Starting phenix.real_space_refine (version: dev) on Tue Feb 28 02:21:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/02_2023/5gap_8014.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/02_2023/5gap_8014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/02_2023/5gap_8014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/02_2023/5gap_8014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/02_2023/5gap_8014.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/02_2023/5gap_8014.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.008 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 Process input model Symmetric amino acids flipped Residue "A GLU 757": "OE1" <-> "OE2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A GLU 933": "OE1" <-> "OE2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A GLU 1037": "OE1" <-> "OE2" Residue "A GLU 1129": "OE1" <-> "OE2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A GLU 1178": "OE1" <-> "OE2" Residue "A GLU 1180": "OE1" <-> "OE2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A GLU 1479": "OE1" <-> "OE2" Residue "A GLU 1708": "OE1" <-> "OE2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "A GLU 1927": "OE1" <-> "OE2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "A GLU 2052": "OE1" <-> "OE2" Residue "A GLU 2062": "OE1" <-> "OE2" Residue "A GLU 2078": "OE1" <-> "OE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H ARG 337": "NH1" <-> "NH2" Residue "J GLU 251": "OE1" <-> "OE2" Residue "J GLU 317": "OE1" <-> "OE2" Residue "J ARG 392": "NH1" <-> "NH2" Residue "J GLU 470": "OE1" <-> "OE2" Residue "J GLU 555": "OE1" <-> "OE2" Residue "J ASP 588": "OD1" <-> "OD2" Residue "J ARG 659": "NH1" <-> "NH2" Residue "J GLU 713": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G GLU 282": "OE1" <-> "OE2" Residue "G GLU 332": "OE1" <-> "OE2" Residue "G ARG 371": "NH1" <-> "NH2" Residue "G GLU 386": "OE1" <-> "OE2" Residue "G GLU 393": "OE1" <-> "OE2" Residue "G GLU 429": "OE1" <-> "OE2" Residue "G GLU 461": "OE1" <-> "OE2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31576 Number of models: 1 Model: "" Number of chains: 12 Chain: "V" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1426 Classifications: {'RNA': 67} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 56} Chain: "W" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1190 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 25} Link IDs: {'rna2p': 6, 'rna3p': 49} Chain breaks: 2 Chain: "U" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'RNA': 20} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 17} Chain: "x" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 410 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'UNK:plan-1': 82} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 11066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 11066 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 56, 'TRANS': 1289} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2789 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 348} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 5822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5822 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 700} Chain breaks: 4 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "D" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1151 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "F" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3218 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 15, 'TRANS': 396} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2632 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 115} Chain: "B" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 522 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 65} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 17.31, per 1000 atoms: 0.55 Number of scatterers: 31576 At special positions: 0 Unit cell: (183.04, 155.87, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 143 15.00 O 6294 8.00 N 5491 7.00 C 19527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.82 Conformation dependent library (CDL) restraints added in 4.1 seconds 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6876 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 19 sheets defined 59.4% alpha, 9.2% beta 44 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 9.55 Creating SS restraints... Processing helix chain 'x' and resid 21 through 46 Processing helix chain 'x' and resid 53 through 62 Processing helix chain 'x' and resid 102 through 120 Processing helix chain 'A' and resid 752 through 770 removed outlier: 4.196A pdb=" N LEU A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 796 removed outlier: 3.664A pdb=" N LYS A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 837 removed outlier: 3.765A pdb=" N SER A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 871 Processing helix chain 'A' and resid 875 through 894 Processing helix chain 'A' and resid 908 through 926 removed outlier: 4.207A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 985 through 1007 removed outlier: 3.665A pdb=" N ILE A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1034 Processing helix chain 'A' and resid 1057 through 1061 Processing helix chain 'A' and resid 1062 through 1074 removed outlier: 3.520A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1087 Processing helix chain 'A' and resid 1109 through 1127 Processing helix chain 'A' and resid 1127 through 1136 Processing helix chain 'A' and resid 1149 through 1156 removed outlier: 3.611A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 Processing helix chain 'A' and resid 1216 through 1234 Processing helix chain 'A' and resid 1273 through 1275 No H-bonds generated for 'chain 'A' and resid 1273 through 1275' Processing helix chain 'A' and resid 1305 through 1321 Processing helix chain 'A' and resid 1327 through 1347 Processing helix chain 'A' and resid 1348 through 1351 Processing helix chain 'A' and resid 1353 through 1376 Processing helix chain 'A' and resid 1385 through 1390 Processing helix chain 'A' and resid 1408 through 1413 removed outlier: 3.553A pdb=" N SER A1413 " --> pdb=" O SER A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1444 removed outlier: 3.924A pdb=" N ILE A1444 " --> pdb=" O PHE A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1471 Processing helix chain 'A' and resid 1490 through 1495 removed outlier: 4.227A pdb=" N LEU A1494 " --> pdb=" O ARG A1490 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A1495 " --> pdb=" O ILE A1491 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1490 through 1495' Processing helix chain 'A' and resid 1498 through 1503 Processing helix chain 'A' and resid 1507 through 1515 Processing helix chain 'A' and resid 1516 through 1518 No H-bonds generated for 'chain 'A' and resid 1516 through 1518' Processing helix chain 'A' and resid 1529 through 1534 Processing helix chain 'A' and resid 1539 through 1550 Processing helix chain 'A' and resid 1551 through 1560 removed outlier: 4.058A pdb=" N THR A1555 " --> pdb=" O GLY A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1566 Processing helix chain 'A' and resid 1577 through 1586 Processing helix chain 'A' and resid 1591 through 1615 Proline residue: A1602 - end of helix Proline residue: A1612 - end of helix Processing helix chain 'A' and resid 1638 through 1649 Processing helix chain 'A' and resid 1652 through 1672 Processing helix chain 'A' and resid 1672 through 1677 removed outlier: 4.096A pdb=" N LEU A1676 " --> pdb=" O GLU A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1693 removed outlier: 4.432A pdb=" N SER A1691 " --> pdb=" O PRO A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1762 removed outlier: 3.709A pdb=" N THR A1761 " --> pdb=" O LEU A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1809 removed outlier: 3.787A pdb=" N LEU A1797 " --> pdb=" O GLY A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1824 Processing helix chain 'A' and resid 1840 through 1845 removed outlier: 3.600A pdb=" N ASN A1845 " --> pdb=" O GLU A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1904 through 1924 Processing helix chain 'A' and resid 1937 through 1939 No H-bonds generated for 'chain 'A' and resid 1937 through 1939' Processing helix chain 'A' and resid 1940 through 1948 Processing helix chain 'A' and resid 1963 through 1969 removed outlier: 4.200A pdb=" N SER A1966 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A1969 " --> pdb=" O SER A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1981 Processing helix chain 'A' and resid 1994 through 1998 Processing helix chain 'A' and resid 2000 through 2018 Processing helix chain 'A' and resid 2018 through 2027 Processing helix chain 'A' and resid 2044 through 2068 Processing helix chain 'A' and resid 2074 through 2084 Processing helix chain 'A' and resid 2092 through 2104 Processing helix chain 'H' and resid 114 through 145 removed outlier: 3.890A pdb=" N PHE H 123 " --> pdb=" O PHE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 removed outlier: 3.916A pdb=" N GLU H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU H 152 " --> pdb=" O THR H 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 170 Processing helix chain 'J' and resid 171 through 177 Processing helix chain 'J' and resid 186 through 198 Proline residue: J 194 - end of helix Processing helix chain 'J' and resid 206 through 210 Processing helix chain 'J' and resid 219 through 236 removed outlier: 3.689A pdb=" N LYS J 225 " --> pdb=" O GLU J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 255 removed outlier: 4.319A pdb=" N ARG J 255 " --> pdb=" O GLU J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 271 removed outlier: 3.645A pdb=" N ASN J 266 " --> pdb=" O LYS J 262 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU J 270 " --> pdb=" O ASN J 266 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N CYS J 271 " --> pdb=" O GLY J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 285 removed outlier: 3.641A pdb=" N TRP J 278 " --> pdb=" O SER J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 303 removed outlier: 3.523A pdb=" N ASN J 301 " --> pdb=" O ALA J 297 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE J 302 " --> pdb=" O THR J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 317 removed outlier: 4.195A pdb=" N TRP J 310 " --> pdb=" O SER J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 334 Processing helix chain 'J' and resid 337 through 348 removed outlier: 4.098A pdb=" N GLU J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 365 Processing helix chain 'J' and resid 368 through 380 removed outlier: 3.763A pdb=" N GLN J 379 " --> pdb=" O TYR J 375 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER J 380 " --> pdb=" O THR J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 395 removed outlier: 3.520A pdb=" N ILE J 394 " --> pdb=" O SER J 390 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 395 " --> pdb=" O PHE J 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 410 removed outlier: 4.082A pdb=" N SER J 405 " --> pdb=" O ILE J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 435 removed outlier: 3.650A pdb=" N LYS J 426 " --> pdb=" O VAL J 422 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU J 432 " --> pdb=" O GLY J 428 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER J 433 " --> pdb=" O LEU J 429 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN J 435 " --> pdb=" O GLU J 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 454 removed outlier: 3.666A pdb=" N LYS J 446 " --> pdb=" O SER J 442 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU J 451 " --> pdb=" O ARG J 447 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA J 454 " --> pdb=" O ALA J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 476 removed outlier: 3.589A pdb=" N ALA J 463 " --> pdb=" O LEU J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 479 through 491 removed outlier: 3.698A pdb=" N ASN J 483 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 509 Processing helix chain 'J' and resid 511 through 526 Processing helix chain 'J' and resid 531 through 543 removed outlier: 3.947A pdb=" N THR J 543 " --> pdb=" O LEU J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 557 Processing helix chain 'J' and resid 559 through 572 Processing helix chain 'J' and resid 576 through 589 Processing helix chain 'J' and resid 594 through 608 removed outlier: 4.317A pdb=" N PHE J 598 " --> pdb=" O LEU J 594 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE J 599 " --> pdb=" O ASP J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 609 through 624 removed outlier: 3.653A pdb=" N SER J 623 " --> pdb=" O GLN J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 625 through 627 No H-bonds generated for 'chain 'J' and resid 625 through 627' Processing helix chain 'J' and resid 633 through 649 removed outlier: 3.681A pdb=" N TYR J 637 " --> pdb=" O GLU J 633 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR J 639 " --> pdb=" O LEU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 652 through 664 removed outlier: 4.380A pdb=" N LEU J 656 " --> pdb=" O ALA J 652 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 661 " --> pdb=" O ASN J 657 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS J 662 " --> pdb=" O GLU J 658 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE J 664 " --> pdb=" O CYS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 667 through 681 removed outlier: 3.846A pdb=" N PHE J 671 " --> pdb=" O CYS J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 683 through 698 Processing helix chain 'J' and resid 701 through 715 removed outlier: 3.731A pdb=" N TRP J 705 " --> pdb=" O CYS J 701 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 733 removed outlier: 3.831A pdb=" N ALA J 722 " --> pdb=" O ASN J 718 " (cutoff:3.500A) Processing helix chain 'J' and resid 737 through 750 Processing helix chain 'J' and resid 753 through 767 Processing helix chain 'J' and resid 770 through 784 removed outlier: 4.133A pdb=" N GLY J 784 " --> pdb=" O LEU J 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 802 Processing helix chain 'J' and resid 804 through 819 Processing helix chain 'J' and resid 820 through 835 Processing helix chain 'J' and resid 839 through 852 removed outlier: 3.689A pdb=" N VAL J 843 " --> pdb=" O GLY J 839 " (cutoff:3.500A) Processing helix chain 'J' and resid 856 through 863 Processing helix chain 'J' and resid 871 through 880 Processing helix chain 'J' and resid 889 through 898 Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.706A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 53 removed outlier: 3.713A pdb=" N GLU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 127 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.592A pdb=" N LEU F 57 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA F 58 " --> pdb=" O PHE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 78 Proline residue: F 75 - end of helix Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 96 through 121 Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 125 through 131 removed outlier: 4.416A pdb=" N SER F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 146 Processing helix chain 'F' and resid 155 through 164 removed outlier: 3.505A pdb=" N HIS F 160 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 161 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 190 through 226 removed outlier: 4.494A pdb=" N SER F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 234 through 246 Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 255 through 260 removed outlier: 3.508A pdb=" N ILE F 259 " --> pdb=" O PRO F 255 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA F 260 " --> pdb=" O SER F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 260' Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.878A pdb=" N PHE F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 293 Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'F' and resid 328 through 346 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.548A pdb=" N LYS F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 389 Processing helix chain 'F' and resid 410 through 414 removed outlier: 3.772A pdb=" N SER F 413 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN F 414 " --> pdb=" O GLY F 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 410 through 414' Processing helix chain 'F' and resid 415 through 422 Processing helix chain 'F' and resid 438 through 457 Processing helix chain 'G' and resid 151 through 164 removed outlier: 3.697A pdb=" N HIS G 164 " --> pdb=" O TYR G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 189 removed outlier: 3.944A pdb=" N MET G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 200 removed outlier: 4.337A pdb=" N GLU G 198 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 262 Processing helix chain 'G' and resid 289 through 330 removed outlier: 3.612A pdb=" N GLU G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 363 removed outlier: 3.846A pdb=" N ARG G 353 " --> pdb=" O ASN G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 398 Processing helix chain 'G' and resid 447 through 456 Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'K' and resid 13 through 30 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 65 through 75 removed outlier: 4.240A pdb=" N LEU K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 92 Processing helix chain 'K' and resid 110 through 126 removed outlier: 4.020A pdb=" N ILE K 126 " --> pdb=" O GLU K 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 412 through 423 removed outlier: 4.191A pdb=" N THR B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Proline residue: B 421 - end of helix Processing helix chain 'B' and resid 425 through 433 Processing sheet with id=AA1, first strand: chain 'A' and resid 981 through 983 removed outlier: 6.293A pdb=" N VAL A 967 " --> pdb=" O ASN A1091 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1013 through 1014 removed outlier: 5.752A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A1249 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1258 through 1262 Processing sheet with id=AA4, first strand: chain 'A' and resid 1414 through 1417 Processing sheet with id=AA5, first strand: chain 'A' and resid 1825 through 1827 Processing sheet with id=AA6, first strand: chain 'A' and resid 1678 through 1683 removed outlier: 6.776A pdb=" N GLU A1704 " --> pdb=" O GLU A1679 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A1681 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR A1702 " --> pdb=" O VAL A1681 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N ILE A1701 " --> pdb=" O GLN A1737 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N GLN A1737 " --> pdb=" O ILE A1701 " (cutoff:3.500A) removed outlier: 12.291A pdb=" N MET A1703 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N ASP A1735 " --> pdb=" O MET A1703 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N SER A1705 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N TRP A1733 " --> pdb=" O SER A1705 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N HIS A1707 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS A1731 " --> pdb=" O HIS A1707 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL A1773 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP A1733 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE A1775 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASP A1735 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A1777 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN A1737 " --> pdb=" O ILE A1777 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1955 through 1957 removed outlier: 6.029A pdb=" N LEU A1850 " --> pdb=" O ILE A1934 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A1881 " --> pdb=" O PHE A1890 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 166 through 172 removed outlier: 5.419A pdb=" N LEU H 167 " --> pdb=" O ASN H 465 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN H 465 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY H 169 " --> pdb=" O LEU H 463 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER H 460 " --> pdb=" O GLY H 456 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY H 456 " --> pdb=" O SER H 460 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 452 " --> pdb=" O TRP H 464 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 180 through 183 removed outlier: 3.622A pdb=" N GLN H 200 " --> pdb=" O THR H 192 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL H 201 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN H 208 " --> pdb=" O ASN H 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 221 through 225 removed outlier: 4.180A pdb=" N ALA H 223 " --> pdb=" O CYS H 237 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 243 " --> pdb=" O ASP H 260 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP H 260 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN H 245 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 268 through 273 Processing sheet with id=AB3, first strand: chain 'H' and resid 310 through 315 removed outlier: 3.569A pdb=" N SER H 340 " --> pdb=" O ASP H 335 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 354 through 357 removed outlier: 3.937A pdb=" N VAL H 375 " --> pdb=" O ASN H 387 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN H 387 " --> pdb=" O VAL H 375 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 396 through 400 removed outlier: 4.138A pdb=" N GLY H 414 " --> pdb=" O LEU H 418 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU H 418 " --> pdb=" O GLY H 414 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 419 " --> pdb=" O SER H 432 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER H 432 " --> pdb=" O ILE H 419 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL H 421 " --> pdb=" O MET H 430 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 8 through 9 Processing sheet with id=AB7, first strand: chain 'G' and resid 366 through 371 Processing sheet with id=AB8, first strand: chain 'G' and resid 366 through 371 removed outlier: 3.907A pdb=" N TYR G 337 " --> pdb=" O LEU G 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 406 through 408 Processing sheet with id=AC1, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.395A pdb=" N ALA K 100 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE K 52 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE K 102 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N VAL K 79 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE K 52 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL K 81 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET K 54 " --> pdb=" O VAL K 81 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 17.25 Time building geometry restraints manager: 15.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4941 1.31 - 1.44: 9190 1.44 - 1.56: 17864 1.56 - 1.69: 301 1.69 - 1.82: 208 Bond restraints: 32504 Sorted by residual: bond pdb=" CA ASN A1369 " pdb=" C ASN A1369 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.30e-02 5.92e+03 2.75e+01 bond pdb=" C ASN A1369 " pdb=" O ASN A1369 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.28e+01 bond pdb=" CA ASP D 78 " pdb=" CB ASP D 78 " ideal model delta sigma weight residual 1.522 1.554 -0.032 7.00e-03 2.04e+04 2.08e+01 bond pdb=" N ILE F 222 " pdb=" CA ILE F 222 " ideal model delta sigma weight residual 1.461 1.508 -0.048 1.24e-02 6.50e+03 1.47e+01 bond pdb=" N ILE A 882 " pdb=" CA ILE A 882 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.23e-02 6.61e+03 1.46e+01 ... (remaining 32499 not shown) Histogram of bond angle deviations from ideal: 97.57 - 105.41: 1206 105.41 - 113.25: 17245 113.25 - 121.09: 15577 121.09 - 128.93: 10277 128.93 - 136.77: 354 Bond angle restraints: 44659 Sorted by residual: angle pdb=" C4' C U 95 " pdb=" C3' C U 95 " pdb=" O3' C U 95 " ideal model delta sigma weight residual 109.40 121.52 -12.12 1.50e+00 4.44e-01 6.52e+01 angle pdb=" O3' A W 49 " pdb=" C3' A W 49 " pdb=" C2' A W 49 " ideal model delta sigma weight residual 109.50 121.14 -11.64 1.50e+00 4.44e-01 6.03e+01 angle pdb=" N THR J 239 " pdb=" CA THR J 239 " pdb=" C THR J 239 " ideal model delta sigma weight residual 111.71 120.62 -8.91 1.15e+00 7.56e-01 6.00e+01 angle pdb=" CA ASN A1369 " pdb=" C ASN A1369 " pdb=" O ASN A1369 " ideal model delta sigma weight residual 120.55 112.66 7.89 1.06e+00 8.90e-01 5.55e+01 angle pdb=" O3' A V 17 " pdb=" C3' A V 17 " pdb=" C2' A V 17 " ideal model delta sigma weight residual 113.70 124.74 -11.04 1.50e+00 4.44e-01 5.41e+01 ... (remaining 44654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 18744 35.72 - 71.45: 639 71.45 - 107.17: 47 107.17 - 142.90: 3 142.90 - 178.62: 9 Dihedral angle restraints: 19442 sinusoidal: 8890 harmonic: 10552 Sorted by residual: dihedral pdb=" C5' G W 31 " pdb=" C4' G W 31 " pdb=" C3' G W 31 " pdb=" O3' G W 31 " ideal model delta sinusoidal sigma weight residual 147.00 72.33 74.67 1 8.00e+00 1.56e-02 1.10e+02 dihedral pdb=" C5' A W 49 " pdb=" C4' A W 49 " pdb=" C3' A W 49 " pdb=" O3' A W 49 " ideal model delta sinusoidal sigma weight residual 147.00 74.90 72.10 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' U W 32 " pdb=" C4' U W 32 " pdb=" C3' U W 32 " pdb=" O3' U W 32 " ideal model delta sinusoidal sigma weight residual 147.00 77.26 69.74 1 8.00e+00 1.56e-02 9.81e+01 ... (remaining 19439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4501 0.134 - 0.268: 561 0.268 - 0.401: 57 0.401 - 0.535: 11 0.535 - 0.669: 6 Chirality restraints: 5136 Sorted by residual: chirality pdb=" C3' U V 31 " pdb=" C4' U V 31 " pdb=" O3' U V 31 " pdb=" C2' U V 31 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C3' C V 39 " pdb=" C4' C V 39 " pdb=" O3' C V 39 " pdb=" C2' C V 39 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.58 2.00e-01 2.50e+01 8.51e+00 chirality pdb=" C3' C W 84 " pdb=" C4' C W 84 " pdb=" O3' C W 84 " pdb=" C2' C W 84 " both_signs ideal model delta sigma weight residual False -2.74 -2.17 -0.57 2.00e-01 2.50e+01 8.23e+00 ... (remaining 5133 not shown) Planarity restraints: 5181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 979 " 0.091 5.00e-02 4.00e+02 1.41e-01 3.17e+01 pdb=" N PRO A 980 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO A 980 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 980 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G V 44 " 0.078 2.00e-02 2.50e+03 3.17e-02 3.01e+01 pdb=" N9 G V 44 " -0.068 2.00e-02 2.50e+03 pdb=" C8 G V 44 " -0.015 2.00e-02 2.50e+03 pdb=" N7 G V 44 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G V 44 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G V 44 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G V 44 " 0.023 2.00e-02 2.50e+03 pdb=" N1 G V 44 " 0.010 2.00e-02 2.50e+03 pdb=" C2 G V 44 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G V 44 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G V 44 " -0.015 2.00e-02 2.50e+03 pdb=" C4 G V 44 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G V 14 " 0.005 2.00e-02 2.50e+03 2.86e-02 2.45e+01 pdb=" N9 G V 14 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G V 14 " -0.007 2.00e-02 2.50e+03 pdb=" N7 G V 14 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G V 14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G V 14 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G V 14 " 0.046 2.00e-02 2.50e+03 pdb=" N1 G V 14 " -0.079 2.00e-02 2.50e+03 pdb=" C2 G V 14 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G V 14 " 0.037 2.00e-02 2.50e+03 pdb=" N3 G V 14 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G V 14 " 0.000 2.00e-02 2.50e+03 ... (remaining 5178 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 757 2.69 - 3.25: 33406 3.25 - 3.80: 53173 3.80 - 4.35: 69491 4.35 - 4.90: 107447 Nonbonded interactions: 264274 Sorted by model distance: nonbonded pdb=" O ASP J 199 " pdb=" N LEU J 201 " model vdw 2.143 2.520 nonbonded pdb=" O ALA K 40 " pdb=" OG1 THR K 43 " model vdw 2.207 2.440 nonbonded pdb=" O2' A W 49 " pdb=" OP2 G W 50 " model vdw 2.225 2.440 nonbonded pdb=" OP2 A V 18 " pdb=" NZ LYS F 378 " model vdw 2.240 2.520 nonbonded pdb=" O PHE A1562 " pdb=" OG1 THR A1565 " model vdw 2.255 2.440 ... (remaining 264269 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 121 5.16 5 C 19527 2.51 5 N 5491 2.21 5 O 6294 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.220 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: 0.040 Extract box with map and model: 14.960 Check model and map are aligned: 0.480 Process input model: 93.440 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.300 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4818 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 : 0.008 0.071 32504 Z= 0.500 Angle : 1.509 15.387 44659 Z= 1.087 Chirality : 0.092 0.669 5136 Planarity : 0.007 0.141 5181 Dihedral : 17.394 178.621 12566 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 1.47 % Allowed : 8.81 % Favored : 89.73 % Rotamer Outliers : 4.23 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.09 % Twisted Proline : 1.46 % Twisted General : 0.09 % 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: -1.15 (0.12), residues: 3475 helix: 1.00 (0.09), residues: 1799 sheet: -2.60 (0.23), residues: 371 loop : -2.79 (0.15), residues: 1305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 948 time to evaluate : 3.745 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: 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: 130 outliers final: 32 residues processed: 1036 average time/residue: 0.4995 time to fit residues: 789.4798 Evaluate side-chains 560 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 528 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.3159 time to fit residues: 23.4139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 287 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1030 GLN A1086 ASN A1087 ASN ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN A1586 GLN A1635 HIS A1677 GLN ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 GLN A1831 GLN A1869 ASN A2054 GLN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 GLN H 316 GLN ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS J 184 ASN J 353 GLN J 363 GLN J 389 ASN J 507 GLN J 676 GLN J 733 ASN J 785 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN F 270 HIS F 320 GLN F 451 GLN G 283 ASN K 45 ASN K 75 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4836 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 32504 Z= 0.319 Angle : 0.795 21.392 44659 Z= 0.406 Chirality : 0.046 0.317 5136 Planarity : 0.005 0.084 5181 Dihedral : 13.597 178.989 5573 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.01 % Favored : 93.70 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.12 % Twisted Proline : 1.46 % Twisted General : 0.03 % 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: 0.63 (0.15), residues: 3475 helix: 2.59 (0.12), residues: 1834 sheet: -2.16 (0.24), residues: 356 loop : -2.20 (0.16), residues: 1285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 597 time to evaluate : 3.731 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: symmetry clash outliers start: 112 outliers final: 51 residues processed: 673 average time/residue: 0.4645 time to fit residues: 494.1895 Evaluate side-chains 511 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 460 time to evaluate : 3.624 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 1 residues processed: 51 average time/residue: 0.3353 time to fit residues: 36.5169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 277 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 360 optimal weight: 10.0000 chunk 297 optimal weight: 0.9990 chunk 331 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 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 861 GLN ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 ASN ** A1600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 GLN ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS ** J 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN G 276 ASN G 283 ASN G 343 GLN K 75 ASN B 407 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4840 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 32504 Z= 0.239 Angle : 0.708 21.003 44659 Z= 0.360 Chirality : 0.043 0.469 5136 Planarity : 0.005 0.098 5181 Dihedral : 13.014 175.247 5573 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.87 % Favored : 93.90 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.09 % Twisted Proline : 1.46 % Twisted General : 0.06 % 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: 0.75 (0.15), residues: 3475 helix: 2.48 (0.12), residues: 1837 sheet: -1.88 (0.25), residues: 348 loop : -1.87 (0.17), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 530 time to evaluate : 3.961 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: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 34 residues processed: 598 average time/residue: 0.4593 time to fit residues: 436.9330 Evaluate side-chains 487 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 453 time to evaluate : 3.336 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.3589 time to fit residues: 27.2278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 8.9990 chunk 251 optimal weight: 0.5980 chunk 173 optimal weight: 5.9990 chunk 36 optimal weight: 0.0770 chunk 159 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 335 optimal weight: 0.0070 chunk 354 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 317 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 870 ASN ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1856 ASN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 ASN H 388 GLN J 382 HIS J 537 GLN ** J 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 641 ASN J 805 HIS J 820 GLN ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS G 187 ASN G 300 GLN G 316 HIS G 343 GLN K 75 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4841 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 32504 Z= 0.194 Angle : 0.684 21.169 44659 Z= 0.342 Chirality : 0.042 0.453 5136 Planarity : 0.005 0.093 5181 Dihedral : 12.702 175.991 5573 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.47 % Favored : 94.30 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.12 % Twisted Proline : 0.73 % Twisted General : 0.03 % 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: 0.70 (0.15), residues: 3475 helix: 2.32 (0.12), residues: 1812 sheet: -1.68 (0.25), residues: 341 loop : -1.67 (0.17), residues: 1322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 531 time to evaluate : 3.816 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 32 residues processed: 583 average time/residue: 0.4727 time to fit residues: 446.2196 Evaluate side-chains 485 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 453 time to evaluate : 3.613 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3156 time to fit residues: 23.5080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 302 optimal weight: 0.6980 chunk 245 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 318 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1618 ASN ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1831 GLN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 HIS J 820 GLN ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN K 25 GLN K 38 ASN K 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4849 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 32504 Z= 0.199 Angle : 0.657 20.753 44659 Z= 0.329 Chirality : 0.040 0.246 5136 Planarity : 0.004 0.100 5181 Dihedral : 12.455 175.521 5573 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.32 % Favored : 94.50 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.06 % 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 (0.15), residues: 3475 helix: 2.16 (0.12), residues: 1823 sheet: -1.48 (0.25), residues: 349 loop : -1.58 (0.17), residues: 1303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 512 time to evaluate : 3.559 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: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 27 residues processed: 557 average time/residue: 0.4454 time to fit residues: 404.5048 Evaluate side-chains 476 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 449 time to evaluate : 3.547 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3276 time to fit residues: 20.9553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 5.9990 chunk 319 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 294 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 117 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1618 ASN ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 820 GLN ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 HIS D 138 ASN F 114 ASN F 331 HIS G 300 GLN G 316 HIS K 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4852 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 32504 Z= 0.196 Angle : 0.655 20.986 44659 Z= 0.326 Chirality : 0.040 0.265 5136 Planarity : 0.005 0.115 5181 Dihedral : 12.322 175.692 5573 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.12 % Twisted Proline : 0.73 % 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 (0.14), residues: 3475 helix: 2.06 (0.12), residues: 1834 sheet: -1.28 (0.25), residues: 343 loop : -1.55 (0.17), residues: 1298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 486 time to evaluate : 3.710 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: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 514 average time/residue: 0.4616 time to fit residues: 385.6892 Evaluate side-chains 465 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 444 time to evaluate : 3.522 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3162 time to fit residues: 17.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 200 optimal weight: 0.2980 chunk 298 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 353 optimal weight: 0.3980 chunk 221 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 ASN A 977 ASN A1618 ASN ** H 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN J 668 HIS J 820 GLN ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4861 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 32504 Z= 0.311 Angle : 0.710 20.789 44659 Z= 0.353 Chirality : 0.043 0.386 5136 Planarity : 0.005 0.111 5181 Dihedral : 12.314 175.675 5573 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.78 % Favored : 94.07 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.12 % Twisted Proline : 0.73 % 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: 0.38 (0.14), residues: 3475 helix: 1.77 (0.12), residues: 1846 sheet: -1.33 (0.26), residues: 332 loop : -1.60 (0.17), residues: 1297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 463 time to evaluate : 3.850 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: 48 outliers final: 33 residues processed: 489 average time/residue: 0.4598 time to fit residues: 362.4614 Evaluate side-chains 452 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 419 time to evaluate : 3.562 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3221 time to fit residues: 25.0755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 106 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1667 GLN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN G 300 GLN G 316 HIS K 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4860 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 32504 Z= 0.286 Angle : 0.700 21.001 44659 Z= 0.349 Chirality : 0.042 0.287 5136 Planarity : 0.005 0.120 5181 Dihedral : 12.295 176.782 5573 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.12 % Twisted Proline : 0.73 % 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: 0.33 (0.14), residues: 3475 helix: 1.71 (0.12), residues: 1835 sheet: -1.39 (0.25), residues: 344 loop : -1.55 (0.17), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 443 time to evaluate : 3.526 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 outliers start: 38 outliers final: 18 residues processed: 461 average time/residue: 0.4637 time to fit residues: 343.9847 Evaluate side-chains 440 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 422 time to evaluate : 3.605 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3340 time to fit residues: 15.8067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 0.0020 chunk 338 optimal weight: 0.7980 chunk 309 optimal weight: 0.6980 chunk 329 optimal weight: 0.0070 chunk 198 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 258 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 chunk 311 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 868 GLN A1500 HIS A1667 GLN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 897 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS G 286 ASN G 316 HIS K 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4853 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 0.063 32504 Z= 0.185 Angle : 0.671 20.960 44659 Z= 0.333 Chirality : 0.040 0.257 5136 Planarity : 0.005 0.118 5181 Dihedral : 12.174 177.504 5573 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.79 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.12 % Twisted Proline : 0.73 % Twisted General : 0.03 % 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: 0.52 (0.14), residues: 3475 helix: 1.81 (0.12), residues: 1836 sheet: -1.20 (0.25), residues: 344 loop : -1.37 (0.17), residues: 1295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 486 time to evaluate : 5.095 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 outliers start: 15 outliers final: 4 residues processed: 494 average time/residue: 0.5008 time to fit residues: 397.2111 Evaluate side-chains 436 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 432 time to evaluate : 3.475 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3521 time to fit residues: 7.5185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 165 optimal weight: 0.0050 chunk 242 optimal weight: 0.9990 chunk 365 optimal weight: 0.8980 chunk 336 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1500 HIS ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 552 ASN J 897 ASN F 113 HIS ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 ASN G 300 GLN G 316 HIS K 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4864 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 32504 Z= 0.259 Angle : 0.698 20.830 44659 Z= 0.346 Chirality : 0.042 0.487 5136 Planarity : 0.005 0.139 5181 Dihedral : 12.124 176.959 5573 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.47 % Favored : 94.39 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.12 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3475 helix: 1.74 (0.12), residues: 1833 sheet: -1.23 (0.25), residues: 351 loop : -1.41 (0.17), residues: 1291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 447 time to evaluate : 3.510 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: 19 outliers final: 8 residues processed: 458 average time/residue: 0.4832 time to fit residues: 355.7785 Evaluate side-chains 434 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 426 time to evaluate : 3.853 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3409 time to fit residues: 10.2244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 268 optimal weight: 5.9990 chunk 42 optimal weight: 0.0050 chunk 80 optimal weight: 0.5980 chunk 291 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 299 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1500 HIS A1737 GLN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 897 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN G 316 HIS K 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129704 restraints weight = 50530.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128849 restraints weight = 41690.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129342 restraints weight = 41748.455| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 32504 Z= 0.192 Angle : 0.676 20.946 44659 Z= 0.335 Chirality : 0.041 0.550 5136 Planarity : 0.005 0.123 5181 Dihedral : 12.051 177.538 5573 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.79 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.12 % Twisted Proline : 0.73 % 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: 0.53 (0.14), residues: 3475 helix: 1.77 (0.12), residues: 1823 sheet: -1.08 (0.26), residues: 348 loop : -1.32 (0.17), residues: 1304 =============================================================================== Job complete usr+sys time: 7652.29 seconds wall clock time: 140 minutes 25.40 seconds (8425.40 seconds total)