Starting phenix.real_space_refine on Sun Mar 17 01:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vpc_21308/03_2024/6vpc_21308_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 154 5.49 5 Mg 3 5.21 5 S 44 5.16 5 C 9806 2.51 5 N 2880 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 664": "NH1" <-> "NH2" Residue "B TYR 1210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1257": "NH1" <-> "NH2" Residue "B GLU 1347": "OE1" <-> "OE2" Residue "B TYR 1439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16309 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1724 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 40, 'rna3p_pyr': 33} Link IDs: {'rna2p': 7, 'rna3p': 73} Chain: "B" Number of atoms: 10766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1332, 10766 Classifications: {'peptide': 1332} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 35, 'TRANS': 1296} Chain breaks: 3 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 824 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "D" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 659 Classifications: {'DNA': 32, 'RNA': 1} Modifications used: {'rna2p': 1} Link IDs: {'rna2p': 1, 'rna3p': 31} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC:plan2': 1, ' DC:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1131 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "F" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1200 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14640 SG CYS E 87 61.313 28.543 137.297 1.00181.35 S ATOM 14661 SG CYS E 90 64.230 28.752 136.279 1.00186.75 S ATOM 15771 SG CYS F 87 60.016 41.060 133.993 1.00183.68 S ATOM 15792 SG CYS F 90 60.736 41.779 137.525 1.00184.30 S Time building chain proxies: 9.35, per 1000 atoms: 0.57 Number of scatterers: 16309 At special positions: 0 Unit cell: (94.94, 124.08, 168.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 44 16.00 P 154 15.00 Mg 3 11.99 O 3420 8.00 N 2880 7.00 C 9806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.17 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 90 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 57 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 87 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 57 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 90 " 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 10 sheets defined 46.4% alpha, 8.5% beta 55 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 8.21 Creating SS restraints... Processing helix chain 'B' and resid 257 through 290 removed outlier: 5.045A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 332 through 341 Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 379 through 392 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 434 through 442 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 481 through 498 removed outlier: 4.801A pdb=" N ASP B 485 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 503 No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 513 through 539 Processing helix chain 'B' and resid 541 through 548 removed outlier: 4.470A pdb=" N LYS B 545 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 548 " --> pdb=" O LYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 Processing helix chain 'B' and resid 566 through 579 Proline residue: B 575 - end of helix Processing helix chain 'B' and resid 584 through 591 removed outlier: 3.822A pdb=" N VAL B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 606 No H-bonds generated for 'chain 'B' and resid 604 through 606' Processing helix chain 'B' and resid 609 through 623 Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 634 through 642 Processing helix chain 'B' and resid 675 through 678 No H-bonds generated for 'chain 'B' and resid 675 through 678' Processing helix chain 'B' and resid 681 through 690 Processing helix chain 'B' and resid 710 through 723 removed outlier: 4.419A pdb=" N LYS B 723 " --> pdb=" O ASN B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 748 Processing helix chain 'B' and resid 758 through 764 Processing helix chain 'B' and resid 766 through 770 Processing helix chain 'B' and resid 789 through 798 Processing helix chain 'B' and resid 801 through 805 Processing helix chain 'B' and resid 807 through 822 removed outlier: 4.580A pdb=" N ASP B 811 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 838 removed outlier: 4.804A pdb=" N THR B 835 " --> pdb=" O GLU B 831 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR B 836 " --> pdb=" O ARG B 832 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N HIS B 838 " --> pdb=" O LYS B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 850 removed outlier: 3.942A pdb=" N ARG B 850 " --> pdb=" O LYS B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 865 Processing helix chain 'B' and resid 876 through 881 Processing helix chain 'B' and resid 890 through 895 Processing helix chain 'B' and resid 901 through 906 Processing helix chain 'B' and resid 917 through 923 Processing helix chain 'B' and resid 928 through 947 Processing helix chain 'B' and resid 974 through 988 Processing helix chain 'B' and resid 992 through 995 No H-bonds generated for 'chain 'B' and resid 992 through 995' Processing helix chain 'B' and resid 1000 through 1002 No H-bonds generated for 'chain 'B' and resid 1000 through 1002' Processing helix chain 'B' and resid 1006 through 1013 Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'B' and resid 1049 through 1051 No H-bonds generated for 'chain 'B' and resid 1049 through 1051' Processing helix chain 'B' and resid 1058 through 1061 Processing helix chain 'B' and resid 1070 through 1085 removed outlier: 5.449A pdb=" N ASN B1078 " --> pdb=" O LYS B1074 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR B1079 " --> pdb=" O LYS B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1101 Processing helix chain 'B' and resid 1123 through 1136 Processing helix chain 'B' and resid 1157 through 1167 Processing helix chain 'B' and resid 1178 through 1197 removed outlier: 3.599A pdb=" N ALA B1184 " --> pdb=" O HIS B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1199 through 1205 removed outlier: 3.787A pdb=" N SER B1203 " --> pdb=" O LYS B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1219 No H-bonds generated for 'chain 'B' and resid 1217 through 1219' Processing helix chain 'B' and resid 1228 through 1243 removed outlier: 3.702A pdb=" N MET B1240 " --> pdb=" O TYR B1236 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN B1241 " --> pdb=" O SER B1237 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE B1242 " --> pdb=" O ASN B1238 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE B1243 " --> pdb=" O ILE B1239 " (cutoff:3.500A) Processing helix chain 'B' and resid 1276 through 1284 Processing helix chain 'B' and resid 1325 through 1328 No H-bonds generated for 'chain 'B' and resid 1325 through 1328' Processing helix chain 'B' and resid 1365 through 1373 removed outlier: 4.777A pdb=" N SER B1369 " --> pdb=" O ILE B1365 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER B1370 " --> pdb=" O MET B1366 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1382 Processing helix chain 'B' and resid 1389 through 1391 No H-bonds generated for 'chain 'B' and resid 1389 through 1391' Processing helix chain 'B' and resid 1404 through 1406 No H-bonds generated for 'chain 'B' and resid 1404 through 1406' Processing helix chain 'B' and resid 1427 through 1437 Processing helix chain 'B' and resid 1446 through 1458 Processing helix chain 'B' and resid 1460 through 1476 Processing helix chain 'B' and resid 1481 through 1493 Processing helix chain 'B' and resid 1499 through 1512 removed outlier: 3.621A pdb=" N PHE B1510 " --> pdb=" O ILE B1506 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B1511 " --> pdb=" O ILE B1507 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B1512 " --> pdb=" O HIS B1508 " (cutoff:3.500A) Processing helix chain 'B' and resid 1538 through 1541 Processing helix chain 'E' and resid 8 through 24 Processing helix chain 'E' and resid 48 through 51 No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 58 through 70 Processing helix chain 'E' and resid 88 through 97 Processing helix chain 'E' and resid 138 through 148 Processing helix chain 'F' and resid 8 through 24 Processing helix chain 'F' and resid 48 through 51 No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 58 through 70 Processing helix chain 'F' and resid 88 through 97 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 154 through 159 Processing sheet with id= A, first strand: chain 'B' and resid 1151 through 1155 removed outlier: 4.333A pdb=" N MET B 960 " --> pdb=" O LEU B1155 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N TYR B 202 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N VAL B 957 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 204 " --> pdb=" O VAL B 957 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLU B 959 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 206 " --> pdb=" O GLU B 959 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1290 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 249 " --> pdb=" O ASN B1290 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B1292 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 226 through 230 Processing sheet with id= C, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.586A pdb=" N GLU B1554 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B1400 " --> pdb=" O ILE B1545 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 1034 through 1037 Processing sheet with id= E, first strand: chain 'B' and resid 1246 through 1249 removed outlier: 3.985A pdb=" N GLU B1253 " --> pdb=" O LEU B1249 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1393 through 1395 removed outlier: 3.640A pdb=" N ILE B1393 " --> pdb=" O LEU B1341 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE B1363 " --> pdb=" O ALA B1337 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER B1339 " --> pdb=" O LEU B1361 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B1361 " --> pdb=" O SER B1339 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU B1341 " --> pdb=" O GLU B1359 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B1359 " --> pdb=" O LEU B1341 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL B1343 " --> pdb=" O VAL B1357 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B1357 " --> pdb=" O VAL B1343 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B1345 " --> pdb=" O LYS B1355 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B1355 " --> pdb=" O LYS B1345 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU B1347 " --> pdb=" O LYS B1353 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS B1353 " --> pdb=" O GLU B1347 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1521 through 1523 Processing sheet with id= H, first strand: chain 'B' and resid 1260 through 1262 Processing sheet with id= I, first strand: chain 'E' and resid 131 through 133 removed outlier: 6.398A pdb=" N LEU E 36 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 131 through 133 removed outlier: 6.302A pdb=" N LEU F 36 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 9.12 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4484 1.34 - 1.46: 3647 1.46 - 1.58: 8413 1.58 - 1.70: 304 1.70 - 1.82: 78 Bond restraints: 16926 Sorted by residual: bond pdb=" C2 8AZ D 26 " pdb=" N3 8AZ D 26 " ideal model delta sigma weight residual 1.504 1.466 0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C5 8AZ D 26 " pdb=" C4 8AZ D 26 " ideal model delta sigma weight residual 1.414 1.386 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C3' DA C 4 " pdb=" O3' DA C 4 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" N9 8AZ D 26 " pdb=" N8 8AZ D 26 " ideal model delta sigma weight residual 1.385 1.361 0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" CA ALA B 496 " pdb=" C ALA B 496 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.38e-02 5.25e+03 1.05e+00 ... (remaining 16921 not shown) Histogram of bond angle deviations from ideal: 99.88 - 107.37: 1299 107.37 - 114.85: 10219 114.85 - 122.34: 9380 122.34 - 129.82: 2477 129.82 - 137.30: 148 Bond angle restraints: 23523 Sorted by residual: angle pdb=" C LEU B 839 " pdb=" N PHE B 840 " pdb=" CA PHE B 840 " ideal model delta sigma weight residual 122.46 114.02 8.44 1.80e+00 3.09e-01 2.20e+01 angle pdb=" C GLU B 781 " pdb=" N ASP B 782 " pdb=" CA ASP B 782 " ideal model delta sigma weight residual 125.02 132.21 -7.19 1.76e+00 3.23e-01 1.67e+01 angle pdb=" C1' 8AZ D 26 " pdb=" N9 8AZ D 26 " pdb=" N8 8AZ D 26 " ideal model delta sigma weight residual 123.98 111.80 12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C1' 8AZ D 26 " pdb=" N9 8AZ D 26 " pdb=" C4 8AZ D 26 " ideal model delta sigma weight residual 126.25 137.30 -11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N GLY F 135 " pdb=" CA GLY F 135 " pdb=" C GLY F 135 " ideal model delta sigma weight residual 115.08 120.66 -5.58 1.54e+00 4.22e-01 1.31e+01 ... (remaining 23518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 9523 34.88 - 69.76: 565 69.76 - 104.65: 37 104.65 - 139.53: 1 139.53 - 174.41: 3 Dihedral angle restraints: 10129 sinusoidal: 5347 harmonic: 4782 Sorted by residual: dihedral pdb=" CA SER F 109 " pdb=" C SER F 109 " pdb=" N LYS F 110 " pdb=" CA LYS F 110 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" C4' DC C 30 " pdb=" C3' DC C 30 " pdb=" O3' DC C 30 " pdb=" P DA C 31 " ideal model delta sinusoidal sigma weight residual -140.00 34.41 -174.41 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA C 4 " pdb=" C3' DA C 4 " pdb=" O3' DA C 4 " pdb=" P DT C 5 " ideal model delta sinusoidal sigma weight residual 220.00 54.65 165.35 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 10126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2091 0.037 - 0.073: 430 0.073 - 0.110: 121 0.110 - 0.146: 42 0.146 - 0.183: 2 Chirality restraints: 2686 Sorted by residual: chirality pdb=" C3' U A 9 " pdb=" C4' U A 9 " pdb=" O3' U A 9 " pdb=" C2' U A 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA ILE B 777 " pdb=" N ILE B 777 " pdb=" C ILE B 777 " pdb=" CB ILE B 777 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA PRO B 700 " pdb=" N PRO B 700 " pdb=" C PRO B 700 " pdb=" CB PRO B 700 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 2683 not shown) Planarity restraints: 2463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 495 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ASP B 495 " -0.077 2.00e-02 2.50e+03 pdb=" O ASP B 495 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA B 496 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1202 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C GLU B1202 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU B1202 " 0.023 2.00e-02 2.50e+03 pdb=" N SER B1203 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 814 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C GLU B 814 " -0.059 2.00e-02 2.50e+03 pdb=" O GLU B 814 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP B 815 " 0.020 2.00e-02 2.50e+03 ... (remaining 2460 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 393 2.68 - 3.23: 14921 3.23 - 3.79: 25611 3.79 - 4.34: 35041 4.34 - 4.90: 53815 Nonbonded interactions: 129781 Sorted by model distance: nonbonded pdb=" O6 8AZ D 26 " pdb="ZN ZN F 201 " model vdw 2.121 2.230 nonbonded pdb=" OP1 C A 6 " pdb=" OH TYR B 712 " model vdw 2.229 2.440 nonbonded pdb=" OH TYR B1439 " pdb=" OE1 GLN B1453 " model vdw 2.254 2.440 nonbonded pdb=" O2' U A 9 " pdb=" OP1 U A 10 " model vdw 2.256 2.440 nonbonded pdb=" OD1 ASP B1464 " pdb=" OH TYR B1491 " model vdw 2.263 2.440 ... (remaining 129776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 5 through 149 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.320 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 55.580 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 0.042 16926 Z= 0.132 Angle : 0.563 12.180 23523 Z= 0.350 Chirality : 0.036 0.183 2686 Planarity : 0.004 0.045 2463 Dihedral : 18.508 174.412 7039 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 8.75 % Favored : 89.68 % 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: -1.99 (0.18), residues: 1621 helix: -1.20 (0.15), residues: 796 sheet: -1.09 (0.41), residues: 145 loop : -1.33 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1323 HIS 0.003 0.001 HIS B 895 PHE 0.017 0.001 PHE B1234 TYR 0.014 0.001 TYR F 10 ARG 0.006 0.001 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 303 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 379 ASP cc_start: 0.6544 (m-30) cc_final: 0.6255 (p0) REVERT: B 766 PHE cc_start: 0.8509 (m-80) cc_final: 0.7946 (m-80) REVERT: B 846 LYS cc_start: 0.8413 (tttp) cc_final: 0.8186 (mtpp) REVERT: B 890 PHE cc_start: 0.7343 (t80) cc_final: 0.7106 (t80) REVERT: B 900 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7433 (t) REVERT: E 96 HIS cc_start: 0.6189 (m-70) cc_final: 0.5637 (m-70) REVERT: F 10 TYR cc_start: 0.9221 (t80) cc_final: 0.8925 (t80) outliers start: 22 outliers final: 4 residues processed: 321 average time/residue: 0.3731 time to fit residues: 162.5189 Evaluate side-chains 158 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 1539 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN B 452 ASN B 462 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 760 GLN B 895 HIS B1005 ASN ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 ASN B1180 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 128 HIS F 46 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16926 Z= 0.263 Angle : 0.570 11.902 23523 Z= 0.306 Chirality : 0.039 0.195 2686 Planarity : 0.004 0.051 2463 Dihedral : 19.213 174.096 3791 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.23 % Allowed : 13.55 % Favored : 83.23 % 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 (0.20), residues: 1621 helix: 0.63 (0.18), residues: 779 sheet: -0.16 (0.40), residues: 161 loop : -0.86 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 45 HIS 0.008 0.001 HIS B 364 PHE 0.015 0.002 PHE B 643 TYR 0.021 0.002 TYR B1009 ARG 0.006 0.001 ARG B1281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 161 time to evaluate : 1.739 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: B 692 MET cc_start: 0.8047 (mtt) cc_final: 0.7813 (mtt) REVERT: B 731 MET cc_start: 0.3582 (ptt) cc_final: 0.2954 (pmm) REVERT: B 766 PHE cc_start: 0.8560 (m-80) cc_final: 0.8166 (m-80) REVERT: B 1196 LYS cc_start: 0.7999 (tttp) cc_final: 0.6965 (tttp) REVERT: F 53 ASP cc_start: 0.7929 (t0) cc_final: 0.7695 (t0) REVERT: F 68 LEU cc_start: 0.8927 (mt) cc_final: 0.8501 (pp) REVERT: F 84 PHE cc_start: 0.6193 (t80) cc_final: 0.5889 (t80) REVERT: F 89 MET cc_start: 0.8718 (ttp) cc_final: 0.7913 (ptm) REVERT: F 96 HIS cc_start: 0.6735 (m90) cc_final: 0.5256 (m90) outliers start: 45 outliers final: 24 residues processed: 195 average time/residue: 0.2943 time to fit residues: 84.5726 Evaluate side-chains 158 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1387 VAL Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1481 ASP Chi-restraints excluded: chain B residue 1536 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 50.0000 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 HIS B1014 GLN B1238 ASN E 57 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS E 127 ASN F 38 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16926 Z= 0.274 Angle : 0.565 11.973 23523 Z= 0.299 Chirality : 0.039 0.189 2686 Planarity : 0.004 0.039 2463 Dihedral : 19.310 173.535 3789 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.94 % Allowed : 13.98 % Favored : 83.08 % 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: 0.12 (0.20), residues: 1621 helix: 0.84 (0.18), residues: 776 sheet: 0.39 (0.44), residues: 144 loop : -0.79 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 45 HIS 0.012 0.001 HIS F 96 PHE 0.019 0.002 PHE F 6 TYR 0.026 0.002 TYR B1009 ARG 0.008 0.001 ARG B1495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 1.282 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: B 437 ASN cc_start: 0.6705 (OUTLIER) cc_final: 0.6439 (t0) REVERT: B 511 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8047 (mtpp) REVERT: B 692 MET cc_start: 0.8077 (mtt) cc_final: 0.7848 (mtt) REVERT: B 731 MET cc_start: 0.4097 (ptt) cc_final: 0.3576 (pmm) REVERT: B 766 PHE cc_start: 0.8578 (m-80) cc_final: 0.8310 (m-80) REVERT: B 1076 MET cc_start: 0.6588 (tpp) cc_final: 0.6219 (tpp) REVERT: B 1402 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: F 61 MET cc_start: 0.8320 (mmm) cc_final: 0.8034 (mmm) REVERT: F 68 LEU cc_start: 0.8927 (mt) cc_final: 0.8514 (pp) REVERT: F 89 MET cc_start: 0.8718 (ttp) cc_final: 0.7961 (ptm) outliers start: 41 outliers final: 25 residues processed: 167 average time/residue: 0.2935 time to fit residues: 72.3984 Evaluate side-chains 151 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 714 TYR Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1481 ASP Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 153 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 HIS B 760 GLN E 71 GLN E 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16926 Z= 0.201 Angle : 0.523 11.147 23523 Z= 0.279 Chirality : 0.038 0.220 2686 Planarity : 0.003 0.037 2463 Dihedral : 19.277 173.723 3789 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.94 % Allowed : 14.84 % Favored : 82.22 % 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: 0.29 (0.21), residues: 1621 helix: 0.99 (0.19), residues: 780 sheet: 0.50 (0.41), residues: 168 loop : -0.78 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1080 HIS 0.024 0.001 HIS E 57 PHE 0.021 0.001 PHE F 6 TYR 0.023 0.001 TYR B1009 ARG 0.009 0.000 ARG B1495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.6720 (OUTLIER) cc_final: 0.6421 (t0) REVERT: B 600 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8345 (mmt90) REVERT: B 692 MET cc_start: 0.8087 (mtt) cc_final: 0.7856 (mtt) REVERT: B 731 MET cc_start: 0.4289 (ptt) cc_final: 0.3718 (pmm) REVERT: B 766 PHE cc_start: 0.8612 (m-80) cc_final: 0.8348 (m-80) REVERT: B 824 GLU cc_start: 0.7733 (pp20) cc_final: 0.7302 (mm-30) REVERT: B 852 ARG cc_start: 0.7510 (ttm110) cc_final: 0.6847 (mmt-90) REVERT: B 1076 MET cc_start: 0.6585 (tpp) cc_final: 0.6205 (tpp) REVERT: B 1240 MET cc_start: 0.9091 (tpp) cc_final: 0.8820 (tpp) REVERT: B 1402 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: F 68 LEU cc_start: 0.8958 (mt) cc_final: 0.8583 (pp) REVERT: F 70 MET cc_start: 0.7477 (ptm) cc_final: 0.6721 (ppp) REVERT: F 89 MET cc_start: 0.8811 (ttp) cc_final: 0.8223 (ptm) outliers start: 41 outliers final: 27 residues processed: 161 average time/residue: 0.3143 time to fit residues: 77.0401 Evaluate side-chains 157 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 714 TYR Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1270 VAL Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 145 optimal weight: 30.0000 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 43 optimal weight: 0.0980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN E 71 GLN E 96 HIS ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16926 Z= 0.166 Angle : 0.517 14.910 23523 Z= 0.271 Chirality : 0.037 0.189 2686 Planarity : 0.003 0.041 2463 Dihedral : 19.239 173.866 3789 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.94 % Allowed : 14.91 % Favored : 82.15 % 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: 0.44 (0.21), residues: 1621 helix: 1.10 (0.19), residues: 781 sheet: 0.51 (0.41), residues: 170 loop : -0.69 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 215 HIS 0.018 0.001 HIS E 57 PHE 0.011 0.001 PHE F 84 TYR 0.015 0.001 TYR B1009 ARG 0.009 0.000 ARG B1495 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 1.586 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: B 437 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.6418 (t0) REVERT: B 692 MET cc_start: 0.8049 (mtt) cc_final: 0.7831 (mtt) REVERT: B 731 MET cc_start: 0.4468 (ptt) cc_final: 0.3888 (pmm) REVERT: B 766 PHE cc_start: 0.8564 (m-80) cc_final: 0.8308 (m-80) REVERT: B 824 GLU cc_start: 0.7854 (pp20) cc_final: 0.7418 (mm-30) REVERT: B 1019 MET cc_start: 0.4626 (mmp) cc_final: 0.4336 (tpp) REVERT: B 1402 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: F 6 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.6410 (t80) REVERT: F 61 MET cc_start: 0.9071 (mmp) cc_final: 0.8190 (mmm) outliers start: 41 outliers final: 25 residues processed: 159 average time/residue: 0.2724 time to fit residues: 66.2376 Evaluate side-chains 154 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1138 THR Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 33 optimal weight: 0.0050 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 40.0000 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16926 Z= 0.209 Angle : 0.539 16.413 23523 Z= 0.281 Chirality : 0.037 0.190 2686 Planarity : 0.003 0.042 2463 Dihedral : 19.298 173.901 3789 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.65 % Allowed : 14.98 % Favored : 82.37 % 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: 0.46 (0.21), residues: 1621 helix: 1.13 (0.19), residues: 779 sheet: 0.46 (0.41), residues: 170 loop : -0.66 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 215 HIS 0.011 0.001 HIS E 57 PHE 0.012 0.001 PHE B 643 TYR 0.014 0.001 TYR B1009 ARG 0.009 0.000 ARG B1495 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.6386 (t0) REVERT: B 600 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8385 (mmt90) REVERT: B 692 MET cc_start: 0.8073 (mtt) cc_final: 0.7864 (mtt) REVERT: B 731 MET cc_start: 0.4632 (ptt) cc_final: 0.4043 (pmm) REVERT: B 766 PHE cc_start: 0.8526 (m-80) cc_final: 0.8287 (m-80) REVERT: B 824 GLU cc_start: 0.7898 (pp20) cc_final: 0.7553 (mm-30) REVERT: B 1019 MET cc_start: 0.5022 (mmp) cc_final: 0.3189 (mmm) REVERT: B 1076 MET cc_start: 0.6203 (tpp) cc_final: 0.5306 (tpp) REVERT: B 1402 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7053 (tt0) REVERT: F 6 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.6379 (t80) REVERT: F 12 MET cc_start: 0.7940 (ttt) cc_final: 0.7418 (ptm) REVERT: F 61 MET cc_start: 0.9075 (mmp) cc_final: 0.8608 (mmm) REVERT: F 89 MET cc_start: 0.8856 (ptm) cc_final: 0.8534 (ptt) outliers start: 37 outliers final: 28 residues processed: 155 average time/residue: 0.2904 time to fit residues: 68.2283 Evaluate side-chains 155 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 714 TYR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 136 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.0970 chunk 19 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16926 Z= 0.159 Angle : 0.528 16.473 23523 Z= 0.273 Chirality : 0.037 0.189 2686 Planarity : 0.003 0.051 2463 Dihedral : 19.266 174.321 3787 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.65 % Allowed : 16.06 % Favored : 81.29 % 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: 0.50 (0.21), residues: 1621 helix: 1.14 (0.19), residues: 778 sheet: 0.51 (0.41), residues: 170 loop : -0.63 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 11 HIS 0.008 0.001 HIS E 57 PHE 0.010 0.001 PHE B1234 TYR 0.016 0.001 TYR B 483 ARG 0.012 0.000 ARG B1495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 731 MET cc_start: 0.5091 (ptt) cc_final: 0.4414 (pmm) REVERT: B 766 PHE cc_start: 0.8511 (m-80) cc_final: 0.8249 (m-80) REVERT: B 824 GLU cc_start: 0.7862 (pp20) cc_final: 0.7486 (mm-30) REVERT: B 1019 MET cc_start: 0.4997 (mmp) cc_final: 0.3328 (mmm) REVERT: B 1076 MET cc_start: 0.6447 (tpp) cc_final: 0.5547 (tpp) REVERT: B 1079 TYR cc_start: 0.7389 (t80) cc_final: 0.7161 (t80) REVERT: B 1402 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: F 6 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.6205 (t80) REVERT: F 61 MET cc_start: 0.9069 (mmp) cc_final: 0.8597 (mmm) outliers start: 37 outliers final: 25 residues processed: 152 average time/residue: 0.2655 time to fit residues: 61.8491 Evaluate side-chains 154 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 714 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 136 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS F 52 HIS ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16926 Z= 0.155 Angle : 0.518 13.585 23523 Z= 0.271 Chirality : 0.037 0.188 2686 Planarity : 0.003 0.053 2463 Dihedral : 19.259 174.540 3787 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.29 % Allowed : 16.06 % Favored : 81.65 % 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: 0.58 (0.21), residues: 1621 helix: 1.18 (0.19), residues: 778 sheet: 0.74 (0.40), residues: 181 loop : -0.61 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 11 HIS 0.005 0.001 HIS E 57 PHE 0.009 0.001 PHE B1234 TYR 0.016 0.001 TYR B 483 ARG 0.013 0.000 ARG B1495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 465 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8653 (mmmm) REVERT: B 731 MET cc_start: 0.5061 (ptt) cc_final: 0.4428 (pmm) REVERT: B 824 GLU cc_start: 0.7879 (pp20) cc_final: 0.7559 (mm-30) REVERT: B 948 MET cc_start: 0.8576 (mtp) cc_final: 0.8358 (mmm) REVERT: B 1019 MET cc_start: 0.5024 (mmp) cc_final: 0.3425 (mmm) REVERT: B 1076 MET cc_start: 0.6509 (tpp) cc_final: 0.5608 (tpp) REVERT: B 1079 TYR cc_start: 0.7399 (t80) cc_final: 0.7184 (t80) REVERT: B 1196 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8117 (ttpp) REVERT: B 1240 MET cc_start: 0.9200 (tpp) cc_final: 0.8911 (tpp) REVERT: B 1402 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: F 6 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6295 (t80) REVERT: F 12 MET cc_start: 0.7672 (ttt) cc_final: 0.6670 (ptm) REVERT: F 89 MET cc_start: 0.8970 (ptp) cc_final: 0.8484 (ptp) outliers start: 32 outliers final: 28 residues processed: 153 average time/residue: 0.2751 time to fit residues: 65.2876 Evaluate side-chains 156 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 714 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 136 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 143 optimal weight: 10.0000 chunk 150 optimal weight: 50.0000 chunk 104 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1418 GLN E 96 HIS F 52 HIS ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16926 Z= 0.278 Angle : 0.589 13.397 23523 Z= 0.308 Chirality : 0.039 0.202 2686 Planarity : 0.004 0.049 2463 Dihedral : 19.454 174.399 3787 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.58 % Allowed : 15.48 % Favored : 81.94 % 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: 0.32 (0.21), residues: 1621 helix: 0.96 (0.19), residues: 779 sheet: 0.55 (0.39), residues: 181 loop : -0.72 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 11 HIS 0.007 0.001 HIS B 364 PHE 0.023 0.002 PHE B 766 TYR 0.017 0.001 TYR B 352 ARG 0.013 0.000 ARG B1495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 465 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8707 (mmmm) REVERT: B 600 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8303 (mmt90) REVERT: B 731 MET cc_start: 0.5390 (ptt) cc_final: 0.4695 (pmm) REVERT: B 824 GLU cc_start: 0.8026 (pp20) cc_final: 0.7809 (mm-30) REVERT: B 948 MET cc_start: 0.8644 (mtp) cc_final: 0.8400 (mmm) REVERT: B 1076 MET cc_start: 0.6609 (tpp) cc_final: 0.6111 (tpp) REVERT: B 1079 TYR cc_start: 0.7456 (t80) cc_final: 0.7241 (t80) REVERT: B 1402 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: F 12 MET cc_start: 0.7712 (ttt) cc_final: 0.6743 (ptm) REVERT: F 61 MET cc_start: 0.8995 (mmp) cc_final: 0.8193 (mmm) REVERT: F 89 MET cc_start: 0.9021 (ptp) cc_final: 0.8778 (ptp) outliers start: 36 outliers final: 30 residues processed: 142 average time/residue: 0.2871 time to fit residues: 61.7948 Evaluate side-chains 150 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 714 TYR Chi-restraints excluded: chain B residue 718 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1387 VAL Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 0.0000 chunk 86 optimal weight: 0.0050 chunk 111 optimal weight: 0.0020 chunk 149 optimal weight: 20.0000 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1177 ASN E 96 HIS F 38 ASN F 52 HIS ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16926 Z= 0.135 Angle : 0.527 13.448 23523 Z= 0.274 Chirality : 0.037 0.236 2686 Planarity : 0.003 0.058 2463 Dihedral : 19.298 174.996 3787 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.86 % Allowed : 16.49 % Favored : 81.65 % 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: 0.61 (0.21), residues: 1621 helix: 1.22 (0.19), residues: 777 sheet: 0.77 (0.39), residues: 180 loop : -0.62 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 11 HIS 0.010 0.001 HIS F 96 PHE 0.028 0.001 PHE B 766 TYR 0.014 0.001 TYR B 483 ARG 0.015 0.000 ARG B1495 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 465 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8663 (mmmm) REVERT: B 731 MET cc_start: 0.5309 (ptt) cc_final: 0.4748 (pmm) REVERT: B 1076 MET cc_start: 0.6690 (tpp) cc_final: 0.6193 (tpp) REVERT: B 1196 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8341 (ttpp) REVERT: B 1240 MET cc_start: 0.9242 (tpp) cc_final: 0.8898 (tpp) REVERT: B 1261 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 1402 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: F 12 MET cc_start: 0.7591 (ttt) cc_final: 0.6256 (ptm) REVERT: F 61 MET cc_start: 0.8954 (mmp) cc_final: 0.8162 (mmm) outliers start: 26 outliers final: 23 residues processed: 147 average time/residue: 0.2794 time to fit residues: 61.8208 Evaluate side-chains 145 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 714 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1474 SER Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS F 52 HIS ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.158074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104201 restraints weight = 33218.024| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.93 r_work: 0.3200 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16926 Z= 0.143 Angle : 0.535 11.597 23523 Z= 0.276 Chirality : 0.036 0.186 2686 Planarity : 0.003 0.058 2463 Dihedral : 19.261 175.064 3787 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.79 % Allowed : 16.92 % Favored : 81.29 % 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: 0.67 (0.21), residues: 1621 helix: 1.29 (0.19), residues: 774 sheet: 0.76 (0.39), residues: 180 loop : -0.61 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 215 HIS 0.013 0.001 HIS F 96 PHE 0.027 0.001 PHE B 766 TYR 0.015 0.001 TYR B 483 ARG 0.015 0.000 ARG B1495 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3507.89 seconds wall clock time: 64 minutes 33.53 seconds (3873.53 seconds total)