Starting phenix.real_space_refine on Sat Mar 16 13:32:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orn_13043/03_2024/7orn_13043_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orn_13043/03_2024/7orn_13043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orn_13043/03_2024/7orn_13043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orn_13043/03_2024/7orn_13043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orn_13043/03_2024/7orn_13043_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orn_13043/03_2024/7orn_13043_updated.pdb" } resolution = 2.8 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= 0.001 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 P 40 5.49 5 Mg 2 5.21 5 S 94 5.16 5 C 9262 2.51 5 N 2454 2.21 5 O 2959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 18": "OD1" <-> "OD2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A ASP 699": "OD1" <-> "OD2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A TYR 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 987": "OD1" <-> "OD2" Residue "A GLU 1008": "OE1" <-> "OE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1188": "OD1" <-> "OD2" Residue "A ASP 1198": "OD1" <-> "OD2" Residue "A GLU 1201": "OE1" <-> "OE2" Residue "A GLU 1214": "OE1" <-> "OE2" Residue "A PHE 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A GLU 1332": "OE1" <-> "OE2" Residue "A GLU 1350": "OE1" <-> "OE2" Residue "A TYR 1355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1380": "OE1" <-> "OE2" Residue "A ASP 1388": "OD1" <-> "OD2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1483": "OE1" <-> "OE2" Residue "A PHE 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1540": "OE1" <-> "OE2" Residue "A TYR 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1612": "OE1" <-> "OE2" Residue "A PHE 1613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1644": "OE1" <-> "OE2" Residue "A TYR 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2099": "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: 14811 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1700, 13900 Classifications: {'peptide': 1700} Link IDs: {'PTRANS': 60, 'TRANS': 1639} Chain breaks: 5 Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 379 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 11} Conformer: "B" Number of residues, atoms: 18, 379 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 7, 'rna3p': 10} bond proxies already assigned to first conformer: 374 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 106 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3, 'water': 73} Link IDs: {None: 75} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A A T 18 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A T 18 " occ=0.50 residue: pdb=" P A C T 19 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B C T 19 " occ=0.50 Time building chain proxies: 8.60, per 1000 atoms: 0.58 Number of scatterers: 14811 At special positions: 0 Unit cell: (105.135, 105.135, 125.775, 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) S 94 16.00 P 40 15.00 Mg 2 11.99 O 2959 8.00 N 2454 7.00 C 9262 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: 6.11 Conformation dependent library (CDL) restraints added in 2.4 seconds 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 13 sheets defined 50.5% alpha, 8.1% beta 8 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 8.36 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 19 through 45 Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 100 through 120 removed outlier: 5.091A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.570A pdb=" N LEU A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 216 through 226 Processing helix chain 'A' and resid 238 through 264 removed outlier: 4.675A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 291 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 341 through 351 removed outlier: 3.700A pdb=" N MET A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 476 through 488 removed outlier: 6.638A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 503 through 521 removed outlier: 3.556A pdb=" N VAL A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 619 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.763A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 660 removed outlier: 3.808A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 3.868A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 Processing helix chain 'A' and resid 681 through 697 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 738 through 750 Proline residue: A 748 - end of helix Processing helix chain 'A' and resid 759 through 780 removed outlier: 4.309A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 809 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 850 through 853 No H-bonds generated for 'chain 'A' and resid 850 through 853' Processing helix chain 'A' and resid 876 through 878 No H-bonds generated for 'chain 'A' and resid 876 through 878' Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.847A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 981 removed outlier: 3.900A pdb=" N GLU A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1022 removed outlier: 3.993A pdb=" N LEU A1001 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A1011 " --> pdb=" O GLU A1008 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A1014 " --> pdb=" O PHE A1011 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR A1015 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A1016 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A1020 " --> pdb=" O ARG A1017 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A1021 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A1022 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1078 removed outlier: 3.716A pdb=" N TRP A1075 " --> pdb=" O LYS A1072 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1078 " --> pdb=" O TRP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 3.591A pdb=" N ASP A1100 " --> pdb=" O CYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1115 Processing helix chain 'A' and resid 1124 through 1128 Processing helix chain 'A' and resid 1149 through 1174 Processing helix chain 'A' and resid 1202 through 1220 removed outlier: 3.835A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1261 removed outlier: 3.975A pdb=" N LEU A1257 " --> pdb=" O ARG A1254 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A1258 " --> pdb=" O PHE A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1284 Processing helix chain 'A' and resid 1289 through 1306 Processing helix chain 'A' and resid 1326 through 1328 No H-bonds generated for 'chain 'A' and resid 1326 through 1328' Processing helix chain 'A' and resid 1331 through 1333 No H-bonds generated for 'chain 'A' and resid 1331 through 1333' Processing helix chain 'A' and resid 1341 through 1346 Processing helix chain 'A' and resid 1349 through 1364 removed outlier: 3.963A pdb=" N GLY A1352 " --> pdb=" O LEU A1349 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A1353 " --> pdb=" O GLU A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1369 No H-bonds generated for 'chain 'A' and resid 1367 through 1369' Processing helix chain 'A' and resid 1374 through 1383 removed outlier: 3.770A pdb=" N GLU A1380 " --> pdb=" O ASN A1376 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A1381 " --> pdb=" O GLN A1377 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS A1382 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN A1383 " --> pdb=" O ALA A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1388 No H-bonds generated for 'chain 'A' and resid 1386 through 1388' Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1435 through 1440 removed outlier: 3.627A pdb=" N LYS A1440 " --> pdb=" O GLY A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1451 Processing helix chain 'A' and resid 1456 through 1466 Processing helix chain 'A' and resid 1468 through 1472 Processing helix chain 'A' and resid 1478 through 1490 removed outlier: 3.947A pdb=" N ASN A1490 " --> pdb=" O ILE A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1497 Processing helix chain 'A' and resid 1503 through 1512 removed outlier: 3.589A pdb=" N ILE A1511 " --> pdb=" O PHE A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1562 Processing helix chain 'A' and resid 1567 through 1577 Processing helix chain 'A' and resid 1582 through 1592 Processing helix chain 'A' and resid 1613 through 1616 Processing helix chain 'A' and resid 1623 through 1632 Processing helix chain 'A' and resid 1642 through 1658 removed outlier: 3.507A pdb=" N ARG A1647 " --> pdb=" O THR A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1676 Processing helix chain 'A' and resid 1681 through 1702 Processing helix chain 'A' and resid 1718 through 1728 Processing sheet with id= A, first strand: chain 'A' and resid 80 through 84 removed outlier: 7.819A pdb=" N ILE A 90 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU A 125 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP A 92 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 127 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LYS A 94 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 129 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 293 through 295 Processing sheet with id= C, first strand: chain 'A' and resid 386 through 388 Processing sheet with id= D, first strand: chain 'A' and resid 398 through 400 removed outlier: 4.863A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 562 through 565 Processing sheet with id= F, first strand: chain 'A' and resid 842 through 846 Processing sheet with id= G, first strand: chain 'A' and resid 959 through 962 removed outlier: 6.488A pdb=" N GLU A1102 " --> pdb=" O PHE A 945 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N PHE A 947 " --> pdb=" O GLU A1102 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE A1104 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N ASN A 949 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A1101 " --> pdb=" O ILE A1139 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1230 through 1232 Processing sheet with id= I, first strand: chain 'A' and resid 1235 through 1238 Processing sheet with id= J, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id= K, first strand: chain 'A' and resid 1599 through 1601 Processing sheet with id= L, first strand: chain 'A' and resid 1606 through 1608 Processing sheet with id= M, first strand: chain 'A' and resid 2087 through 2090 removed outlier: 4.316A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2579 1.33 - 1.45: 3959 1.45 - 1.57: 8324 1.57 - 1.69: 78 1.69 - 1.81: 157 Bond restraints: 15097 Sorted by residual: bond pdb=" N THR A2093 " pdb=" CA THR A2093 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.06e+01 bond pdb=" N ILE A2095 " pdb=" CA ILE A2095 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.22e-02 6.72e+03 9.92e+00 bond pdb=" N ARG A1141 " pdb=" CA ARG A1141 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.26e-02 6.30e+03 9.26e+00 bond pdb=" N ILE A1378 " pdb=" CA ILE A1378 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 8.30e+00 bond pdb=" N ILE A 518 " pdb=" CA ILE A 518 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.88e+00 ... (remaining 15092 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.80: 761 107.80 - 115.78: 9282 115.78 - 123.77: 10028 123.77 - 131.75: 450 131.75 - 139.73: 27 Bond angle restraints: 20548 Sorted by residual: angle pdb=" N PRO A2094 " pdb=" CA PRO A2094 " pdb=" C PRO A2094 " ideal model delta sigma weight residual 112.47 100.01 12.46 2.06e+00 2.36e-01 3.66e+01 angle pdb=" C2' C T 21 " pdb=" C1' C T 21 " pdb=" N1 C T 21 " ideal model delta sigma weight residual 114.00 121.42 -7.42 1.50e+00 4.44e-01 2.45e+01 angle pdb=" CA ILE A1578 " pdb=" C ILE A1578 " pdb=" O ILE A1578 " ideal model delta sigma weight residual 120.70 117.39 3.31 8.50e-01 1.38e+00 1.51e+01 angle pdb=" C THR A1365 " pdb=" CA THR A1365 " pdb=" CB THR A1365 " ideal model delta sigma weight residual 109.41 115.59 -6.18 1.62e+00 3.81e-01 1.46e+01 angle pdb=" N GLY A 720 " pdb=" CA GLY A 720 " pdb=" C GLY A 720 " ideal model delta sigma weight residual 111.56 115.40 -3.84 1.01e+00 9.80e-01 1.44e+01 ... (remaining 20543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8442 17.69 - 35.39: 634 35.39 - 53.08: 123 53.08 - 70.77: 67 70.77 - 88.46: 15 Dihedral angle restraints: 9281 sinusoidal: 4220 harmonic: 5061 Sorted by residual: dihedral pdb=" O4' C T 21 " pdb=" C1' C T 21 " pdb=" N1 C T 21 " pdb=" C2 C T 21 " ideal model delta sinusoidal sigma weight residual 232.00 152.16 79.84 1 1.70e+01 3.46e-03 2.74e+01 dihedral pdb=" C THR A 552 " pdb=" N THR A 552 " pdb=" CA THR A 552 " pdb=" CB THR A 552 " ideal model delta harmonic sigma weight residual -122.00 -132.94 10.94 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C LEU A1144 " pdb=" N LEU A1144 " pdb=" CA LEU A1144 " pdb=" CB LEU A1144 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 9278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2062 0.066 - 0.132: 218 0.132 - 0.197: 25 0.197 - 0.263: 4 0.263 - 0.329: 3 Chirality restraints: 2312 Sorted by residual: chirality pdb=" CA THR A 552 " pdb=" N THR A 552 " pdb=" C THR A 552 " pdb=" CB THR A 552 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA LEU A1144 " pdb=" N LEU A1144 " pdb=" C LEU A1144 " pdb=" CB LEU A1144 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA TRP A1143 " pdb=" N TRP A1143 " pdb=" C TRP A1143 " pdb=" CB TRP A1143 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 2309 not shown) Planarity restraints: 2461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1143 " -0.024 2.00e-02 2.50e+03 1.37e-02 4.69e+00 pdb=" CG TRP A1143 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1143 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A1143 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1143 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A1143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1143 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1143 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1143 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1140 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C LYS A1140 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A1140 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A1141 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1187 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ASP A1187 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A1187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A1188 " -0.011 2.00e-02 2.50e+03 ... (remaining 2458 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 81 2.56 - 3.15: 11649 3.15 - 3.73: 23997 3.73 - 4.32: 35969 4.32 - 4.90: 57230 Nonbonded interactions: 128926 Sorted by model distance: nonbonded pdb=" O1B ATP A2301 " pdb="MG MG A2303 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP A1060 " pdb="MG MG A2303 " model vdw 2.089 2.170 nonbonded pdb=" OD1 ASP A1187 " pdb="MG MG A2302 " model vdw 2.115 2.170 nonbonded pdb=" OD2 ASP A1187 " pdb="MG MG A2303 " model vdw 2.157 2.170 nonbonded pdb=" OD1 ASP A1060 " pdb="MG MG A2302 " model vdw 2.191 2.170 ... (remaining 128921 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=0.50 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: 4.810 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: 0.010 Extract box with map and model: 20.200 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.460 Find NCS groups from input model: 0.360 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.004 0.044 15097 Z= 0.233 Angle : 0.592 12.461 20548 Z= 0.372 Chirality : 0.044 0.329 2312 Planarity : 0.004 0.042 2461 Dihedral : 14.139 88.463 5995 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.19 % Allowed : 0.32 % Favored : 99.49 % Cbeta Deviations : 0.06 % 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: 1.14 (0.21), residues: 1688 helix: 1.71 (0.18), residues: 891 sheet: 1.21 (0.43), residues: 140 loop : -0.66 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1143 HIS 0.004 0.001 HIS A 814 PHE 0.019 0.001 PHE A1395 TYR 0.018 0.001 TYR A1442 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 231 time to evaluate : 1.668 Fit side-chains REVERT: A 35 ASP cc_start: 0.6258 (m-30) cc_final: 0.6032 (m-30) REVERT: A 487 ASP cc_start: 0.7454 (m-30) cc_final: 0.7103 (m-30) REVERT: A 1160 MET cc_start: 0.8822 (mmp) cc_final: 0.8479 (mmp) REVERT: A 1258 THR cc_start: 0.8674 (m) cc_final: 0.8406 (m) outliers start: 3 outliers final: 0 residues processed: 233 average time/residue: 1.5867 time to fit residues: 402.0330 Evaluate side-chains 184 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 86 ASN A 289 GLN A 424 HIS A 497 HIS A1600 GLN A1620 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15097 Z= 0.182 Angle : 0.466 8.192 20548 Z= 0.249 Chirality : 0.039 0.226 2312 Planarity : 0.004 0.039 2461 Dihedral : 12.138 83.728 2445 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 7.44 % Favored : 91.22 % 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: 1.24 (0.21), residues: 1688 helix: 1.77 (0.18), residues: 891 sheet: 1.24 (0.43), residues: 140 loop : -0.59 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1143 HIS 0.010 0.001 HIS A1620 PHE 0.019 0.001 PHE A1395 TYR 0.018 0.001 TYR A1576 ARG 0.006 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 2.077 Fit side-chains REVERT: A 35 ASP cc_start: 0.6235 (m-30) cc_final: 0.6031 (m-30) REVERT: A 487 ASP cc_start: 0.7464 (m-30) cc_final: 0.7115 (m-30) REVERT: A 597 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7539 (p0) REVERT: A 1210 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7124 (mmm) REVERT: A 1258 THR cc_start: 0.8647 (m) cc_final: 0.8296 (m) REVERT: A 1665 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8948 (ttt) outliers start: 21 outliers final: 5 residues processed: 203 average time/residue: 1.4924 time to fit residues: 330.3208 Evaluate side-chains 186 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 156 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 46 ASN A 159 ASN A1383 ASN A1600 GLN A1658 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15097 Z= 0.232 Angle : 0.479 7.507 20548 Z= 0.256 Chirality : 0.040 0.238 2312 Planarity : 0.004 0.039 2461 Dihedral : 12.150 84.944 2445 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.46 % Allowed : 8.91 % Favored : 89.63 % 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: 1.16 (0.21), residues: 1688 helix: 1.69 (0.18), residues: 894 sheet: 1.17 (0.43), residues: 134 loop : -0.58 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1143 HIS 0.012 0.001 HIS A1620 PHE 0.020 0.001 PHE A1395 TYR 0.020 0.001 TYR A1576 ARG 0.007 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 1.827 Fit side-chains REVERT: A 487 ASP cc_start: 0.7531 (m-30) cc_final: 0.7210 (m-30) REVERT: A 597 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7625 (p0) REVERT: A 758 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: A 1056 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: A 1210 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7165 (mmm) REVERT: A 1665 MET cc_start: 0.9188 (ttm) cc_final: 0.8948 (ttt) REVERT: A 1734 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7813 (pp20) outliers start: 23 outliers final: 9 residues processed: 204 average time/residue: 1.4789 time to fit residues: 330.1422 Evaluate side-chains 195 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1466 GLU Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 46 ASN A 159 ASN A 506 GLN A 523 GLN A1383 ASN A1658 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15097 Z= 0.177 Angle : 0.452 8.279 20548 Z= 0.241 Chirality : 0.039 0.255 2312 Planarity : 0.003 0.035 2461 Dihedral : 12.057 87.667 2445 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.46 % Allowed : 9.99 % Favored : 88.55 % 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: 1.27 (0.21), residues: 1688 helix: 1.78 (0.18), residues: 894 sheet: 1.30 (0.43), residues: 136 loop : -0.55 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.018 0.001 TYR A1576 ARG 0.007 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 1.699 Fit side-chains REVERT: A 487 ASP cc_start: 0.7481 (m-30) cc_final: 0.7154 (m-30) REVERT: A 597 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7604 (p0) REVERT: A 758 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: A 1017 ARG cc_start: 0.7295 (mtp-110) cc_final: 0.7048 (mtm180) REVERT: A 1056 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: A 1210 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7273 (mmm) REVERT: A 1665 MET cc_start: 0.9189 (ttm) cc_final: 0.8974 (ttt) REVERT: A 1734 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7802 (pp20) outliers start: 23 outliers final: 9 residues processed: 194 average time/residue: 1.4320 time to fit residues: 304.9991 Evaluate side-chains 193 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1466 GLU Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 0.0970 chunk 149 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 46 ASN A 159 ASN A 523 GLN ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15097 Z= 0.196 Angle : 0.458 7.763 20548 Z= 0.244 Chirality : 0.039 0.261 2312 Planarity : 0.003 0.034 2461 Dihedral : 12.099 89.311 2445 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.65 % Allowed : 10.62 % Favored : 87.72 % 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: 1.23 (0.21), residues: 1688 helix: 1.75 (0.18), residues: 895 sheet: 1.25 (0.44), residues: 130 loop : -0.55 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1143 HIS 0.012 0.001 HIS A1620 PHE 0.019 0.001 PHE A1395 TYR 0.018 0.001 TYR A1576 ARG 0.005 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.598 Fit side-chains REVERT: A 487 ASP cc_start: 0.7474 (m-30) cc_final: 0.7182 (m-30) REVERT: A 597 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7572 (p0) REVERT: A 758 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: A 1056 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: A 1210 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7268 (mmm) REVERT: A 1665 MET cc_start: 0.9182 (ttm) cc_final: 0.8950 (ttt) REVERT: A 1734 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7856 (pp20) outliers start: 26 outliers final: 10 residues processed: 202 average time/residue: 1.4609 time to fit residues: 323.1743 Evaluate side-chains 196 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1466 GLU Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 46 ASN A 159 ASN A 523 GLN ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1600 GLN A1658 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15097 Z= 0.211 Angle : 0.465 7.583 20548 Z= 0.248 Chirality : 0.040 0.264 2312 Planarity : 0.004 0.043 2461 Dihedral : 12.156 86.332 2445 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.53 % Allowed : 11.13 % Favored : 87.34 % 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: 1.23 (0.21), residues: 1688 helix: 1.74 (0.18), residues: 894 sheet: 1.37 (0.45), residues: 120 loop : -0.53 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.019 0.001 PHE A1395 TYR 0.018 0.001 TYR A1576 ARG 0.011 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.672 Fit side-chains REVERT: A 136 ARG cc_start: 0.7334 (mmm-85) cc_final: 0.6876 (mmm-85) REVERT: A 487 ASP cc_start: 0.7477 (m-30) cc_final: 0.7174 (m-30) REVERT: A 597 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7643 (p0) REVERT: A 758 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: A 1017 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.6961 (mtm180) REVERT: A 1056 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: A 1210 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7287 (mmm) REVERT: A 1665 MET cc_start: 0.9185 (ttm) cc_final: 0.8950 (ttt) REVERT: A 1734 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7879 (pp20) outliers start: 24 outliers final: 12 residues processed: 202 average time/residue: 1.4354 time to fit residues: 318.1219 Evaluate side-chains 203 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1466 GLU Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1725 MET Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 66 optimal weight: 0.0070 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 46 ASN A 159 ASN A 985 ASN ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15097 Z= 0.173 Angle : 0.448 8.337 20548 Z= 0.238 Chirality : 0.039 0.266 2312 Planarity : 0.003 0.036 2461 Dihedral : 12.078 85.580 2445 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.40 % Allowed : 11.32 % Favored : 87.28 % 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: 1.34 (0.21), residues: 1688 helix: 1.83 (0.18), residues: 892 sheet: 1.46 (0.45), residues: 120 loop : -0.49 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.017 0.001 TYR A1576 ARG 0.008 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 1.775 Fit side-chains REVERT: A 136 ARG cc_start: 0.7305 (mmm-85) cc_final: 0.6876 (mmm-85) REVERT: A 487 ASP cc_start: 0.7477 (m-30) cc_final: 0.7214 (m-30) REVERT: A 597 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7610 (p0) REVERT: A 758 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: A 1056 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: A 1210 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7326 (mmm) REVERT: A 1482 MET cc_start: 0.8302 (mtt) cc_final: 0.7853 (mtm) REVERT: A 1665 MET cc_start: 0.9175 (ttm) cc_final: 0.8954 (ttt) REVERT: A 1734 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7896 (pp20) outliers start: 22 outliers final: 11 residues processed: 199 average time/residue: 1.4013 time to fit residues: 305.9612 Evaluate side-chains 195 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1466 GLU Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 144 optimal weight: 0.0040 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 159 ASN ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15097 Z= 0.215 Angle : 0.470 8.377 20548 Z= 0.250 Chirality : 0.040 0.271 2312 Planarity : 0.004 0.053 2461 Dihedral : 12.171 84.955 2445 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.46 % Allowed : 11.39 % Favored : 87.15 % 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: 1.26 (0.21), residues: 1688 helix: 1.75 (0.18), residues: 892 sheet: 1.46 (0.45), residues: 126 loop : -0.53 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.019 0.001 TYR A1576 ARG 0.012 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.785 Fit side-chains REVERT: A 136 ARG cc_start: 0.7337 (mmm-85) cc_final: 0.6906 (mmm-85) REVERT: A 487 ASP cc_start: 0.7486 (m-30) cc_final: 0.7206 (m-30) REVERT: A 597 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7593 (p0) REVERT: A 758 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: A 1017 ARG cc_start: 0.7273 (mtp-110) cc_final: 0.6896 (mtm180) REVERT: A 1056 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: A 1210 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7291 (mmm) REVERT: A 1665 MET cc_start: 0.9189 (ttm) cc_final: 0.8973 (ttt) REVERT: A 1734 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7870 (pp20) outliers start: 23 outliers final: 12 residues processed: 194 average time/residue: 1.4086 time to fit residues: 299.9664 Evaluate side-chains 195 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1466 GLU Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.6980 chunk 158 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 159 ASN ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15097 Z= 0.193 Angle : 0.460 7.874 20548 Z= 0.245 Chirality : 0.039 0.273 2312 Planarity : 0.003 0.050 2461 Dihedral : 12.129 84.750 2445 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.40 % Allowed : 11.45 % Favored : 87.15 % 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: 1.30 (0.21), residues: 1688 helix: 1.79 (0.18), residues: 892 sheet: 1.49 (0.45), residues: 126 loop : -0.51 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.018 0.001 TYR A1576 ARG 0.011 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.755 Fit side-chains REVERT: A 487 ASP cc_start: 0.7471 (m-30) cc_final: 0.7194 (m-30) REVERT: A 597 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7641 (p0) REVERT: A 758 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: A 1017 ARG cc_start: 0.7309 (mtp-110) cc_final: 0.6936 (mtm180) REVERT: A 1056 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: A 1210 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7283 (mmm) REVERT: A 1665 MET cc_start: 0.9194 (ttm) cc_final: 0.8980 (ttt) REVERT: A 1734 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7874 (pp20) outliers start: 22 outliers final: 12 residues processed: 194 average time/residue: 1.4375 time to fit residues: 306.5611 Evaluate side-chains 193 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1466 GLU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15097 Z= 0.184 Angle : 0.452 8.089 20548 Z= 0.241 Chirality : 0.039 0.168 2312 Planarity : 0.003 0.048 2461 Dihedral : 12.104 84.384 2445 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.27 % Allowed : 11.64 % Favored : 87.09 % 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: 1.31 (0.21), residues: 1688 helix: 1.79 (0.18), residues: 893 sheet: 1.49 (0.45), residues: 126 loop : -0.50 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1143 HIS 0.014 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.018 0.001 TYR A1576 ARG 0.011 0.000 ARG A1017 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 1.713 Fit side-chains REVERT: A 487 ASP cc_start: 0.7470 (m-30) cc_final: 0.7186 (m-30) REVERT: A 597 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 758 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: A 1017 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.6930 (mtm180) REVERT: A 1056 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: A 1210 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7338 (mmm) REVERT: A 1665 MET cc_start: 0.9190 (ttm) cc_final: 0.8978 (ttt) REVERT: A 1734 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7877 (pp20) outliers start: 20 outliers final: 11 residues processed: 193 average time/residue: 1.3673 time to fit residues: 289.9859 Evaluate side-chains 192 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1210 MET Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1466 GLU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 0.0010 chunk 57 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1658 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.092031 restraints weight = 21580.068| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.45 r_work: 0.2737 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15097 Z= 0.146 Angle : 0.441 9.219 20548 Z= 0.233 Chirality : 0.038 0.307 2312 Planarity : 0.003 0.046 2461 Dihedral : 11.965 84.199 2445 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.21 % Allowed : 11.77 % Favored : 87.02 % 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: 1.44 (0.21), residues: 1688 helix: 1.89 (0.18), residues: 892 sheet: 1.56 (0.45), residues: 126 loop : -0.44 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.017 0.001 PHE A1395 TYR 0.015 0.001 TYR A1442 ARG 0.010 0.000 ARG A1017 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6128.38 seconds wall clock time: 111 minutes 36.38 seconds (6696.38 seconds total)