Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 23:53:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p04_13143/08_2023/7p04_13143_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p04_13143/08_2023/7p04_13143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p04_13143/08_2023/7p04_13143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p04_13143/08_2023/7p04_13143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p04_13143/08_2023/7p04_13143_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p04_13143/08_2023/7p04_13143_trim_updated.pdb" } resolution = 2.85 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 5 5.49 5 S 68 5.16 5 C 7022 2.51 5 N 1794 2.21 5 O 1979 1.98 5 H 10675 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A ARG 630": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A ARG 810": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 872": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A GLU 963": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1008": "OE1" <-> "OE2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A GLU 1077": "OE1" <-> "OE2" Residue "A GLU 1098": "OE1" <-> "OE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A ARG 1146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A PHE 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1267": "OE1" <-> "OE2" Residue "A ARG 1274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1353": "OE1" <-> "OE2" Residue "A PHE 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1408": "OD1" <-> "OD2" Residue "A GLU 1418": "OE1" <-> "OE2" Residue "A GLU 1473": "OE1" <-> "OE2" Residue "A PHE 1495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 21543 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1355, 21543 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1353, 'undetermined': 2} Link IDs: {'PTRANS': 52, 'TRANS': 1300, None: 2} Not linked: pdbres="PRO A1502 " pdbres="ATP A1601 " Not linked: pdbres="ATP A1601 " pdbres="ADP A1602 " Chain breaks: 5 Time building chain proxies: 9.01, per 1000 atoms: 0.42 Number of scatterers: 21543 At special positions: 0 Unit cell: (103.668, 95.844, 150.612, 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 68 16.00 P 5 15.00 O 1979 8.00 N 1794 7.00 C 7022 6.00 H 10675 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1411 " - pdb=" SG CYS A1455 " distance=2.03 Simple disulfide: pdb=" SG CYS A1427 " - pdb=" SG CYS A1452 " distance=2.02 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: 19.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 8 sheets defined 55.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.825A pdb=" N VAL A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 341 through 358 Processing helix chain 'A' and resid 371 through 376 removed outlier: 4.106A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.578A pdb=" N ALA A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS A 398 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.571A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.756A pdb=" N GLN A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 518 Processing helix chain 'A' and resid 520 through 541 Processing helix chain 'A' and resid 550 through 590 removed outlier: 3.619A pdb=" N PHE A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TYR A 554 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 571 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 572 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 575 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 596 through 626 removed outlier: 3.758A pdb=" N GLU A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Proline residue: A 609 - end of helix removed outlier: 3.886A pdb=" N ASN A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 659 Processing helix chain 'A' and resid 663 through 679 removed outlier: 4.334A pdb=" N VAL A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Proline residue: A 669 - end of helix Processing helix chain 'A' and resid 695 through 699 Processing helix chain 'A' and resid 702 through 715 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 756 through 763 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 773 through 795 Processing helix chain 'A' and resid 810 through 815 removed outlier: 4.026A pdb=" N ARG A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 961 through 972 Processing helix chain 'A' and resid 979 through 992 Processing helix chain 'A' and resid 1012 through 1024 Processing helix chain 'A' and resid 1043 through 1059 Processing helix chain 'A' and resid 1072 through 1077 removed outlier: 3.845A pdb=" N GLU A1077 " --> pdb=" O ILE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 5.904A pdb=" N THR A1102 " --> pdb=" O GLY A1099 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A1109 " --> pdb=" O TYR A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1149 through 1165 removed outlier: 3.751A pdb=" N LEU A1165 " --> pdb=" O MET A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1199 Processing helix chain 'A' and resid 1203 through 1223 Processing helix chain 'A' and resid 1231 through 1269 removed outlier: 3.865A pdb=" N THR A1245 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A1246 " --> pdb=" O PHE A1242 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE A1247 " --> pdb=" O MET A1243 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE A1248 " --> pdb=" O PHE A1244 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASN A1249 " --> pdb=" O THR A1245 " (cutoff:3.500A) Proline residue: A1250 - end of helix Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1278 through 1308 removed outlier: 3.644A pdb=" N GLU A1289 " --> pdb=" O GLN A1285 " (cutoff:3.500A) Proline residue: A1291 - end of helix removed outlier: 4.264A pdb=" N TYR A1306 " --> pdb=" O PHE A1302 " (cutoff:3.500A) Proline residue: A1307 - end of helix Processing helix chain 'A' and resid 1310 through 1317 removed outlier: 3.540A pdb=" N ALA A1317 " --> pdb=" O ASN A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1348 removed outlier: 4.408A pdb=" N PHE A1348 " --> pdb=" O LEU A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1368 Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.633A pdb=" N ILE A1384 " --> pdb=" O ARG A1381 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A1385 " --> pdb=" O PHE A1382 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1389 " --> pdb=" O MET A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1427 through 1437 Proline residue: A1433 - end of helix Processing helix chain 'A' and resid 1460 through 1467 removed outlier: 3.543A pdb=" N ASN A1466 " --> pdb=" O ASP A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1499 removed outlier: 3.708A pdb=" N ARG A1474 " --> pdb=" O TYR A1471 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP A1475 " --> pdb=" O SER A1472 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A1499 " --> pdb=" O TYR A1496 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 387 through 393 removed outlier: 6.611A pdb=" N VAL A 382 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 391 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 380 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA A 362 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 191 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 364 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 719 through 721 Processing sheet with id= D, first strand: chain 'A' and resid 893 through 895 Processing sheet with id= E, first strand: chain 'A' and resid 926 through 928 removed outlier: 3.763A pdb=" N LEU A 888 " --> pdb=" O TYR A 876 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 878 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ARG A 886 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1089 through 1095 removed outlier: 6.855A pdb=" N PHE A1083 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A1093 " --> pdb=" O LEU A1081 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1081 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A1063 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU A 903 " --> pdb=" O ILE A1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS A1065 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A1032 " --> pdb=" O LEU A1064 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A1066 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A1034 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1417 through 1419 removed outlier: 3.632A pdb=" N PHE A1419 " --> pdb=" O CYS A1452 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 136 through 139 removed outlier: 6.664A pdb=" N GLY A 138 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN A 174 " --> pdb=" O GLY A 138 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.68 Time building geometry restraints manager: 19.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10653 1.03 - 1.23: 48 1.23 - 1.42: 4809 1.42 - 1.62: 6206 1.62 - 1.81: 108 Bond restraints: 21824 Sorted by residual: bond pdb=" C4 ATP A1601 " pdb=" C5 ATP A1601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.35e+01 bond pdb=" C5 ATP A1601 " pdb=" C6 ATP A1601 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.88e+01 bond pdb=" C5 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.32e+01 bond pdb=" C4 ATP A1601 " pdb=" N9 ATP A1601 " ideal model delta sigma weight residual 1.374 1.329 0.045 1.00e-02 1.00e+04 2.00e+01 bond pdb=" C8 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.93e+01 ... (remaining 21819 not shown) Histogram of bond angle deviations from ideal: 74.10 - 86.44: 6 86.44 - 98.78: 0 98.78 - 111.12: 23269 111.12 - 123.47: 14212 123.47 - 135.81: 1790 Bond angle restraints: 39277 Sorted by residual: angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 122.01 17.86 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 122.54 14.29 1.00e+00 1.00e+00 2.04e+02 angle pdb=" N ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 110.00 75.08 34.92 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 109.00 74.10 34.90 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 110.00 75.45 34.55 3.00e+00 1.11e-01 1.33e+02 ... (remaining 39272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 8423 21.84 - 43.68: 385 43.68 - 65.52: 39 65.52 - 87.35: 19 87.35 - 109.19: 5 Dihedral angle restraints: 8871 sinusoidal: 3973 harmonic: 4898 Sorted by residual: dihedral pdb=" CA TYR A1199 " pdb=" C TYR A1199 " pdb=" N TRP A1200 " pdb=" CA TRP A1200 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" O1B ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PB ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 49.19 -109.19 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" C4' ADP A1602 " pdb=" C5' ADP A1602 " pdb=" O5' ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual 180.00 75.72 104.28 1 2.00e+01 2.50e-03 2.99e+01 ... (remaining 8868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1589 0.093 - 0.186: 56 0.186 - 0.280: 0 0.280 - 0.373: 0 0.373 - 0.466: 2 Chirality restraints: 1647 Sorted by residual: chirality pdb=" CA ARG A 517 " pdb=" N ARG A 517 " pdb=" C ARG A 517 " pdb=" CB ARG A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA ASP A 120 " pdb=" N ASP A 120 " pdb=" C ASP A 120 " pdb=" CB ASP A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA TYR A 591 " pdb=" N TYR A 591 " pdb=" C TYR A 591 " pdb=" CB TYR A 591 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1644 not shown) Planarity restraints: 3197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 808 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.44e+00 pdb=" N PRO A 809 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 809 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 809 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1256 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A1257 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1257 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1257 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 685 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 686 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 686 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 686 " 0.020 5.00e-02 4.00e+02 ... (remaining 3194 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1586 2.20 - 2.80: 45403 2.80 - 3.40: 62238 3.40 - 4.00: 82626 4.00 - 4.60: 127582 Nonbonded interactions: 319435 Sorted by model distance: nonbonded pdb="HH22 ARG A 872 " pdb=" OD1 ASP A1159 " model vdw 1.602 1.850 nonbonded pdb=" O ARG A1388 " pdb=" HH TYR A1394 " model vdw 1.609 1.850 nonbonded pdb=" HH TYR A 732 " pdb=" O TYR A1430 " model vdw 1.612 1.850 nonbonded pdb=" H ASP A 120 " pdb=" HA ASP A 120 " model vdw 1.612 1.816 nonbonded pdb=" HG SER A 597 " pdb=" OE1 GLU A 794 " model vdw 1.613 1.850 ... (remaining 319430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 31.610 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 70.530 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.005 0.080 11149 Z= 0.325 Angle : 0.659 17.859 15119 Z= 0.404 Chirality : 0.043 0.466 1647 Planarity : 0.004 0.063 1901 Dihedral : 13.938 109.192 4001 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % 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: -0.21 (0.23), residues: 1341 helix: 0.42 (0.18), residues: 771 sheet: -1.29 (0.47), residues: 105 loop : -0.62 (0.30), residues: 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 2.5711 time to fit residues: 431.2542 Evaluate side-chains 106 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.622 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 11149 Z= 0.272 Angle : 0.576 7.660 15119 Z= 0.305 Chirality : 0.042 0.464 1647 Planarity : 0.005 0.061 1901 Dihedral : 7.174 93.694 1496 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.08 % 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 (0.23), residues: 1341 helix: 0.44 (0.18), residues: 773 sheet: -1.12 (0.47), residues: 105 loop : -0.50 (0.31), residues: 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 124 average time/residue: 2.4336 time to fit residues: 330.5969 Evaluate side-chains 113 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.3818 time to fit residues: 3.3131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 122 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 11149 Z= 0.161 Angle : 0.523 7.615 15119 Z= 0.273 Chirality : 0.039 0.417 1647 Planarity : 0.004 0.058 1901 Dihedral : 6.791 91.341 1496 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1341 helix: 0.63 (0.18), residues: 773 sheet: -0.88 (0.53), residues: 91 loop : -0.36 (0.31), residues: 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 122 average time/residue: 2.2861 time to fit residues: 308.1989 Evaluate side-chains 110 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 0.3314 time to fit residues: 2.8324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 0.0270 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11149 Z= 0.182 Angle : 0.513 7.755 15119 Z= 0.266 Chirality : 0.040 0.421 1647 Planarity : 0.004 0.055 1901 Dihedral : 6.417 90.744 1496 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.08 % 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: 0.40 (0.24), residues: 1341 helix: 0.84 (0.19), residues: 777 sheet: -0.75 (0.54), residues: 91 loop : -0.31 (0.31), residues: 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 2.2473 time to fit residues: 302.6388 Evaluate side-chains 111 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 2 average time/residue: 0.3508 time to fit residues: 3.2379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 11149 Z= 0.302 Angle : 0.554 7.945 15119 Z= 0.290 Chirality : 0.041 0.424 1647 Planarity : 0.004 0.055 1901 Dihedral : 6.471 93.093 1496 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.08 % 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: 0.26 (0.23), residues: 1341 helix: 0.72 (0.18), residues: 780 sheet: -0.76 (0.49), residues: 105 loop : -0.35 (0.31), residues: 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.689 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 2.1403 time to fit residues: 266.1230 Evaluate side-chains 111 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.6949 time to fit residues: 5.6475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11149 Z= 0.215 Angle : 0.525 7.685 15119 Z= 0.272 Chirality : 0.040 0.422 1647 Planarity : 0.004 0.054 1901 Dihedral : 6.317 91.351 1496 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.08 % 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: 0.41 (0.23), residues: 1341 helix: 0.83 (0.19), residues: 779 sheet: -0.75 (0.49), residues: 105 loop : -0.25 (0.31), residues: 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 113 average time/residue: 2.2347 time to fit residues: 280.8110 Evaluate side-chains 110 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.3677 time to fit residues: 3.9769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11149 Z= 0.162 Angle : 0.504 7.627 15119 Z= 0.259 Chirality : 0.039 0.417 1647 Planarity : 0.004 0.052 1901 Dihedral : 6.045 90.636 1496 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.08 % 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: 0.66 (0.24), residues: 1341 helix: 1.03 (0.19), residues: 777 sheet: -0.62 (0.55), residues: 91 loop : -0.16 (0.31), residues: 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.701 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 2.1566 time to fit residues: 284.2348 Evaluate side-chains 113 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.3709 time to fit residues: 4.0511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11149 Z= 0.260 Angle : 0.534 7.883 15119 Z= 0.277 Chirality : 0.040 0.421 1647 Planarity : 0.004 0.051 1901 Dihedral : 6.083 92.669 1496 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.08 % 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 (0.24), residues: 1341 helix: 0.95 (0.19), residues: 778 sheet: -0.69 (0.50), residues: 105 loop : -0.16 (0.31), residues: 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.618 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 113 average time/residue: 2.1421 time to fit residues: 268.7986 Evaluate side-chains 112 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.9345 time to fit residues: 7.8805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 0.0070 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11149 Z= 0.190 Angle : 0.515 8.115 15119 Z= 0.265 Chirality : 0.040 0.418 1647 Planarity : 0.004 0.051 1901 Dihedral : 5.944 91.388 1496 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.08 % 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: 0.68 (0.24), residues: 1341 helix: 1.02 (0.19), residues: 778 sheet: -0.57 (0.56), residues: 91 loop : -0.13 (0.31), residues: 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.761 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 2.1399 time to fit residues: 264.5878 Evaluate side-chains 109 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.4106 time to fit residues: 2.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 85 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11149 Z= 0.137 Angle : 0.502 11.887 15119 Z= 0.254 Chirality : 0.039 0.413 1647 Planarity : 0.004 0.049 1901 Dihedral : 5.693 90.743 1496 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.08 % 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: 0.90 (0.24), residues: 1341 helix: 1.19 (0.19), residues: 778 sheet: -0.48 (0.55), residues: 91 loop : -0.01 (0.31), residues: 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.842 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 2.1271 time to fit residues: 272.5953 Evaluate side-chains 110 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 2.1013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103283 restraints weight = 48169.103| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.96 r_work: 0.3263 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11149 Z= 0.177 Angle : 0.509 9.553 15119 Z= 0.258 Chirality : 0.039 0.413 1647 Planarity : 0.004 0.047 1901 Dihedral : 5.634 91.446 1496 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.08 % 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: 0.93 (0.24), residues: 1341 helix: 1.22 (0.19), residues: 778 sheet: -0.48 (0.56), residues: 91 loop : -0.00 (0.32), residues: 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6952.69 seconds wall clock time: 123 minutes 22.74 seconds (7402.74 seconds total)