Starting phenix.real_space_refine on Fri Feb 16 04:26:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgj_14707/02_2024/7zgj_14707_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgj_14707/02_2024/7zgj_14707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgj_14707/02_2024/7zgj_14707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgj_14707/02_2024/7zgj_14707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgj_14707/02_2024/7zgj_14707_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgj_14707/02_2024/7zgj_14707_neut.pdb" } resolution = 3.58 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= 0.009 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 9073 2.51 5 N 2434 2.21 5 O 2743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "B GLU 718": "OE1" <-> "OE2" Residue "B GLU 1040": "OE1" <-> "OE2" Residue "B GLU 1120": "OE1" <-> "OE2" Residue "B GLU 1221": "OE1" <-> "OE2" Residue "B GLU 1323": "OE1" <-> "OE2" Residue "B ASP 1499": "OD1" <-> "OD2" Residue "B TYR 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1560": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14314 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5014 Classifications: {'peptide': 643} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 604} Chain: "B" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7765 Classifications: {'peptide': 970} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 927} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1535 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Time building chain proxies: 7.79, per 1000 atoms: 0.54 Number of scatterers: 14314 At special positions: 0 Unit cell: (92.02, 148.78, 159.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2743 8.00 N 2434 7.00 C 9073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS B 816 " distance=2.03 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 693 " - pdb=" SG CYS B 720 " distance=2.03 Simple disulfide: pdb=" SG CYS B 694 " - pdb=" SG CYS B 727 " distance=2.03 Simple disulfide: pdb=" SG CYS B 707 " - pdb=" SG CYS B 728 " distance=2.03 Simple disulfide: pdb=" SG CYS B 873 " - pdb=" SG CYS B1513 " distance=2.03 Simple disulfide: pdb=" SG CYS B1101 " - pdb=" SG CYS B1158 " distance=2.03 Simple disulfide: pdb=" SG CYS B1358 " - pdb=" SG CYS B1489 " distance=2.03 Simple disulfide: pdb=" SG CYS B1389 " - pdb=" SG CYS B1458 " distance=2.04 Simple disulfide: pdb=" SG CYS B1506 " - pdb=" SG CYS B1511 " distance=2.03 Simple disulfide: pdb=" SG CYS B1518 " - pdb=" SG CYS B1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1537 " - pdb=" SG CYS B1661 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 2.6 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 23 sheets defined 29.2% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 303 through 311 removed outlier: 4.011A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 612 through 623 removed outlier: 3.755A pdb=" N ALA A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.706A pdb=" N PHE A 639 " --> pdb=" O TYR A 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 685 removed outlier: 3.894A pdb=" N LYS B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 699 Processing helix chain 'B' and resid 706 through 712 removed outlier: 3.777A pdb=" N ARG B 712 " --> pdb=" O GLN B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 739 removed outlier: 4.165A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS B 722 " --> pdb=" O GLU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 removed outlier: 3.664A pdb=" N VAL B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 996 " --> pdb=" O GLU B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 removed outlier: 3.781A pdb=" N ILE B1004 " --> pdb=" O LYS B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.715A pdb=" N GLY B1017 " --> pdb=" O ASN B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1031 removed outlier: 3.582A pdb=" N THR B1031 " --> pdb=" O TYR B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1038 Processing helix chain 'B' and resid 1040 through 1057 removed outlier: 4.044A pdb=" N GLY B1044 " --> pdb=" O GLU B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1060 No H-bonds generated for 'chain 'B' and resid 1058 through 1060' Processing helix chain 'B' and resid 1075 through 1091 removed outlier: 4.546A pdb=" N ASN B1091 " --> pdb=" O SER B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1110 removed outlier: 3.723A pdb=" N LEU B1100 " --> pdb=" O ASP B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1154 removed outlier: 3.691A pdb=" N LYS B1139 " --> pdb=" O ASN B1135 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B1153 " --> pdb=" O ILE B1149 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B1154 " --> pdb=" O SER B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1179 Processing helix chain 'B' and resid 1185 through 1200 Processing helix chain 'B' and resid 1204 through 1213 removed outlier: 3.516A pdb=" N ASN B1208 " --> pdb=" O GLY B1204 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1244 removed outlier: 3.751A pdb=" N VAL B1230 " --> pdb=" O GLN B1226 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B1231 " --> pdb=" O LEU B1227 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1258 removed outlier: 4.250A pdb=" N VAL B1252 " --> pdb=" O PHE B1248 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP B1255 " --> pdb=" O PRO B1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1285 Processing helix chain 'B' and resid 1414 through 1424 removed outlier: 3.610A pdb=" N LEU B1418 " --> pdb=" O ASP B1414 " (cutoff:3.500A) Processing helix chain 'B' and resid 1509 through 1515 Processing helix chain 'B' and resid 1528 through 1537 Processing helix chain 'B' and resid 1590 through 1595 removed outlier: 4.162A pdb=" N LYS B1595 " --> pdb=" O ARG B1591 " (cutoff:3.500A) Processing helix chain 'B' and resid 1609 through 1611 No H-bonds generated for 'chain 'B' and resid 1609 through 1611' Processing helix chain 'B' and resid 1644 through 1655 removed outlier: 3.646A pdb=" N SER B1655 " --> pdb=" O ALA B1651 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.520A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.928A pdb=" N GLY C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.649A pdb=" N ALA C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 119 removed outlier: 3.572A pdb=" N GLU C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 145 removed outlier: 3.569A pdb=" N ALA C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.566A pdb=" N GLU C 206 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR C 209 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 226 removed outlier: 4.372A pdb=" N ALA C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 300 removed outlier: 3.722A pdb=" N THR C 264 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 292 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 3.662A pdb=" N VAL C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 88 removed outlier: 8.529A pdb=" N THR A 41 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 5.890A pdb=" N VAL A 59 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER A 70 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.701A pdb=" N VAL A 163 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A 179 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 165 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN A 177 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 167 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 238 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 293 removed outlier: 5.379A pdb=" N PHE A 273 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLU A 286 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N VAL A 271 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N LEU A 288 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N ALA A 269 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N ARG A 290 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N GLY A 267 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 345 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 339 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA8, first strand: chain 'A' and resid 370 through 375 Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 460 removed outlier: 3.963A pdb=" N GLU A 469 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 521 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 499 through 507 removed outlier: 5.393A pdb=" N LEU A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 496 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 502 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR A 489 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR A 536 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 564 through 566 removed outlier: 3.513A pdb=" N GLY A 587 " --> pdb=" O SER B 787 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 580 through 581 Processing sheet with id=AB4, first strand: chain 'B' and resid 771 through 777 removed outlier: 5.481A pdb=" N LEU B 772 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 597 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 774 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 771 through 777 removed outlier: 5.481A pdb=" N LEU B 772 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 597 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 774 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 829 through 834 removed outlier: 3.685A pdb=" N ARG B 848 " --> pdb=" O ARG B 834 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 853 " --> pdb=" O SER B 892 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 892 " --> pdb=" O ASN B 853 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 839 through 840 removed outlier: 3.503A pdb=" N LEU B 866 " --> pdb=" O HIS B 882 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N HIS B 882 " --> pdb=" O LEU B 866 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 844 through 845 removed outlier: 3.628A pdb=" N GLN B 844 " --> pdb=" O GLU B1470 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 872 through 874 Processing sheet with id=AC1, first strand: chain 'B' and resid 936 through 947 removed outlier: 6.539A pdb=" N VAL B1344 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 944 " --> pdb=" O LEU B1342 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B1342 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR B 946 " --> pdb=" O GLY B1340 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY B1340 " --> pdb=" O THR B 946 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 958 through 962 removed outlier: 4.375A pdb=" N THR B1331 " --> pdb=" O GLN B1299 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B1299 " --> pdb=" O THR B1331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1364 through 1369 Processing sheet with id=AC4, first strand: chain 'B' and resid 1431 through 1432 removed outlier: 3.531A pdb=" N LYS B1431 " --> pdb=" O TYR B1447 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B1476 " --> pdb=" O SER B1406 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1620 through 1621 removed outlier: 3.615A pdb=" N GLU B1560 " --> pdb=" O GLN B1553 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA B1564 " --> pdb=" O LEU B1549 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU B1549 " --> pdb=" O ALA B1564 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLU B1566 " --> pdb=" O THR B1547 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B1547 " --> pdb=" O GLU B1566 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B1568 " --> pdb=" O TYR B1545 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR B1545 " --> pdb=" O THR B1568 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS B1570 " --> pdb=" O TYR B1543 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR B1543 " --> pdb=" O LYS B1570 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B1543 " --> pdb=" O GLY B1606 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B1606 " --> pdb=" O TYR B1543 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1689 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: 5.79 Time building geometry restraints manager: 5.49 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: 2697 1.33 - 1.45: 3460 1.45 - 1.57: 8335 1.57 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 14593 Sorted by residual: bond pdb=" N CYS B1389 " pdb=" CA CYS B1389 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.15e-02 7.56e+03 9.44e+00 bond pdb=" N ILE C 309 " pdb=" CA ILE C 309 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.70e+00 bond pdb=" N GLN C 301 " pdb=" CA GLN C 301 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.09e-02 8.42e+03 8.65e+00 bond pdb=" N ASP B1508 " pdb=" CA ASP B1508 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.14e-02 7.69e+03 8.38e+00 bond pdb=" N LYS C 303 " pdb=" CA LYS C 303 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.88e+00 ... (remaining 14588 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.12: 432 107.12 - 113.86: 8260 113.86 - 120.61: 5605 120.61 - 127.36: 5300 127.36 - 134.10: 154 Bond angle restraints: 19751 Sorted by residual: angle pdb=" N LYS C 298 " pdb=" CA LYS C 298 " pdb=" C LYS C 298 " ideal model delta sigma weight residual 111.40 105.90 5.50 1.22e+00 6.72e-01 2.03e+01 angle pdb=" N VAL C 299 " pdb=" CA VAL C 299 " pdb=" C VAL C 299 " ideal model delta sigma weight residual 112.04 106.43 5.61 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CA LEU C 305 " pdb=" C LEU C 305 " pdb=" O LEU C 305 " ideal model delta sigma weight residual 120.92 116.71 4.21 1.12e+00 7.97e-01 1.41e+01 angle pdb=" CA VAL C 295 " pdb=" C VAL C 295 " pdb=" O VAL C 295 " ideal model delta sigma weight residual 120.64 116.54 4.10 1.09e+00 8.42e-01 1.41e+01 angle pdb=" N PRO C 304 " pdb=" CA PRO C 304 " pdb=" C PRO C 304 " ideal model delta sigma weight residual 111.57 117.20 -5.63 1.52e+00 4.33e-01 1.37e+01 ... (remaining 19746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8183 17.87 - 35.74: 595 35.74 - 53.60: 132 53.60 - 71.47: 28 71.47 - 89.34: 13 Dihedral angle restraints: 8951 sinusoidal: 3684 harmonic: 5267 Sorted by residual: dihedral pdb=" CB CYS B1537 " pdb=" SG CYS B1537 " pdb=" SG CYS B1661 " pdb=" CB CYS B1661 " ideal model delta sinusoidal sigma weight residual 93.00 -178.37 -88.63 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B1518 " pdb=" SG CYS B1518 " pdb=" SG CYS B1590 " pdb=" CB CYS B1590 " ideal model delta sinusoidal sigma weight residual 93.00 150.28 -57.28 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS B1389 " pdb=" SG CYS B1389 " pdb=" SG CYS B1458 " pdb=" CB CYS B1458 " ideal model delta sinusoidal sigma weight residual -86.00 -29.44 -56.56 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 8948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1601 0.035 - 0.069: 350 0.069 - 0.104: 140 0.104 - 0.138: 121 0.138 - 0.173: 7 Chirality restraints: 2219 Sorted by residual: chirality pdb=" CA ILE B1388 " pdb=" N ILE B1388 " pdb=" C ILE B1388 " pdb=" CB ILE B1388 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA VAL C 299 " pdb=" N VAL C 299 " pdb=" C VAL C 299 " pdb=" CB VAL C 299 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA LEU B1459 " pdb=" N LEU B1459 " pdb=" C LEU B1459 " pdb=" CB LEU B1459 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 2216 not shown) Planarity restraints: 2551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 303 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C LYS C 303 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS C 303 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO C 304 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 223 " -0.015 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP C 223 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 223 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 223 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 223 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 223 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 223 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 223 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B1507 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C ARG B1507 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG B1507 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP B1508 " -0.011 2.00e-02 2.50e+03 ... (remaining 2548 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 16 2.34 - 2.98: 6875 2.98 - 3.62: 19341 3.62 - 4.26: 28918 4.26 - 4.90: 50292 Nonbonded interactions: 105442 Sorted by model distance: nonbonded pdb=" SG CYS B1010 " pdb=" CD GLN B1013 " model vdw 1.696 3.630 nonbonded pdb=" O LEU B1109 " pdb=" NH2 ARG C 77 " model vdw 1.829 2.520 nonbonded pdb=" O ALA C 219 " pdb=" OG SER C 222 " model vdw 2.025 2.440 nonbonded pdb=" OD1 ASP C 210 " pdb=" OG SER C 212 " model vdw 2.025 2.440 nonbonded pdb=" OG1 THR C 35 " pdb=" OE1 GLU C 37 " model vdw 2.108 2.440 ... (remaining 105437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.790 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 39.760 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14593 Z= 0.158 Angle : 0.475 5.633 19751 Z= 0.278 Chirality : 0.043 0.173 2219 Planarity : 0.003 0.033 2551 Dihedral : 13.365 89.340 5513 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 0.82 % Allowed : 0.32 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.20), residues: 1791 helix: 3.10 (0.26), residues: 430 sheet: 0.94 (0.22), residues: 545 loop : -0.55 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 223 HIS 0.003 0.000 HIS B1494 PHE 0.005 0.001 PHE A 475 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.000 ARG B1512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 300 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1430 SER cc_start: 0.7871 (m) cc_final: 0.7427 (t) REVERT: C 257 TRP cc_start: 0.1945 (m-10) cc_final: 0.1735 (m-10) outliers start: 13 outliers final: 5 residues processed: 309 average time/residue: 0.2999 time to fit residues: 129.7282 Evaluate side-chains 176 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1013 GLN Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 309 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN B1119 GLN B1259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14593 Z= 0.191 Angle : 0.567 12.073 19751 Z= 0.289 Chirality : 0.043 0.209 2219 Planarity : 0.004 0.051 2551 Dihedral : 3.752 68.363 1957 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.71 % Allowed : 8.84 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.17 (0.20), residues: 1791 helix: 2.74 (0.24), residues: 451 sheet: 1.10 (0.23), residues: 525 loop : -0.60 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 81 HIS 0.007 0.001 HIS B 918 PHE 0.010 0.001 PHE A 475 TYR 0.020 0.001 TYR A 261 ARG 0.007 0.000 ARG B 736 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1388 ILE cc_start: 0.8394 (pt) cc_final: 0.8111 (pt) outliers start: 27 outliers final: 15 residues processed: 182 average time/residue: 0.2720 time to fit residues: 73.4387 Evaluate side-chains 149 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1456 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.0270 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN B 858 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14593 Z= 0.223 Angle : 0.556 14.406 19751 Z= 0.288 Chirality : 0.043 0.255 2219 Planarity : 0.004 0.036 2551 Dihedral : 3.743 32.693 1949 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.27 % Allowed : 9.60 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.20), residues: 1791 helix: 2.60 (0.24), residues: 448 sheet: 1.01 (0.22), residues: 538 loop : -0.85 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 223 HIS 0.006 0.001 HIS B1464 PHE 0.021 0.001 PHE B1519 TYR 0.022 0.001 TYR A 261 ARG 0.005 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 171 average time/residue: 0.2670 time to fit residues: 67.6311 Evaluate side-chains 148 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1499 ASP Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.0070 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1453 HIS C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14593 Z= 0.170 Angle : 0.507 10.680 19751 Z= 0.262 Chirality : 0.042 0.202 2219 Planarity : 0.003 0.038 2551 Dihedral : 3.633 27.849 1949 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.34 % Allowed : 10.49 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.91 (0.20), residues: 1791 helix: 2.65 (0.24), residues: 447 sheet: 0.95 (0.22), residues: 545 loop : -0.87 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 223 HIS 0.004 0.001 HIS A 47 PHE 0.025 0.001 PHE B1519 TYR 0.017 0.001 TYR A 261 ARG 0.003 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.5606 (mmm) cc_final: 0.5136 (mmm) REVERT: A 373 MET cc_start: 0.6741 (mmm) cc_final: 0.6338 (mmm) REVERT: B 826 MET cc_start: 0.7105 (pmm) cc_final: 0.6401 (pmm) outliers start: 37 outliers final: 21 residues processed: 160 average time/residue: 0.2779 time to fit residues: 65.8909 Evaluate side-chains 136 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 0.0060 chunk 43 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14593 Z= 0.274 Angle : 0.566 10.908 19751 Z= 0.295 Chirality : 0.043 0.219 2219 Planarity : 0.004 0.043 2551 Dihedral : 3.920 27.660 1949 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.40 % Allowed : 11.62 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.74 (0.20), residues: 1791 helix: 2.30 (0.24), residues: 455 sheet: 0.85 (0.22), residues: 545 loop : -0.87 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 223 HIS 0.007 0.001 HIS B 919 PHE 0.027 0.002 PHE B1659 TYR 0.014 0.001 TYR B1261 ARG 0.005 0.000 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6673 (mmm) cc_final: 0.6299 (mmm) REVERT: B 826 MET cc_start: 0.7163 (pmm) cc_final: 0.6607 (pmm) REVERT: C 136 THR cc_start: 0.6792 (p) cc_final: 0.6588 (p) outliers start: 38 outliers final: 27 residues processed: 153 average time/residue: 0.2655 time to fit residues: 62.3550 Evaluate side-chains 139 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS A 579 GLN B1423 ASN C 120 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14593 Z= 0.420 Angle : 0.645 11.658 19751 Z= 0.338 Chirality : 0.045 0.243 2219 Planarity : 0.004 0.037 2551 Dihedral : 4.508 38.874 1949 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.84 % Allowed : 12.13 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.42 (0.20), residues: 1791 helix: 2.11 (0.24), residues: 440 sheet: 0.57 (0.22), residues: 553 loop : -1.01 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 223 HIS 0.008 0.001 HIS B1464 PHE 0.021 0.002 PHE B1519 TYR 0.018 0.002 TYR B 852 ARG 0.004 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 124 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6673 (mmm) cc_final: 0.6360 (mmm) REVERT: B 826 MET cc_start: 0.6968 (pmm) cc_final: 0.6580 (pmm) REVERT: B 937 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7233 (ttm-80) REVERT: B 990 MET cc_start: 0.8045 (mtm) cc_final: 0.7758 (mtt) REVERT: C 136 THR cc_start: 0.6786 (p) cc_final: 0.6234 (p) outliers start: 45 outliers final: 35 residues processed: 159 average time/residue: 0.2626 time to fit residues: 62.9248 Evaluate side-chains 149 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 113 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1595 LYS Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 265 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 173 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14593 Z= 0.223 Angle : 0.545 10.201 19751 Z= 0.286 Chirality : 0.043 0.201 2219 Planarity : 0.003 0.039 2551 Dihedral : 4.135 36.374 1949 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.65 % Allowed : 12.82 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.57 (0.20), residues: 1791 helix: 2.33 (0.24), residues: 445 sheet: 0.65 (0.22), residues: 546 loop : -0.97 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.026 0.001 PHE B1519 TYR 0.012 0.001 TYR A 261 ARG 0.004 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6596 (mmm) cc_final: 0.6324 (mmm) REVERT: B 826 MET cc_start: 0.6911 (pmm) cc_final: 0.6565 (pmm) REVERT: B 937 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7319 (ttm-80) REVERT: B 990 MET cc_start: 0.7966 (mtm) cc_final: 0.7692 (mtt) REVERT: C 45 MET cc_start: 0.6680 (mmt) cc_final: 0.6456 (mmm) outliers start: 42 outliers final: 33 residues processed: 162 average time/residue: 0.2622 time to fit residues: 64.5722 Evaluate side-chains 154 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1479 VAL Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1595 LYS Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.0670 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 136 optimal weight: 1.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14593 Z= 0.143 Angle : 0.514 8.926 19751 Z= 0.269 Chirality : 0.042 0.166 2219 Planarity : 0.003 0.039 2551 Dihedral : 3.805 29.349 1949 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.96 % Allowed : 13.77 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.69 (0.20), residues: 1791 helix: 2.48 (0.24), residues: 445 sheet: 0.80 (0.23), residues: 515 loop : -0.93 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 223 HIS 0.006 0.001 HIS C 135 PHE 0.028 0.001 PHE B1519 TYR 0.014 0.001 TYR B1545 ARG 0.003 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6524 (mmm) cc_final: 0.6265 (mmm) REVERT: B 826 MET cc_start: 0.6925 (pmm) cc_final: 0.6554 (pmm) outliers start: 31 outliers final: 25 residues processed: 152 average time/residue: 0.2734 time to fit residues: 62.3047 Evaluate side-chains 145 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 161 optimal weight: 0.0070 chunk 97 optimal weight: 0.2980 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 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 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14593 Z= 0.202 Angle : 0.542 9.229 19751 Z= 0.282 Chirality : 0.042 0.194 2219 Planarity : 0.003 0.038 2551 Dihedral : 3.826 25.903 1949 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.90 % Allowed : 14.47 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.64 (0.20), residues: 1791 helix: 2.40 (0.24), residues: 445 sheet: 0.74 (0.23), residues: 522 loop : -0.93 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.026 0.001 PHE B1519 TYR 0.012 0.001 TYR A 261 ARG 0.003 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 826 MET cc_start: 0.6938 (pmm) cc_final: 0.6600 (pmm) outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 0.2694 time to fit residues: 58.9396 Evaluate side-chains 142 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1557 ASP Chi-restraints excluded: chain B residue 1595 LYS Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14593 Z= 0.164 Angle : 0.522 8.830 19751 Z= 0.272 Chirality : 0.042 0.179 2219 Planarity : 0.003 0.039 2551 Dihedral : 3.754 24.588 1949 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.58 % Allowed : 14.85 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.71 (0.20), residues: 1791 helix: 2.48 (0.24), residues: 446 sheet: 0.80 (0.23), residues: 516 loop : -0.91 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.027 0.001 PHE B1519 TYR 0.015 0.001 TYR B1545 ARG 0.003 0.000 ARG A 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 826 MET cc_start: 0.6961 (pmm) cc_final: 0.6622 (pmm) REVERT: B 990 MET cc_start: 0.7832 (mtm) cc_final: 0.7535 (mtt) REVERT: C 136 THR cc_start: 0.6539 (p) cc_final: 0.5932 (p) outliers start: 25 outliers final: 23 residues processed: 148 average time/residue: 0.2617 time to fit residues: 58.7423 Evaluate side-chains 144 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1458 CYS Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061627 restraints weight = 39776.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064078 restraints weight = 19325.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065649 restraints weight = 12706.227| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14593 Z= 0.176 Angle : 0.527 9.915 19751 Z= 0.276 Chirality : 0.042 0.175 2219 Planarity : 0.003 0.042 2551 Dihedral : 3.722 22.783 1949 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.64 % Allowed : 15.03 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.72 (0.20), residues: 1791 helix: 2.46 (0.24), residues: 443 sheet: 0.79 (0.23), residues: 531 loop : -0.88 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 223 HIS 0.007 0.001 HIS C 135 PHE 0.026 0.001 PHE B1519 TYR 0.012 0.001 TYR A 261 ARG 0.004 0.000 ARG C 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.91 seconds wall clock time: 53 minutes 51.05 seconds (3231.05 seconds total)