GLU A1523 " pdb=" OG SER A1527 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR A1519 " pdb=" O SER A1527 " model vdw 2.263 2.440 nonbonded pdb=" O GLN A 172 " pdb=" OG SER A 176 " model vdw 2.267 2.440 nonbonded pdb=" O ILE A1648 " pdb=" OG1 THR A1651 " model vdw 2.269 2.440 ... (remaining 89642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.000 Extract box with map and model: 1.850 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 39.940 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.002 0.039 11725 Z= 0.159 Angle : 0.560 8.344 15832 Z= 0.321 Chirality : 0.038 0.185 1819 Planarity : 0.003 0.040 2001 Dihedral : 13.089 88.684 4318 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.20), residues: 1426 helix: -0.18 (0.16), residues: 792 sheet: -1.51 (0.52), residues: 92 loop : -3.41 (0.21), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1666 HIS 0.003 0.001 HIS A1287 PHE 0.015 0.001 PHE A 541 TYR 0.008 0.001 TYR A 654 ARG 0.002 0.000 ARG A1476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 LEU cc_start: 0.8757 (mt) cc_final: 0.8530 (mt) REVERT: A 456 TYR cc_start: 0.7543 (t80) cc_final: 0.6928 (t80) REVERT: A 511 LYS cc_start: 0.8365 (pptt) cc_final: 0.8144 (pttm) REVERT: A 593 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7889 (tp-100) REVERT: A 647 MET cc_start: 0.8154 (tpt) cc_final: 0.7928 (tpt) REVERT: A 664 GLU cc_start: 0.7943 (tp30) cc_final: 0.7476 (tp30) REVERT: A 665 GLU cc_start: 0.8030 (tt0) cc_final: 0.7813 (mm-30) REVERT: A 753 ASP cc_start: 0.8306 (m-30) cc_final: 0.7544 (m-30) REVERT: A 1150 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7289 (tp30) REVERT: A 1154 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8158 (tp30) REVERT: A 1199 MET cc_start: 0.8216 (mmt) cc_final: 0.7895 (mmt) REVERT: A 1240 MET cc_start: 0.6876 (mtt) cc_final: 0.6591 (mtt) REVERT: A 1299 LEU cc_start: 0.8694 (mt) cc_final: 0.8489 (mt) REVERT: A 1300 HIS cc_start: 0.7524 (t-170) cc_final: 0.7077 (t-170) REVERT: A 1301 ASN cc_start: 0.8892 (m-40) cc_final: 0.8018 (m-40) REVERT: A 1408 HIS cc_start: 0.6762 (m-70) cc_final: 0.6558 (m90) REVERT: A 1463 ASN cc_start: 0.8437 (t0) cc_final: 0.8216 (t0) REVERT: A 1470 ASP cc_start: 0.7427 (p0) cc_final: 0.7123 (p0) REVERT: A 1531 LEU cc_start: 0.8981 (pp) cc_final: 0.8745 (pp) REVERT: A 1672 LEU cc_start: 0.8064 (tp) cc_final: 0.7863 (tt) REVERT: B 26 LEU cc_start: 0.6300 (mp) cc_final: 0.5624 (mp) REVERT: B 43 GLU cc_start: 0.8983 (tt0) cc_final: 0.8641 (tp30) REVERT: B 47 HIS cc_start: 0.7851 (p90) cc_final: 0.7502 (p90) REVERT: B 48 TYR cc_start: 0.8301 (m-10) cc_final: 0.8021 (m-10) REVERT: B 51 LEU cc_start: 0.8946 (tp) cc_final: 0.8731 (tt) REVERT: B 56 LEU cc_start: 0.8742 (tp) cc_final: 0.8434 (tt) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2651 time to fit residues: 121.8762 Evaluate side-chains 227 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN A 321 GLN A 567 ASN A 593 GLN A 655 HIS A 703 ASN A 794 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 ASN A1287 HIS A1315 ASN A1408 HIS A1409 ASN A1432 ASN ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN A1518 ASN A1587 GLN A1638 ASN A1664 GLN B 52 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11725 Z= 0.172 Angle : 0.599 9.938 15832 Z= 0.293 Chirality : 0.039 0.185 1819 Planarity : 0.004 0.042 2001 Dihedral : 3.907 23.913 1557 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.73 % Favored : 93.20 % Rotamer: Outliers : 1.65 % Allowed : 13.83 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1426 helix: 0.99 (0.18), residues: 801 sheet: -1.11 (0.53), residues: 89 loop : -3.09 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1688 HIS 0.004 0.001 HIS A 76 PHE 0.029 0.001 PHE A1214 TYR 0.013 0.001 TYR A 706 ARG 0.007 0.000 ARG A1349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.6801 (mp0) cc_final: 0.6595 (mp0) REVERT: A 333 LYS cc_start: 0.8095 (tptt) cc_final: 0.7758 (tppt) REVERT: A 456 TYR cc_start: 0.7861 (t80) cc_final: 0.7564 (t80) REVERT: A 511 LYS cc_start: 0.8361 (pptt) cc_final: 0.8155 (pttm) REVERT: A 593 GLN cc_start: 0.8257 (tp40) cc_final: 0.7774 (tp-100) REVERT: A 621 LYS cc_start: 0.8748 (tttt) cc_final: 0.8382 (mtpt) REVERT: A 647 MET cc_start: 0.8195 (tpt) cc_final: 0.7981 (tpt) REVERT: A 664 GLU cc_start: 0.7914 (tp30) cc_final: 0.7566 (tp30) REVERT: A 665 GLU cc_start: 0.8087 (tt0) cc_final: 0.7872 (mm-30) REVERT: A 755 MET cc_start: 0.8877 (tpp) cc_final: 0.8610 (tpt) REVERT: A 1094 MET cc_start: 0.6702 (tpt) cc_final: 0.6484 (tpt) REVERT: A 1134 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7671 (mm-30) REVERT: A 1147 ARG cc_start: 0.8126 (tpt90) cc_final: 0.7788 (mtp85) REVERT: A 1150 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7177 (tp30) REVERT: A 1154 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8038 (tp30) REVERT: A 1199 MET cc_start: 0.8460 (mmt) cc_final: 0.8024 (mmt) REVERT: A 1276 TYR cc_start: 0.8003 (m-80) cc_final: 0.7760 (m-80) REVERT: A 1299 LEU cc_start: 0.8679 (mt) cc_final: 0.8152 (mt) REVERT: A 1300 HIS cc_start: 0.7483 (t-170) cc_final: 0.7087 (t-170) REVERT: A 1301 ASN cc_start: 0.8881 (m-40) cc_final: 0.7716 (t0) REVERT: A 1312 ARG cc_start: 0.7856 (ttt90) cc_final: 0.7618 (mtp85) REVERT: A 1524 HIS cc_start: 0.8893 (m90) cc_final: 0.8568 (m-70) REVERT: A 1793 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7796 (mp0) REVERT: B 26 LEU cc_start: 0.6319 (mp) cc_final: 0.5696 (mp) REVERT: B 43 GLU cc_start: 0.9022 (tt0) cc_final: 0.8700 (tp30) outliers start: 21 outliers final: 11 residues processed: 247 average time/residue: 0.2292 time to fit residues: 82.5070 Evaluate side-chains 225 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 214 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1409 ASN Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1438 LEU Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN A1504 ASN B 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11725 Z= 0.157 Angle : 0.585 10.697 15832 Z= 0.287 Chirality : 0.039 0.205 1819 Planarity : 0.003 0.047 2001 Dihedral : 3.903 20.182 1557 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 1.57 % Allowed : 16.26 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1426 helix: 1.45 (0.19), residues: 803 sheet: -0.78 (0.54), residues: 89 loop : -2.95 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 325 HIS 0.003 0.001 HIS A 76 PHE 0.032 0.001 PHE A1214 TYR 0.013 0.001 TYR A1125 ARG 0.003 0.000 ARG A1501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 227 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6598 (mmt-90) REVERT: A 329 LEU cc_start: 0.8700 (mt) cc_final: 0.8417 (mt) REVERT: A 456 TYR cc_start: 0.7739 (t80) cc_final: 0.7487 (t80) REVERT: A 539 GLN cc_start: 0.7372 (tp40) cc_final: 0.6614 (mm110) REVERT: A 647 MET cc_start: 0.8171 (tpt) cc_final: 0.7955 (tpt) REVERT: A 664 GLU cc_start: 0.7921 (tp30) cc_final: 0.7562 (tp30) REVERT: A 665 GLU cc_start: 0.8092 (tt0) cc_final: 0.7867 (mm-30) REVERT: A 755 MET cc_start: 0.8890 (tpp) cc_final: 0.8642 (tpp) REVERT: A 1147 ARG cc_start: 0.8002 (tpt90) cc_final: 0.7685 (mtp85) REVERT: A 1150 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7167 (tp30) REVERT: A 1154 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8012 (tp30) REVERT: A 1191 MET cc_start: 0.7760 (mtp) cc_final: 0.7520 (mpp) REVERT: A 1199 MET cc_start: 0.8451 (mmt) cc_final: 0.8037 (mmt) REVERT: A 1228 TYR cc_start: 0.7550 (m-80) cc_final: 0.6992 (m-80) REVERT: A 1276 TYR cc_start: 0.8088 (m-80) cc_final: 0.7757 (m-80) REVERT: A 1299 LEU cc_start: 0.8686 (mt) cc_final: 0.8234 (mt) REVERT: A 1300 HIS cc_start: 0.7472 (t-170) cc_final: 0.7040 (t-170) REVERT: A 1301 ASN cc_start: 0.8842 (m-40) cc_final: 0.7621 (t0) REVERT: A 1312 ARG cc_start: 0.7878 (ttt90) cc_final: 0.7628 (mtp85) REVERT: A 1366 ASP cc_start: 0.7920 (t0) cc_final: 0.7697 (t0) REVERT: A 1530 ASN cc_start: 0.8324 (m110) cc_final: 0.8064 (m-40) REVERT: A 1793 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7784 (mp0) REVERT: B 26 LEU cc_start: 0.6086 (mp) cc_final: 0.5629 (mp) REVERT: B 43 GLU cc_start: 0.9007 (tt0) cc_final: 0.8702 (tp30) REVERT: B 48 TYR cc_start: 0.8385 (m-10) cc_final: 0.8016 (m-10) outliers start: 20 outliers final: 10 residues processed: 240 average time/residue: 0.2243 time to fit residues: 78.6558 Evaluate side-chains 220 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 4.9990 chunk 99 optimal weight: 0.0370 chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN A1103 GLN A1181 ASN A1278 ASN A1409 ASN A1504 ASN A1524 HIS A1556 HIS B 52 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11725 Z= 0.220 Angle : 0.616 9.829 15832 Z= 0.305 Chirality : 0.040 0.192 1819 Planarity : 0.004 0.048 2001 Dihedral : 4.004 18.696 1557 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 2.67 % Allowed : 18.85 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1426 helix: 1.60 (0.19), residues: 806 sheet: -0.77 (0.52), residues: 94 loop : -2.89 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 602 HIS 0.004 0.001 HIS A1361 PHE 0.028 0.002 PHE A1274 TYR 0.016 0.001 TYR A1503 ARG 0.003 0.000 ARG A1476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6624 (mmt-90) REVERT: A 333 LYS cc_start: 0.8181 (tptt) cc_final: 0.7955 (tptp) REVERT: A 456 TYR cc_start: 0.7962 (t80) cc_final: 0.7730 (t80) REVERT: A 539 GLN cc_start: 0.7639 (tp40) cc_final: 0.6838 (mm-40) REVERT: A 593 GLN cc_start: 0.8251 (tp40) cc_final: 0.8050 (tp-100) REVERT: A 647 MET cc_start: 0.8364 (tpt) cc_final: 0.8103 (tpt) REVERT: A 754 ASP cc_start: 0.8827 (m-30) cc_final: 0.8441 (p0) REVERT: A 755 MET cc_start: 0.8885 (tpp) cc_final: 0.8421 (tpp) REVERT: A 1147 ARG cc_start: 0.8099 (tpt90) cc_final: 0.7774 (mtp85) REVERT: A 1154 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8186 (tp30) REVERT: A 1199 MET cc_start: 0.8386 (mmt) cc_final: 0.7961 (mmt) REVERT: A 1200 MET cc_start: 0.7988 (mmt) cc_final: 0.7628 (tpp) REVERT: A 1228 TYR cc_start: 0.7509 (m-80) cc_final: 0.7155 (m-80) REVERT: A 1251 MET cc_start: 0.8976 (mmt) cc_final: 0.8595 (mmp) REVERT: A 1276 TYR cc_start: 0.8130 (m-80) cc_final: 0.7875 (m-80) REVERT: A 1294 MET cc_start: 0.7497 (ttp) cc_final: 0.7045 (ttt) REVERT: A 1311 GLU cc_start: 0.7767 (tp30) cc_final: 0.7473 (tp30) REVERT: A 1312 ARG cc_start: 0.8029 (ttt90) cc_final: 0.7743 (mtp85) REVERT: A 1388 ARG cc_start: 0.8340 (mmt90) cc_final: 0.7891 (ttm110) REVERT: A 1512 HIS cc_start: 0.7112 (m170) cc_final: 0.6772 (m-70) REVERT: A 1793 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7840 (mp0) REVERT: B 26 LEU cc_start: 0.6186 (mp) cc_final: 0.5788 (mp) REVERT: B 43 GLU cc_start: 0.8939 (tt0) cc_final: 0.8621 (tp30) outliers start: 34 outliers final: 21 residues processed: 231 average time/residue: 0.2223 time to fit residues: 75.1435 Evaluate side-chains 217 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1409 ASN Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 0.0370 chunk 125 optimal weight: 0.0040 chunk 35 optimal weight: 0.7980 overall best weight: 0.7472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN A1409 ASN A1416 HIS A1504 ASN ** A1530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11725 Z= 0.153 Angle : 0.593 11.145 15832 Z= 0.294 Chirality : 0.039 0.187 1819 Planarity : 0.003 0.048 2001 Dihedral : 3.921 18.224 1557 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.73 % Allowed : 20.90 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1426 helix: 1.81 (0.19), residues: 807 sheet: -0.68 (0.56), residues: 84 loop : -2.74 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1549 HIS 0.007 0.001 HIS A1408 PHE 0.032 0.001 PHE A1214 TYR 0.015 0.001 TYR A1125 ARG 0.002 0.000 ARG A1118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7377 (m-40) cc_final: 0.6949 (m-40) REVERT: A 185 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6316 (mmt-90) REVERT: A 295 SER cc_start: 0.8340 (t) cc_final: 0.7697 (p) REVERT: A 329 LEU cc_start: 0.8807 (mt) cc_final: 0.8295 (mt) REVERT: A 510 MET cc_start: 0.7985 (tpt) cc_final: 0.7769 (tpt) REVERT: A 539 GLN cc_start: 0.7529 (tp40) cc_final: 0.6682 (mm-40) REVERT: A 593 GLN cc_start: 0.8057 (tp40) cc_final: 0.7857 (tp-100) REVERT: A 647 MET cc_start: 0.8284 (tpt) cc_final: 0.8028 (tpt) REVERT: A 665 GLU cc_start: 0.8436 (pt0) cc_final: 0.7831 (pt0) REVERT: A 755 MET cc_start: 0.8896 (tpp) cc_final: 0.8613 (tpp) REVERT: A 1094 MET cc_start: 0.6853 (tpt) cc_final: 0.6173 (ppp) REVERT: A 1147 ARG cc_start: 0.8000 (tpt90) cc_final: 0.7726 (mtp85) REVERT: A 1150 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7734 (tp30) REVERT: A 1154 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8123 (tp30) REVERT: A 1191 MET cc_start: 0.7794 (mtp) cc_final: 0.7488 (mpp) REVERT: A 1199 MET cc_start: 0.8505 (mmt) cc_final: 0.8091 (mmt) REVERT: A 1209 LEU cc_start: 0.9212 (tt) cc_final: 0.8976 (tt) REVERT: A 1228 TYR cc_start: 0.7477 (m-80) cc_final: 0.7104 (m-80) REVERT: A 1276 TYR cc_start: 0.8158 (m-80) cc_final: 0.7808 (m-80) REVERT: A 1294 MET cc_start: 0.7432 (ttp) cc_final: 0.6949 (ttt) REVERT: A 1301 ASN cc_start: 0.8875 (m-40) cc_final: 0.7855 (t0) REVERT: A 1312 ARG cc_start: 0.7990 (ttt90) cc_final: 0.7674 (mtp85) REVERT: A 1512 HIS cc_start: 0.7060 (m170) cc_final: 0.6730 (m-70) REVERT: A 1524 HIS cc_start: 0.8745 (m-70) cc_final: 0.8300 (m-70) REVERT: A 1654 ILE cc_start: 0.5822 (OUTLIER) cc_final: 0.5473 (pt) REVERT: A 1793 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7807 (mp0) REVERT: B 26 LEU cc_start: 0.6143 (mp) cc_final: 0.5662 (mp) REVERT: B 43 GLU cc_start: 0.8925 (tt0) cc_final: 0.8614 (tp30) REVERT: B 48 TYR cc_start: 0.8402 (m-10) cc_final: 0.8096 (m-10) REVERT: B 69 MET cc_start: 0.8554 (tpp) cc_final: 0.8324 (mmm) outliers start: 22 outliers final: 12 residues processed: 223 average time/residue: 0.2306 time to fit residues: 77.3092 Evaluate side-chains 209 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11725 Z= 0.183 Angle : 0.626 14.672 15832 Z= 0.304 Chirality : 0.040 0.183 1819 Planarity : 0.003 0.048 2001 Dihedral : 3.958 19.261 1557 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.36 % Allowed : 21.60 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1426 helix: 1.85 (0.19), residues: 801 sheet: -0.62 (0.56), residues: 84 loop : -2.66 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1666 HIS 0.005 0.001 HIS A 213 PHE 0.033 0.001 PHE A1274 TYR 0.015 0.001 TYR A1125 ARG 0.002 0.000 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7439 (m-40) cc_final: 0.7011 (m-40) REVERT: A 185 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6383 (mmt-90) REVERT: A 295 SER cc_start: 0.8389 (t) cc_final: 0.7665 (p) REVERT: A 329 LEU cc_start: 0.8880 (mt) cc_final: 0.8345 (mt) REVERT: A 497 GLU cc_start: 0.7581 (tp30) cc_final: 0.7341 (tp30) REVERT: A 539 GLN cc_start: 0.7535 (tp40) cc_final: 0.6750 (mm-40) REVERT: A 647 MET cc_start: 0.8358 (tpt) cc_final: 0.8084 (tpt) REVERT: A 665 GLU cc_start: 0.8466 (pt0) cc_final: 0.8145 (pt0) REVERT: A 755 MET cc_start: 0.8895 (tpp) cc_final: 0.8664 (tpp) REVERT: A 1094 MET cc_start: 0.6711 (tpt) cc_final: 0.6155 (ppp) REVERT: A 1147 ARG cc_start: 0.7937 (tpt90) cc_final: 0.7697 (mtp85) REVERT: A 1154 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8258 (tp30) REVERT: A 1191 MET cc_start: 0.7815 (mtp) cc_final: 0.7546 (mpp) REVERT: A 1199 MET cc_start: 0.8433 (mmt) cc_final: 0.8036 (mmt) REVERT: A 1209 LEU cc_start: 0.9281 (tt) cc_final: 0.9052 (tt) REVERT: A 1228 TYR cc_start: 0.7478 (m-80) cc_final: 0.7251 (m-80) REVERT: A 1276 TYR cc_start: 0.8137 (m-80) cc_final: 0.7829 (m-80) REVERT: A 1294 MET cc_start: 0.7525 (ttp) cc_final: 0.6968 (ttt) REVERT: A 1311 GLU cc_start: 0.7585 (tp30) cc_final: 0.7335 (tp30) REVERT: A 1312 ARG cc_start: 0.8029 (ttt90) cc_final: 0.7705 (mtp85) REVERT: A 1524 HIS cc_start: 0.8751 (m-70) cc_final: 0.8338 (m-70) REVERT: A 1793 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7851 (mp0) REVERT: B 26 LEU cc_start: 0.6136 (mp) cc_final: 0.5661 (mp) REVERT: B 43 GLU cc_start: 0.8929 (tt0) cc_final: 0.8618 (tp30) REVERT: B 69 MET cc_start: 0.8589 (tpp) cc_final: 0.8332 (mmm) outliers start: 30 outliers final: 21 residues processed: 220 average time/residue: 0.2090 time to fit residues: 69.0654 Evaluate side-chains 215 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN A1504 ASN ** A1530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11725 Z= 0.149 Angle : 0.616 13.894 15832 Z= 0.297 Chirality : 0.039 0.177 1819 Planarity : 0.003 0.047 2001 Dihedral : 3.880 17.656 1557 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.96 % Allowed : 22.31 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1426 helix: 1.89 (0.19), residues: 801 sheet: -0.47 (0.58), residues: 84 loop : -2.59 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1666 HIS 0.005 0.001 HIS A 213 PHE 0.027 0.001 PHE A1214 TYR 0.016 0.001 TYR A1125 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7354 (m-40) cc_final: 0.6940 (m-40) REVERT: A 185 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6372 (mmt-90) REVERT: A 192 MET cc_start: 0.6497 (mmm) cc_final: 0.6287 (mmm) REVERT: A 295 SER cc_start: 0.8418 (t) cc_final: 0.7781 (p) REVERT: A 329 LEU cc_start: 0.8877 (mt) cc_final: 0.8241 (mt) REVERT: A 539 GLN cc_start: 0.7498 (tp40) cc_final: 0.6758 (mm-40) REVERT: A 593 GLN cc_start: 0.8075 (tp40) cc_final: 0.7853 (tp-100) REVERT: A 647 MET cc_start: 0.8304 (tpt) cc_final: 0.8066 (tpt) REVERT: A 664 GLU cc_start: 0.7928 (tp30) cc_final: 0.7726 (tp30) REVERT: A 665 GLU cc_start: 0.8518 (pt0) cc_final: 0.8205 (pt0) REVERT: A 755 MET cc_start: 0.8880 (tpp) cc_final: 0.8587 (tpp) REVERT: A 1094 MET cc_start: 0.6731 (tpt) cc_final: 0.6209 (ppp) REVERT: A 1147 ARG cc_start: 0.7915 (tpt90) cc_final: 0.7662 (mtp85) REVERT: A 1154 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8224 (tp30) REVERT: A 1199 MET cc_start: 0.8338 (mmt) cc_final: 0.7930 (mmt) REVERT: A 1228 TYR cc_start: 0.7457 (m-80) cc_final: 0.7202 (m-80) REVERT: A 1276 TYR cc_start: 0.8158 (m-80) cc_final: 0.7806 (m-80) REVERT: A 1294 MET cc_start: 0.7550 (ttp) cc_final: 0.7299 (ttt) REVERT: A 1312 ARG cc_start: 0.8022 (ttt90) cc_final: 0.7709 (mtp85) REVERT: A 1524 HIS cc_start: 0.8742 (m-70) cc_final: 0.8288 (m-70) REVERT: A 1793 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7817 (mp0) outliers start: 25 outliers final: 16 residues processed: 225 average time/residue: 0.2219 time to fit residues: 74.3250 Evaluate side-chains 216 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Chi-restraints excluded: chain B residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN A1530 ASN B 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11725 Z= 0.176 Angle : 0.656 14.086 15832 Z= 0.315 Chirality : 0.040 0.190 1819 Planarity : 0.003 0.047 2001 Dihedral : 3.901 17.346 1557 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.81 % Allowed : 22.94 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1426 helix: 1.92 (0.19), residues: 794 sheet: -0.49 (0.56), residues: 90 loop : -2.58 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1666 HIS 0.004 0.001 HIS A 213 PHE 0.020 0.001 PHE A1274 TYR 0.015 0.001 TYR A1125 ARG 0.005 0.000 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7364 (m-40) cc_final: 0.6956 (m-40) REVERT: A 185 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6363 (mmt-90) REVERT: A 295 SER cc_start: 0.8341 (t) cc_final: 0.7673 (p) REVERT: A 329 LEU cc_start: 0.8907 (mt) cc_final: 0.8296 (mt) REVERT: A 497 GLU cc_start: 0.7569 (tp30) cc_final: 0.7318 (tp30) REVERT: A 510 MET cc_start: 0.7946 (tpt) cc_final: 0.7649 (tpt) REVERT: A 539 GLN cc_start: 0.7765 (tp40) cc_final: 0.7006 (mm-40) REVERT: A 593 GLN cc_start: 0.8055 (tp40) cc_final: 0.7807 (tp-100) REVERT: A 647 MET cc_start: 0.8347 (tpt) cc_final: 0.8077 (tpt) REVERT: A 665 GLU cc_start: 0.8631 (pt0) cc_final: 0.8318 (pt0) REVERT: A 707 MET cc_start: 0.8579 (mtt) cc_final: 0.7931 (mtt) REVERT: A 755 MET cc_start: 0.8885 (tpp) cc_final: 0.8667 (tpp) REVERT: A 1094 MET cc_start: 0.6712 (tpt) cc_final: 0.6212 (ppp) REVERT: A 1147 ARG cc_start: 0.7836 (tpt90) cc_final: 0.7600 (mtp85) REVERT: A 1154 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8255 (tp30) REVERT: A 1199 MET cc_start: 0.8473 (mmt) cc_final: 0.8056 (mmt) REVERT: A 1228 TYR cc_start: 0.7461 (m-80) cc_final: 0.7220 (m-80) REVERT: A 1276 TYR cc_start: 0.8156 (m-80) cc_final: 0.7827 (m-80) REVERT: A 1294 MET cc_start: 0.7610 (ttp) cc_final: 0.7403 (ttt) REVERT: A 1311 GLU cc_start: 0.7711 (tp30) cc_final: 0.7406 (tp30) REVERT: A 1312 ARG cc_start: 0.8041 (ttt90) cc_final: 0.7720 (mtp85) REVERT: A 1366 ASP cc_start: 0.7901 (t0) cc_final: 0.7700 (t0) REVERT: A 1388 ARG cc_start: 0.8388 (mmt90) cc_final: 0.7909 (ttm110) REVERT: A 1524 HIS cc_start: 0.8802 (m-70) cc_final: 0.8339 (m-70) REVERT: A 1793 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7840 (mp0) REVERT: B 43 GLU cc_start: 0.9037 (tt0) cc_final: 0.8707 (tp30) outliers start: 23 outliers final: 19 residues processed: 222 average time/residue: 0.2273 time to fit residues: 76.2484 Evaluate side-chains 216 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 133 optimal weight: 0.0050 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN B 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11725 Z= 0.190 Angle : 0.653 13.355 15832 Z= 0.317 Chirality : 0.040 0.180 1819 Planarity : 0.003 0.046 2001 Dihedral : 3.938 18.327 1557 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.96 % Allowed : 23.64 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1426 helix: 1.89 (0.19), residues: 794 sheet: -0.46 (0.58), residues: 85 loop : -2.55 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1235 HIS 0.004 0.001 HIS A 213 PHE 0.029 0.001 PHE A1214 TYR 0.016 0.001 TYR A1125 ARG 0.005 0.000 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7382 (m-40) cc_final: 0.6971 (m-40) REVERT: A 185 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6356 (mmt-90) REVERT: A 295 SER cc_start: 0.8346 (t) cc_final: 0.7673 (p) REVERT: A 329 LEU cc_start: 0.8951 (mt) cc_final: 0.8433 (mt) REVERT: A 539 GLN cc_start: 0.7579 (tp40) cc_final: 0.6851 (mm-40) REVERT: A 593 GLN cc_start: 0.8053 (tp40) cc_final: 0.7832 (tp-100) REVERT: A 647 MET cc_start: 0.8358 (tpt) cc_final: 0.8089 (tpt) REVERT: A 707 MET cc_start: 0.8630 (mtt) cc_final: 0.8108 (mtt) REVERT: A 755 MET cc_start: 0.8917 (tpp) cc_final: 0.8694 (tpp) REVERT: A 1094 MET cc_start: 0.6593 (tpt) cc_final: 0.6191 (ppp) REVERT: A 1147 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7611 (mtp85) REVERT: A 1154 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8348 (tp30) REVERT: A 1199 MET cc_start: 0.8469 (mmt) cc_final: 0.8057 (mmt) REVERT: A 1228 TYR cc_start: 0.7466 (m-80) cc_final: 0.7218 (m-80) REVERT: A 1274 PHE cc_start: 0.9220 (t80) cc_final: 0.8951 (t80) REVERT: A 1275 PHE cc_start: 0.9341 (m-80) cc_final: 0.9049 (m-80) REVERT: A 1276 TYR cc_start: 0.8201 (m-80) cc_final: 0.7854 (m-80) REVERT: A 1294 MET cc_start: 0.7604 (ttp) cc_final: 0.7398 (ttt) REVERT: A 1311 GLU cc_start: 0.7738 (tp30) cc_final: 0.7443 (tp30) REVERT: A 1312 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7728 (mtp85) REVERT: A 1388 ARG cc_start: 0.8399 (mmt90) cc_final: 0.7884 (ttm110) REVERT: A 1524 HIS cc_start: 0.8808 (m-70) cc_final: 0.8319 (m-70) REVERT: A 1793 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7842 (mp0) REVERT: B 43 GLU cc_start: 0.9062 (tt0) cc_final: 0.8727 (tp30) REVERT: B 48 TYR cc_start: 0.8515 (m-10) cc_final: 0.8243 (m-10) outliers start: 25 outliers final: 21 residues processed: 210 average time/residue: 0.2282 time to fit residues: 72.6899 Evaluate side-chains 213 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 144 optimal weight: 7.9990 chunk 132 optimal weight: 0.2980 chunk 115 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN B 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11725 Z= 0.163 Angle : 0.693 13.086 15832 Z= 0.329 Chirality : 0.040 0.287 1819 Planarity : 0.003 0.048 2001 Dihedral : 3.877 18.968 1557 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.26 % Allowed : 24.74 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1426 helix: 2.03 (0.19), residues: 794 sheet: -0.35 (0.59), residues: 83 loop : -2.48 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1549 HIS 0.004 0.000 HIS A 213 PHE 0.021 0.001 PHE A1245 TYR 0.016 0.001 TYR A1125 ARG 0.005 0.000 ARG A 435 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7376 (m-40) cc_final: 0.6965 (m-40) REVERT: A 185 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6263 (mmt-90) REVERT: A 295 SER cc_start: 0.8325 (t) cc_final: 0.7682 (p) REVERT: A 329 LEU cc_start: 0.8938 (mt) cc_final: 0.8407 (mt) REVERT: A 435 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8392 (ptm-80) REVERT: A 539 GLN cc_start: 0.7538 (tp40) cc_final: 0.6812 (mm-40) REVERT: A 593 GLN cc_start: 0.7977 (tp40) cc_final: 0.7733 (tp-100) REVERT: A 647 MET cc_start: 0.8292 (tpt) cc_final: 0.8031 (tpt) REVERT: A 707 MET cc_start: 0.8682 (mtt) cc_final: 0.8106 (mtt) REVERT: A 755 MET cc_start: 0.8887 (tpp) cc_final: 0.8628 (tpp) REVERT: A 1094 MET cc_start: 0.6588 (tpt) cc_final: 0.6208 (ppp) REVERT: A 1147 ARG cc_start: 0.7809 (tpt90) cc_final: 0.7518 (mtp85) REVERT: A 1154 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8347 (tp30) REVERT: A 1199 MET cc_start: 0.8466 (mmt) cc_final: 0.8075 (mmt) REVERT: A 1228 TYR cc_start: 0.7415 (m-80) cc_final: 0.7200 (m-80) REVERT: A 1240 MET cc_start: 0.7366 (mpt) cc_final: 0.6852 (mtt) REVERT: A 1274 PHE cc_start: 0.9172 (t80) cc_final: 0.8962 (t80) REVERT: A 1275 PHE cc_start: 0.9339 (m-80) cc_final: 0.9015 (m-80) REVERT: A 1276 TYR cc_start: 0.8195 (m-80) cc_final: 0.7850 (m-80) REVERT: A 1312 ARG cc_start: 0.8013 (ttt90) cc_final: 0.7717 (mtp85) REVERT: A 1524 HIS cc_start: 0.8775 (m-70) cc_final: 0.8287 (m-70) REVERT: A 1663 VAL cc_start: 0.7926 (t) cc_final: 0.7408 (t) REVERT: A 1793 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7818 (mp0) REVERT: B 43 GLU cc_start: 0.9059 (tt0) cc_final: 0.8726 (tp30) REVERT: B 48 TYR cc_start: 0.8521 (m-10) cc_final: 0.8258 (m-10) REVERT: B 68 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8685 (mtmm) REVERT: B 69 MET cc_start: 0.8407 (tpt) cc_final: 0.7984 (tpp) outliers start: 16 outliers final: 14 residues processed: 215 average time/residue: 0.2145 time to fit residues: 68.3005 Evaluate side-chains 214 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1475 ASN Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN A1335 GLN A1504 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.148968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105567 restraints weight = 22373.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105620 restraints weight = 12398.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106649 restraints weight = 10027.443| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11725 Z= 0.198 Angle : 0.697 12.670 15832 Z= 0.334 Chirality : 0.041 0.293 1819 Planarity : 0.004 0.046 2001 Dihedral : 3.917 19.814 1557 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.73 % Allowed : 24.51 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1426 helix: 1.99 (0.19), residues: 794 sheet: -0.51 (0.53), residues: 93 loop : -2.48 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1688 HIS 0.002 0.001 HIS A1361 PHE 0.032 0.001 PHE A1214 TYR 0.061 0.002 TYR A1152 ARG 0.004 0.000 ARG A 435 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.05 seconds wall clock time: 46 minutes 20.51 seconds (2780.51 seconds total)