Starting phenix.real_space_refine on Sun Mar 17 09:37:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ori_13038/03_2024/7ori_13038_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ori_13038/03_2024/7ori_13038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ori_13038/03_2024/7ori_13038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ori_13038/03_2024/7ori_13038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ori_13038/03_2024/7ori_13038_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ori_13038/03_2024/7ori_13038_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 46 5.49 5 Mg 1 5.21 5 S 108 5.16 5 C 10917 2.51 5 N 2879 2.21 5 O 3374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 35": "OD1" <-> "OD2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 765": "OD1" <-> "OD2" Residue "A GLU 1697": "OE1" <-> "OE2" Residue "A ASP 2072": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17326 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "T" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 439 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain breaks: 1 Chain: "P" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "A" Number of atoms: 16394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2010, 16394 Unusual residues: {' MG': 1, ' ZN': 1, 'POP': 1} Classifications: {'peptide': 2007, 'undetermined': 3} Link IDs: {'PTRANS': 67, 'TRANS': 1939, None: 3} Not linked: pdbres="PHE A2238 " pdbres=" ZN A2301 " Not linked: pdbres=" ZN A2301 " pdbres=" MG A2302 " Not linked: pdbres=" MG A2302 " pdbres="POP A2303 " Chain breaks: 7 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15963 SG CYS A2064 66.994 30.063 27.886 1.00143.63 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O POP A2303 " occ=0.74 ... (7 atoms not shown) pdb=" P2 POP A2303 " occ=0.74 Time building chain proxies: 9.04, per 1000 atoms: 0.52 Number of scatterers: 17326 At special positions: 0 Unit cell: (111.065, 132.82, 136.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 108 16.00 P 46 15.00 Mg 1 11.99 O 3374 8.00 N 2879 7.00 C 10917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2182 " 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 14 sheets defined 52.3% alpha, 7.0% beta 12 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 9.83 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 19 through 45 removed outlier: 3.588A pdb=" N LYS A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 100 through 120 removed outlier: 4.773A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.748A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 removed outlier: 4.643A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 291 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 357 through 373 removed outlier: 4.027A pdb=" N SER A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 476 through 488 removed outlier: 5.809A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 598 through 619 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.744A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 660 removed outlier: 3.604A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.109A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 Processing helix chain 'A' and resid 681 through 699 removed outlier: 3.605A pdb=" N PHE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 738 through 751 Proline residue: A 748 - end of helix removed outlier: 3.763A pdb=" N PHE A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 779 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 850 through 853 No H-bonds generated for 'chain 'A' and resid 850 through 853' Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 965 through 984 removed outlier: 4.214A pdb=" N LEU A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1027 removed outlier: 5.248A pdb=" N GLU A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1048 Processing helix chain 'A' and resid 1070 through 1078 removed outlier: 3.863A pdb=" N TRP A1075 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 3.742A pdb=" N ASP A1100 " --> pdb=" O CYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1114 Processing helix chain 'A' and resid 1124 through 1128 Processing helix chain 'A' and resid 1149 through 1174 Processing helix chain 'A' and resid 1202 through 1219 Processing helix chain 'A' and resid 1253 through 1260 removed outlier: 3.712A pdb=" N SER A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1285 removed outlier: 3.603A pdb=" N SER A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1306 Processing helix chain 'A' and resid 1331 through 1333 No H-bonds generated for 'chain 'A' and resid 1331 through 1333' Processing helix chain 'A' and resid 1341 through 1347 Processing helix chain 'A' and resid 1351 through 1364 Processing helix chain 'A' and resid 1374 through 1383 removed outlier: 5.410A pdb=" N LYS A1382 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN A1383 " --> pdb=" O ALA A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1402 Processing helix chain 'A' and resid 1419 through 1421 No H-bonds generated for 'chain 'A' and resid 1419 through 1421' Processing helix chain 'A' and resid 1442 through 1452 Processing helix chain 'A' and resid 1456 through 1466 Processing helix chain 'A' and resid 1468 through 1471 Processing helix chain 'A' and resid 1478 through 1490 removed outlier: 3.843A pdb=" N TYR A1489 " --> pdb=" O VAL A1485 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A1490 " --> pdb=" O ILE A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1498 Processing helix chain 'A' and resid 1503 through 1514 removed outlier: 3.755A pdb=" N SER A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1527 Processing helix chain 'A' and resid 1549 through 1562 removed outlier: 3.783A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1577 Processing helix chain 'A' and resid 1582 through 1592 Processing helix chain 'A' and resid 1623 through 1631 Processing helix chain 'A' and resid 1642 through 1659 Processing helix chain 'A' and resid 1661 through 1676 Processing helix chain 'A' and resid 1681 through 1698 Processing helix chain 'A' and resid 1718 through 1728 Processing helix chain 'A' and resid 1761 through 1778 Processing helix chain 'A' and resid 1784 through 1794 Processing helix chain 'A' and resid 1802 through 1810 Processing helix chain 'A' and resid 1816 through 1825 removed outlier: 4.165A pdb=" N ILE A1819 " --> pdb=" O THR A1816 " (cutoff:3.500A) Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1831 through 1839 Processing helix chain 'A' and resid 1984 through 1990 removed outlier: 3.575A pdb=" N TYR A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2020 removed outlier: 3.784A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2038 Processing helix chain 'A' and resid 2041 through 2043 No H-bonds generated for 'chain 'A' and resid 2041 through 2043' Processing helix chain 'A' and resid 2047 through 2051 Processing helix chain 'A' and resid 2055 through 2061 removed outlier: 3.979A pdb=" N LYS A2060 " --> pdb=" O ILE A2056 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU A2061 " --> pdb=" O SER A2057 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2074 Processing helix chain 'A' and resid 2110 through 2128 Processing helix chain 'A' and resid 2139 through 2154 Processing helix chain 'A' and resid 2159 through 2175 Processing helix chain 'A' and resid 2178 through 2181 No H-bonds generated for 'chain 'A' and resid 2178 through 2181' Processing helix chain 'A' and resid 2201 through 2209 Processing helix chain 'A' and resid 2219 through 2237 Processing sheet with id= A, first strand: chain 'A' and resid 80 through 84 Processing sheet with id= B, first strand: chain 'A' and resid 293 through 295 Processing sheet with id= C, first strand: chain 'A' and resid 308 through 310 removed outlier: 3.518A pdb=" N TRP A 309 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 386 through 388 Processing sheet with id= E, first strand: chain 'A' and resid 398 through 400 Processing sheet with id= F, first strand: chain 'A' and resid 562 through 565 Processing sheet with id= G, first strand: chain 'A' and resid 842 through 846 Processing sheet with id= H, first strand: chain 'A' and resid 945 through 949 Processing sheet with id= I, first strand: chain 'A' and resid 1230 through 1232 Processing sheet with id= J, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 3.741A pdb=" N LYS A1101 " --> pdb=" O ILE A1139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1236 through 1238 Processing sheet with id= L, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id= M, first strand: chain 'A' and resid 1606 through 1609 Processing sheet with id= N, first strand: chain 'A' and resid 2083 through 2089 751 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 8.74 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4167 1.33 - 1.45: 3696 1.45 - 1.57: 9639 1.57 - 1.69: 86 1.69 - 1.81: 179 Bond restraints: 17767 Sorted by residual: bond pdb=" N VAL A1239 " pdb=" CA VAL A1239 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" N PHE A1242 " pdb=" CA PHE A1242 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.32e+00 bond pdb=" N VAL A 134 " pdb=" CA VAL A 134 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.21e+00 bond pdb=" N TYR A1528 " pdb=" CA TYR A1528 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.16e-02 7.43e+03 6.88e+00 bond pdb=" N LEU A1241 " pdb=" CA LEU A1241 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.24e-02 6.50e+03 6.81e+00 ... (remaining 17762 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.82: 521 105.82 - 112.86: 9585 112.86 - 119.90: 5983 119.90 - 126.94: 7823 126.94 - 133.98: 255 Bond angle restraints: 24167 Sorted by residual: angle pdb=" C ASP A 137 " pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta sigma weight residual 109.48 116.63 -7.15 1.68e+00 3.54e-01 1.81e+01 angle pdb=" P1 POP A2303 " pdb=" O POP A2303 " pdb=" P2 POP A2303 " ideal model delta sigma weight residual 120.50 132.54 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CA ARG A 136 " pdb=" C ARG A 136 " pdb=" O ARG A 136 " ideal model delta sigma weight residual 122.64 118.25 4.39 1.25e+00 6.40e-01 1.23e+01 angle pdb=" O LYS A1370 " pdb=" C LYS A1370 " pdb=" N ARG A1371 " ideal model delta sigma weight residual 122.12 125.67 -3.55 1.06e+00 8.90e-01 1.12e+01 angle pdb=" N GLN A 387 " pdb=" CA GLN A 387 " pdb=" C GLN A 387 " ideal model delta sigma weight residual 108.23 113.92 -5.69 1.72e+00 3.38e-01 1.10e+01 ... (remaining 24162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.40: 10072 23.40 - 46.81: 634 46.81 - 70.21: 125 70.21 - 93.61: 21 93.61 - 117.02: 3 Dihedral angle restraints: 10855 sinusoidal: 4892 harmonic: 5963 Sorted by residual: dihedral pdb=" O4 POP A2303 " pdb=" O POP A2303 " pdb=" P2 POP A2303 " pdb=" P1 POP A2303 " ideal model delta sinusoidal sigma weight residual -57.42 59.60 -117.02 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" O2 POP A2303 " pdb=" O POP A2303 " pdb=" P1 POP A2303 " pdb=" P2 POP A2303 " ideal model delta sinusoidal sigma weight residual -88.77 -176.65 87.88 1 2.00e+01 2.50e-03 2.31e+01 dihedral pdb=" CA TRP A1143 " pdb=" C TRP A1143 " pdb=" N LEU A1144 " pdb=" CA LEU A1144 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 10852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2401 0.063 - 0.126: 283 0.126 - 0.188: 33 0.188 - 0.251: 4 0.251 - 0.314: 3 Chirality restraints: 2724 Sorted by residual: chirality pdb=" CA ASN A1334 " pdb=" N ASN A1334 " pdb=" C ASN A1334 " pdb=" CB ASN A1334 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ASP A1799 " pdb=" N ASP A1799 " pdb=" C ASP A1799 " pdb=" CB ASP A1799 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE A 421 " pdb=" CA ILE A 421 " pdb=" CG1 ILE A 421 " pdb=" CG2 ILE A 421 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2721 not shown) Planarity restraints: 2898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 135 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C SER A 135 " 0.039 2.00e-02 2.50e+03 pdb=" O SER A 135 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 136 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 939 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.31e+00 pdb=" C ASP A 939 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP A 939 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS A 940 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 668 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ASP A 668 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 668 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 669 " -0.011 2.00e-02 2.50e+03 ... (remaining 2895 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 73 2.51 - 3.11: 13270 3.11 - 3.70: 28310 3.70 - 4.30: 39796 4.30 - 4.90: 64566 Nonbonded interactions: 146015 Sorted by model distance: nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2301 " model vdw 1.911 2.230 nonbonded pdb=" O2' U T 30 " pdb=" O2 U T 30 " model vdw 2.244 2.440 nonbonded pdb=" O PHE A 210 " pdb=" OG SER A 213 " model vdw 2.271 2.440 nonbonded pdb=" O GLU A1469 " pdb=" OG1 THR A1473 " model vdw 2.279 2.440 nonbonded pdb=" O GLU A1654 " pdb=" ND2 ASN A1658 " model vdw 2.281 2.520 ... (remaining 146010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.74 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 55.830 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.003 0.042 17767 Z= 0.202 Angle : 0.581 12.039 24167 Z= 0.342 Chirality : 0.043 0.314 2724 Planarity : 0.003 0.038 2898 Dihedral : 15.420 117.017 6981 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.30 % Allowed : 1.24 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1991 helix: 1.91 (0.16), residues: 1076 sheet: 1.20 (0.45), residues: 137 loop : -0.84 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1293 HIS 0.007 0.001 HIS A1156 PHE 0.019 0.001 PHE A1795 TYR 0.012 0.001 TYR A1528 ARG 0.004 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8635 (t0) REVERT: A 400 MET cc_start: 0.8668 (tpt) cc_final: 0.8359 (tpt) REVERT: A 510 ASP cc_start: 0.8233 (m-30) cc_final: 0.7890 (m-30) REVERT: A 696 ASP cc_start: 0.8430 (m-30) cc_final: 0.7747 (p0) REVERT: A 1056 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7258 (mm-30) REVERT: A 1236 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8077 (mtpt) REVERT: A 1240 SER cc_start: 0.9167 (m) cc_final: 0.8855 (p) REVERT: A 1439 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7558 (mmm160) REVERT: A 1472 VAL cc_start: 0.9668 (m) cc_final: 0.9404 (p) REVERT: A 2227 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7577 (tptp) outliers start: 24 outliers final: 6 residues processed: 184 average time/residue: 0.3008 time to fit residues: 84.3937 Evaluate side-chains 134 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1236 LYS Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2134 ASN Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1704 HIS ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17767 Z= 0.222 Angle : 0.492 5.840 24167 Z= 0.257 Chirality : 0.039 0.189 2724 Planarity : 0.003 0.037 2898 Dihedral : 12.610 109.109 2846 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.81 % Allowed : 7.88 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 1991 helix: 2.03 (0.16), residues: 1079 sheet: 0.90 (0.44), residues: 143 loop : -0.75 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1735 HIS 0.008 0.001 HIS A1156 PHE 0.013 0.001 PHE A1795 TYR 0.017 0.001 TYR A1696 ARG 0.004 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.980 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8432 (tpp) cc_final: 0.8129 (tpp) REVERT: A 400 MET cc_start: 0.8620 (tpt) cc_final: 0.8212 (tpt) REVERT: A 510 ASP cc_start: 0.8288 (m-30) cc_final: 0.7928 (m-30) REVERT: A 696 ASP cc_start: 0.8488 (m-30) cc_final: 0.7858 (p0) REVERT: A 900 MET cc_start: 0.8048 (tmm) cc_final: 0.7696 (tmm) REVERT: A 1056 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 1472 VAL cc_start: 0.9690 (m) cc_final: 0.9440 (p) outliers start: 15 outliers final: 12 residues processed: 139 average time/residue: 0.2718 time to fit residues: 60.5602 Evaluate side-chains 135 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17767 Z= 0.262 Angle : 0.503 6.526 24167 Z= 0.261 Chirality : 0.039 0.157 2724 Planarity : 0.003 0.039 2898 Dihedral : 12.289 111.209 2831 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.97 % Allowed : 10.69 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 1991 helix: 2.07 (0.16), residues: 1076 sheet: 0.93 (0.45), residues: 137 loop : -0.71 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1293 HIS 0.010 0.001 HIS A1156 PHE 0.015 0.001 PHE A1795 TYR 0.014 0.001 TYR A1696 ARG 0.002 0.000 ARG A1602 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.981 Fit side-chains REVERT: A 7 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: A 400 MET cc_start: 0.8592 (tpt) cc_final: 0.8215 (tpt) REVERT: A 510 ASP cc_start: 0.8307 (m-30) cc_final: 0.7952 (m-30) REVERT: A 900 MET cc_start: 0.8191 (tmm) cc_final: 0.7801 (tmm) REVERT: A 1056 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 1472 VAL cc_start: 0.9715 (m) cc_final: 0.9451 (p) REVERT: A 2037 MET cc_start: 0.8896 (mpp) cc_final: 0.8609 (mpp) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.2672 time to fit residues: 58.8135 Evaluate side-chains 137 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 5.9990 chunk 140 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17767 Z= 0.152 Angle : 0.451 5.756 24167 Z= 0.236 Chirality : 0.038 0.157 2724 Planarity : 0.003 0.035 2898 Dihedral : 12.176 112.109 2831 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.08 % Allowed : 12.15 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 1991 helix: 2.12 (0.16), residues: 1078 sheet: 1.04 (0.46), residues: 136 loop : -0.64 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1143 HIS 0.010 0.001 HIS A 760 PHE 0.012 0.001 PHE A1795 TYR 0.014 0.001 TYR A1696 ARG 0.002 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.951 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: A 365 MET cc_start: 0.8400 (tpp) cc_final: 0.8125 (tpp) REVERT: A 400 MET cc_start: 0.8661 (tpt) cc_final: 0.8292 (tpt) REVERT: A 450 MET cc_start: 0.9532 (mmt) cc_final: 0.9327 (mmm) REVERT: A 510 ASP cc_start: 0.8218 (m-30) cc_final: 0.7877 (m-30) REVERT: A 657 MET cc_start: 0.9366 (mmm) cc_final: 0.9165 (mmm) REVERT: A 900 MET cc_start: 0.8143 (tmm) cc_final: 0.7544 (tmm) REVERT: A 1056 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 1472 VAL cc_start: 0.9722 (m) cc_final: 0.9480 (p) outliers start: 20 outliers final: 14 residues processed: 150 average time/residue: 0.2564 time to fit residues: 62.6549 Evaluate side-chains 139 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1739 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17767 Z= 0.306 Angle : 0.527 8.163 24167 Z= 0.273 Chirality : 0.039 0.171 2724 Planarity : 0.003 0.036 2898 Dihedral : 12.193 111.259 2831 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.51 % Allowed : 13.23 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1991 helix: 2.02 (0.16), residues: 1076 sheet: 0.68 (0.44), residues: 147 loop : -0.71 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2219 HIS 0.011 0.001 HIS A1156 PHE 0.018 0.001 PHE A1507 TYR 0.012 0.001 TYR A1696 ARG 0.004 0.000 ARG A1439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: A 400 MET cc_start: 0.8548 (tpt) cc_final: 0.8007 (tpt) REVERT: A 424 HIS cc_start: 0.5191 (OUTLIER) cc_final: 0.4679 (t-170) REVERT: A 510 ASP cc_start: 0.8352 (m-30) cc_final: 0.7985 (m-30) REVERT: A 657 MET cc_start: 0.9384 (mmm) cc_final: 0.9136 (mmm) REVERT: A 900 MET cc_start: 0.8269 (tmm) cc_final: 0.6970 (tmm) REVERT: A 959 GLU cc_start: 0.8285 (pm20) cc_final: 0.8055 (pm20) REVERT: A 1056 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 1472 VAL cc_start: 0.9729 (m) cc_final: 0.9469 (p) REVERT: A 2037 MET cc_start: 0.9004 (mpp) cc_final: 0.8690 (mpp) REVERT: A 2203 MET cc_start: 0.8158 (ppp) cc_final: 0.7946 (ppp) outliers start: 28 outliers final: 18 residues processed: 142 average time/residue: 0.2666 time to fit residues: 61.4891 Evaluate side-chains 142 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1509 GLU Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.5980 chunk 178 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17767 Z= 0.146 Angle : 0.466 7.546 24167 Z= 0.241 Chirality : 0.038 0.172 2724 Planarity : 0.003 0.037 2898 Dihedral : 12.127 112.039 2827 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.30 % Allowed : 14.20 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 1991 helix: 2.09 (0.16), residues: 1076 sheet: 0.97 (0.46), residues: 136 loop : -0.68 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A2219 HIS 0.008 0.001 HIS A1156 PHE 0.021 0.001 PHE A1507 TYR 0.014 0.001 TYR A1696 ARG 0.002 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 2.082 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: A 214 MET cc_start: 0.7947 (mpp) cc_final: 0.7707 (mpp) REVERT: A 365 MET cc_start: 0.8367 (tpp) cc_final: 0.8076 (tpp) REVERT: A 400 MET cc_start: 0.8631 (tpt) cc_final: 0.8251 (tpt) REVERT: A 424 HIS cc_start: 0.5109 (OUTLIER) cc_final: 0.4594 (t-170) REVERT: A 510 ASP cc_start: 0.8228 (m-30) cc_final: 0.7893 (m-30) REVERT: A 900 MET cc_start: 0.8165 (tmm) cc_final: 0.6855 (tmm) REVERT: A 959 GLU cc_start: 0.8185 (pm20) cc_final: 0.7926 (pm20) REVERT: A 1056 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 1071 TYR cc_start: 0.8580 (m-80) cc_final: 0.8297 (m-80) REVERT: A 1472 VAL cc_start: 0.9725 (m) cc_final: 0.9492 (p) outliers start: 24 outliers final: 15 residues processed: 146 average time/residue: 0.2774 time to fit residues: 65.3099 Evaluate side-chains 143 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 chunk 113 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 197 optimal weight: 0.6980 chunk 123 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN A1243 ASN A1308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17767 Z= 0.129 Angle : 0.471 8.491 24167 Z= 0.241 Chirality : 0.037 0.168 2724 Planarity : 0.003 0.035 2898 Dihedral : 12.070 111.829 2827 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.19 % Allowed : 14.52 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.19), residues: 1991 helix: 2.15 (0.16), residues: 1071 sheet: 1.06 (0.46), residues: 136 loop : -0.62 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A2219 HIS 0.007 0.001 HIS A1156 PHE 0.022 0.001 PHE A1507 TYR 0.013 0.001 TYR A1696 ARG 0.002 0.000 ARG A1602 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 1.783 Fit side-chains REVERT: A 7 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: A 365 MET cc_start: 0.8425 (tpp) cc_final: 0.8117 (tpp) REVERT: A 400 MET cc_start: 0.8604 (tpt) cc_final: 0.8231 (tpt) REVERT: A 424 HIS cc_start: 0.5088 (OUTLIER) cc_final: 0.4648 (t-170) REVERT: A 510 ASP cc_start: 0.8195 (m-30) cc_final: 0.7879 (m-30) REVERT: A 900 MET cc_start: 0.8132 (tmm) cc_final: 0.6861 (tmm) REVERT: A 1056 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7942 (mm-30) REVERT: A 1343 MET cc_start: 0.8844 (tpp) cc_final: 0.8634 (mmm) REVERT: A 1472 VAL cc_start: 0.9717 (m) cc_final: 0.9479 (p) REVERT: A 2037 MET cc_start: 0.9045 (mtm) cc_final: 0.8764 (pmm) REVERT: A 2108 MET cc_start: 0.8003 (ptp) cc_final: 0.7754 (ptm) outliers start: 22 outliers final: 16 residues processed: 156 average time/residue: 0.2697 time to fit residues: 67.4164 Evaluate side-chains 142 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1308 ASN Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2085 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 179 optimal weight: 0.0070 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17767 Z= 0.142 Angle : 0.476 7.896 24167 Z= 0.244 Chirality : 0.038 0.179 2724 Planarity : 0.003 0.035 2898 Dihedral : 12.011 111.285 2827 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.19 % Allowed : 15.12 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 1991 helix: 2.16 (0.16), residues: 1070 sheet: 1.19 (0.47), residues: 136 loop : -0.62 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1143 HIS 0.007 0.001 HIS A1156 PHE 0.022 0.001 PHE A1507 TYR 0.028 0.001 TYR A1073 ARG 0.002 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 2.166 Fit side-chains REVERT: A 7 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: A 365 MET cc_start: 0.8439 (tpp) cc_final: 0.8117 (tpp) REVERT: A 400 MET cc_start: 0.8617 (tpt) cc_final: 0.8235 (tpt) REVERT: A 424 HIS cc_start: 0.5192 (OUTLIER) cc_final: 0.4751 (t-170) REVERT: A 510 ASP cc_start: 0.8195 (m-30) cc_final: 0.7872 (m-30) REVERT: A 696 ASP cc_start: 0.8252 (m-30) cc_final: 0.7744 (p0) REVERT: A 900 MET cc_start: 0.8148 (tmm) cc_final: 0.6872 (tmm) REVERT: A 1056 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7924 (mm-30) REVERT: A 1169 GLU cc_start: 0.8794 (tp30) cc_final: 0.8585 (tp30) REVERT: A 1343 MET cc_start: 0.8854 (tpp) cc_final: 0.8648 (mmm) REVERT: A 1472 VAL cc_start: 0.9707 (m) cc_final: 0.9479 (p) REVERT: A 2108 MET cc_start: 0.7981 (ptp) cc_final: 0.7728 (ptm) outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 0.2806 time to fit residues: 65.0342 Evaluate side-chains 140 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1308 ASN Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2085 THR Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN A1308 ASN A2209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17767 Z= 0.154 Angle : 0.482 9.329 24167 Z= 0.245 Chirality : 0.037 0.147 2724 Planarity : 0.003 0.035 2898 Dihedral : 11.980 110.651 2825 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.03 % Allowed : 15.60 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 1991 helix: 2.18 (0.16), residues: 1064 sheet: 1.17 (0.47), residues: 136 loop : -0.61 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1143 HIS 0.008 0.001 HIS A1156 PHE 0.021 0.001 PHE A1507 TYR 0.025 0.001 TYR A1989 ARG 0.002 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 2.142 Fit side-chains REVERT: A 7 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: A 400 MET cc_start: 0.8617 (tpt) cc_final: 0.8326 (tpt) REVERT: A 424 HIS cc_start: 0.5196 (OUTLIER) cc_final: 0.4760 (t-170) REVERT: A 510 ASP cc_start: 0.8197 (m-30) cc_final: 0.7876 (m-30) REVERT: A 696 ASP cc_start: 0.8281 (m-30) cc_final: 0.7831 (p0) REVERT: A 900 MET cc_start: 0.8169 (tmm) cc_final: 0.6850 (tmm) REVERT: A 1056 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7918 (mm-30) REVERT: A 1099 MET cc_start: 0.8601 (mmm) cc_final: 0.8361 (mmm) REVERT: A 1169 GLU cc_start: 0.8832 (tp30) cc_final: 0.8492 (tp30) REVERT: A 1343 MET cc_start: 0.8866 (tpp) cc_final: 0.8647 (mmm) REVERT: A 1472 VAL cc_start: 0.9711 (m) cc_final: 0.9487 (p) REVERT: A 2108 MET cc_start: 0.7970 (ptp) cc_final: 0.7708 (ptm) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 0.2754 time to fit residues: 62.3285 Evaluate side-chains 142 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1308 ASN Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2085 THR Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 0.0870 chunk 204 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 0.0870 chunk 99 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN A1308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17767 Z= 0.257 Angle : 0.530 9.262 24167 Z= 0.269 Chirality : 0.039 0.160 2724 Planarity : 0.003 0.033 2898 Dihedral : 11.990 109.333 2825 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.86 % Allowed : 15.60 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1991 helix: 2.15 (0.16), residues: 1074 sheet: 0.91 (0.45), residues: 146 loop : -0.67 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2219 HIS 0.010 0.001 HIS A1156 PHE 0.020 0.001 PHE A1148 TYR 0.025 0.001 TYR A1307 ARG 0.002 0.000 ARG A1439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 2.148 Fit side-chains REVERT: A 7 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: A 400 MET cc_start: 0.8580 (tpt) cc_final: 0.8208 (tpt) REVERT: A 424 HIS cc_start: 0.5176 (OUTLIER) cc_final: 0.4674 (t-170) REVERT: A 510 ASP cc_start: 0.8234 (m-30) cc_final: 0.7882 (m-30) REVERT: A 631 MET cc_start: 0.8433 (mtt) cc_final: 0.8205 (mtm) REVERT: A 696 ASP cc_start: 0.8387 (m-30) cc_final: 0.7908 (p0) REVERT: A 900 MET cc_start: 0.8145 (tmm) cc_final: 0.7578 (tmm) REVERT: A 1056 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 1073 TYR cc_start: 0.9390 (m-10) cc_final: 0.9105 (m-80) REVERT: A 1169 GLU cc_start: 0.8828 (tp30) cc_final: 0.8587 (tp30) REVERT: A 1472 VAL cc_start: 0.9723 (m) cc_final: 0.9483 (p) REVERT: A 2203 MET cc_start: 0.8177 (ppp) cc_final: 0.7893 (ppp) outliers start: 16 outliers final: 14 residues processed: 136 average time/residue: 0.2673 time to fit residues: 58.9932 Evaluate side-chains 140 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1308 ASN Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2085 THR Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 167 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN A1308 ASN A2209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.060390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.048883 restraints weight = 65784.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.050591 restraints weight = 33104.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051745 restraints weight = 20537.216| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17767 Z= 0.157 Angle : 0.500 8.547 24167 Z= 0.252 Chirality : 0.038 0.145 2724 Planarity : 0.003 0.034 2898 Dihedral : 11.990 109.587 2825 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.03 % Allowed : 15.33 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.19), residues: 1991 helix: 2.13 (0.16), residues: 1068 sheet: 1.11 (0.47), residues: 136 loop : -0.61 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A2219 HIS 0.008 0.001 HIS A1156 PHE 0.022 0.001 PHE A1507 TYR 0.018 0.001 TYR A1307 ARG 0.001 0.000 ARG A 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2750.06 seconds wall clock time: 51 minutes 51.76 seconds (3111.76 seconds total)