Starting phenix.real_space_refine on Fri Dec 8 05:24:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xib_33201/12_2023/7xib_33201_updated.pdb" } resolution = 2.23 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 22 5.49 5 S 41 5.16 5 C 4355 2.51 5 N 1236 2.21 5 O 1521 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A ASP 802": "OD1" <-> "OD2" Residue "A ASP 810": "OD1" <-> "OD2" Residue "A ASP 822": "OD1" <-> "OD2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A ASP 916": "OD1" <-> "OD2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A ASP 965": "OD1" <-> "OD2" Residue "A ASP 967": "OD1" <-> "OD2" Residue "A ASP 978": "OD1" <-> "OD2" Residue "A GLU 998": "OE1" <-> "OE2" Residue "A ASP 1013": "OD1" <-> "OD2" Residue "A ARG 1017": "NH1" <-> "NH2" Residue "A ASP 1052": "OD1" <-> "OD2" Residue "A ARG 1059": "NH1" <-> "NH2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1171": "OD1" <-> "OD2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1259": "NH1" <-> "NH2" Residue "A GLU 1329": "OE1" <-> "OE2" Residue "A ARG 1337": "NH1" <-> "NH2" Residue "A ARG 1398": "NH1" <-> "NH2" Residue "A TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1410": "NH1" <-> "NH2" Residue "A ASP 1416": "OD1" <-> "OD2" Residue "A ARG 1456": "NH1" <-> "NH2" Residue "A TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1461": "OD1" <-> "OD2" Residue "A GLU 1480": "OE1" <-> "OE2" Residue "A PHE 1492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1516": "NH1" <-> "NH2" Residue "A ARG 1546": "NH1" <-> "NH2" Residue "A ARG 1551": "NH1" <-> "NH2" Residue "A ARG 1574": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7178 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6490 Classifications: {'peptide': 815} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 763} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 171 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2, 'water': 169} Link IDs: {None: 170} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5452 SG CYS A1476 20.776 25.722 22.658 1.00 53.95 S ATOM 5464 SG CYS A1478 19.739 26.560 26.288 1.00 57.76 S ATOM 5509 SG CYS A1485 21.681 23.342 25.823 1.00 61.18 S ATOM 638 SG CYS A 820 22.900 34.632 87.923 1.00 60.15 S ATOM 1119 SG CYS A 893 25.557 33.570 89.809 1.00 63.01 S ATOM 1138 SG CYS A 896 23.622 37.138 90.302 1.00 57.17 S Time building chain proxies: 4.11, per 1000 atoms: 0.57 Number of scatterers: 7178 At special positions: 0 Unit cell: (74.7, 89.64, 110.39, 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 2 29.99 S 41 16.00 P 22 15.00 F 1 9.00 O 1521 8.00 N 1236 7.00 C 4355 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A1502 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1478 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1476 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1485 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 793 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 893 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 820 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 896 " Number of angles added : 6 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 12 sheets defined 24.7% alpha, 16.7% beta 8 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 894 through 903 Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1031 through 1034 Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1065 through 1067 No H-bonds generated for 'chain 'A' and resid 1065 through 1067' Processing helix chain 'A' and resid 1072 through 1076 Processing helix chain 'A' and resid 1150 through 1158 Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1191 through 1199 Processing helix chain 'A' and resid 1239 through 1258 removed outlier: 3.681A pdb=" N LEU A1247 " --> pdb=" O PHE A1243 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL A1249 " --> pdb=" O ASN A1245 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1250 " --> pdb=" O SER A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1272 Processing helix chain 'A' and resid 1274 through 1290 removed outlier: 4.857A pdb=" N VAL A1279 " --> pdb=" O LYS A1275 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A1280 " --> pdb=" O ARG A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1304 Processing helix chain 'A' and resid 1336 through 1338 No H-bonds generated for 'chain 'A' and resid 1336 through 1338' Processing helix chain 'A' and resid 1367 through 1371 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1419 through 1426 Processing helix chain 'A' and resid 1436 through 1438 No H-bonds generated for 'chain 'A' and resid 1436 through 1438' Processing helix chain 'A' and resid 1477 through 1479 No H-bonds generated for 'chain 'A' and resid 1477 through 1479' Processing helix chain 'A' and resid 1498 through 1506 removed outlier: 5.137A pdb=" N ASN A1505 " --> pdb=" O PRO A1501 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A1506 " --> pdb=" O HIS A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1510 No H-bonds generated for 'chain 'A' and resid 1508 through 1510' Processing helix chain 'A' and resid 1550 through 1556 Processing helix chain 'A' and resid 1569 through 1578 Processing helix chain 'A' and resid 1582 through 1607 removed outlier: 3.509A pdb=" N CYS A1595 " --> pdb=" O GLU A1591 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 762 through 765 removed outlier: 6.491A pdb=" N HIS A 793 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 797 through 799 removed outlier: 6.358A pdb=" N PHE A 864 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 816 " --> pdb=" O PHE A 864 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLN A 866 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 867 through 870 Processing sheet with id= D, first strand: chain 'A' and resid 909 through 911 Processing sheet with id= E, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.783A pdb=" N LEU A 922 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP A 916 " --> pdb=" O ARG A 920 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ARG A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 999 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG A1017 " --> pdb=" O LYS A 997 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE A 999 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LYS A1015 " --> pdb=" O ILE A 999 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 992 through 995 removed outlier: 4.154A pdb=" N GLY A1058 " --> pdb=" O TYR A 940 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1021 through 1023 Processing sheet with id= H, first strand: chain 'A' and resid 1061 through 1064 Processing sheet with id= I, first strand: chain 'A' and resid 1087 through 1090 Processing sheet with id= J, first strand: chain 'A' and resid 1293 through 1300 removed outlier: 7.648A pdb=" N ASP A1143 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A1166 " --> pdb=" O ASP A1143 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR A1185 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1343 through 1345 Processing sheet with id= L, first strand: chain 'A' and resid 1385 through 1387 175 hydrogen bonds defined for protein. 480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.03 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: 1092 1.31 - 1.43: 2086 1.43 - 1.56: 3915 1.56 - 1.68: 48 1.68 - 1.81: 59 Bond restraints: 7200 Sorted by residual: bond pdb=" C2' 5CM B 6 " pdb=" C1' 5CM B 6 " ideal model delta sigma weight residual 1.521 1.268 0.253 2.00e-02 2.50e+03 1.61e+02 bond pdb=" N3 EIX C 18 " pdb=" C4 EIX C 18 " ideal model delta sigma weight residual 1.473 1.265 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C2 EIX C 18 " pdb=" N3 EIX C 18 " ideal model delta sigma weight residual 1.526 1.332 0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C2 5CM B 6 " pdb=" N3 5CM B 6 " ideal model delta sigma weight residual 1.494 1.313 0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C4' EIX C 18 " pdb=" O4' EIX C 18 " ideal model delta sigma weight residual 1.613 1.435 0.178 2.00e-02 2.50e+03 7.95e+01 ... (remaining 7195 not shown) Histogram of bond angle deviations from ideal: 93.40 - 101.52: 27 101.52 - 109.65: 1083 109.65 - 117.78: 4252 117.78 - 125.91: 4294 125.91 - 134.03: 191 Bond angle restraints: 9847 Sorted by residual: angle pdb=" C ARG A1210 " pdb=" N LEU A1211 " pdb=" CA LEU A1211 " ideal model delta sigma weight residual 120.68 127.74 -7.06 1.52e+00 4.33e-01 2.16e+01 angle pdb=" C3' EIX C 18 " pdb=" C2' EIX C 18 " pdb=" C1' EIX C 18 " ideal model delta sigma weight residual 105.59 93.40 12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O4' EIX C 18 " pdb=" C1' EIX C 18 " pdb=" N1 EIX C 18 " ideal model delta sigma weight residual 110.14 121.44 -11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C4 EIX C 18 " pdb=" C5 EIX C 18 " pdb=" C6 EIX C 18 " ideal model delta sigma weight residual 119.72 108.62 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" N PRO A1582 " pdb=" CA PRO A1582 " pdb=" C PRO A1582 " ideal model delta sigma weight residual 110.70 113.96 -3.26 1.22e+00 6.72e-01 7.16e+00 ... (remaining 9842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.13: 3979 31.13 - 62.27: 260 62.27 - 93.40: 16 93.40 - 124.53: 0 124.53 - 155.67: 1 Dihedral angle restraints: 4256 sinusoidal: 1895 harmonic: 2361 Sorted by residual: dihedral pdb=" CA THR A 620 " pdb=" C THR A 620 " pdb=" N THR A 621 " pdb=" CA THR A 621 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" N3 EIX C 18 " pdb=" C4 EIX C 18 " pdb=" C5 EIX C 18 " pdb=" CM5 EIX C 18 " ideal model delta sinusoidal sigma weight residual 236.82 81.15 155.67 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CA TYR A1292 " pdb=" C TYR A1292 " pdb=" N GLN A1293 " pdb=" CA GLN A1293 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 4253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.043: 1047 1.043 - 2.086: 0 2.086 - 3.129: 0 3.129 - 4.172: 0 4.172 - 5.215: 1 Chirality restraints: 1048 Sorted by residual: chirality pdb=" C5 EIX C 18 " pdb=" C4 EIX C 18 " pdb=" C6 EIX C 18 " pdb=" CM5 EIX C 18 " both_signs ideal model delta sigma weight residual False 2.64 -2.57 5.21 2.00e-01 2.50e+01 6.80e+02 chirality pdb=" C1' EIX C 18 " pdb=" O4' EIX C 18 " pdb=" C2' EIX C 18 " pdb=" N1 EIX C 18 " both_signs ideal model delta sigma weight residual False -2.37 -2.04 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1' 5CM B 6 " pdb=" O4' 5CM B 6 " pdb=" C2' 5CM B 6 " pdb=" N1 5CM B 6 " both_signs ideal model delta sigma weight residual False 2.50 2.24 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1045 not shown) Planarity restraints: 1199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' EIX C 18 " -0.546 2.00e-02 2.50e+03 3.48e-01 2.73e+03 pdb=" N1 EIX C 18 " -0.052 2.00e-02 2.50e+03 pdb=" C2 EIX C 18 " 0.098 2.00e-02 2.50e+03 pdb=" O2 EIX C 18 " 0.366 2.00e-02 2.50e+03 pdb=" N3 EIX C 18 " -0.071 2.00e-02 2.50e+03 pdb=" C4 EIX C 18 " -0.019 2.00e-02 2.50e+03 pdb=" N4 EIX C 18 " -0.510 2.00e-02 2.50e+03 pdb=" C5 EIX C 18 " 0.605 2.00e-02 2.50e+03 pdb=" C6 EIX C 18 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1360 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A1361 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1361 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1361 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1171 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A1172 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1172 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1172 " 0.028 5.00e-02 4.00e+02 ... (remaining 1196 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 504 2.73 - 3.27: 6996 3.27 - 3.81: 13245 3.81 - 4.36: 17044 4.36 - 4.90: 25897 Nonbonded interactions: 63686 Sorted by model distance: nonbonded pdb=" OG1 THR A1528 " pdb=" OP2 DG C 19 " model vdw 2.184 2.440 nonbonded pdb=" O ILE A1365 " pdb=" O HOH A1801 " model vdw 2.186 2.440 nonbonded pdb=" O ARG A1276 " pdb=" O HOH A1802 " model vdw 2.194 2.440 nonbonded pdb=" NH2 ARG A1368 " pdb=" OD1 ASP A1520 " model vdw 2.215 2.520 nonbonded pdb=" O ARG A1289 " pdb=" O HOH A1803 " model vdw 2.223 2.440 ... (remaining 63681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.840 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.530 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.009 0.253 7200 Z= 0.545 Angle : 0.711 12.195 9847 Z= 0.391 Chirality : 0.168 5.215 1048 Planarity : 0.011 0.348 1199 Dihedral : 18.395 155.668 2738 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.14 % Allowed : 14.71 % Favored : 81.14 % 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: -1.86 (0.27), residues: 801 helix: -1.29 (0.32), residues: 200 sheet: -0.94 (0.43), residues: 121 loop : -1.28 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 843 HIS 0.002 0.001 HIS A1509 PHE 0.024 0.002 PHE A1523 TYR 0.021 0.002 TYR A1304 ARG 0.003 0.000 ARG A1462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.824 Fit side-chains outliers start: 29 outliers final: 10 residues processed: 117 average time/residue: 1.4231 time to fit residues: 174.6746 Evaluate side-chains 94 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.0913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 GLN A 972 HIS A1102 HIS A1156 HIS A1157 GLN A1192 ASN A1270 ASN A1573 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7200 Z= 0.237 Angle : 0.763 30.003 9847 Z= 0.356 Chirality : 0.072 1.818 1048 Planarity : 0.005 0.047 1199 Dihedral : 15.994 72.721 1156 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.00 % Allowed : 14.71 % Favored : 80.29 % 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: -1.09 (0.28), residues: 801 helix: -0.41 (0.35), residues: 200 sheet: -0.67 (0.44), residues: 119 loop : -0.84 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 843 HIS 0.003 0.001 HIS A 972 PHE 0.022 0.002 PHE A1523 TYR 0.019 0.002 TYR A1304 ARG 0.004 0.000 ARG A1276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 85 time to evaluate : 0.739 Fit side-chains outliers start: 35 outliers final: 19 residues processed: 112 average time/residue: 1.4382 time to fit residues: 169.2490 Evaluate side-chains 101 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.8553 time to fit residues: 2.9024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 HIS A1270 ASN A1340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7200 Z= 0.205 Angle : 0.734 26.118 9847 Z= 0.340 Chirality : 0.068 1.683 1048 Planarity : 0.005 0.044 1199 Dihedral : 15.857 71.352 1156 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.86 % Allowed : 14.57 % Favored : 80.57 % 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: -0.57 (0.29), residues: 801 helix: 0.17 (0.37), residues: 200 sheet: -0.27 (0.43), residues: 118 loop : -0.60 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 843 HIS 0.002 0.001 HIS A1102 PHE 0.019 0.002 PHE A1523 TYR 0.016 0.001 TYR A1304 ARG 0.002 0.000 ARG A1368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 82 time to evaluate : 0.751 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 111 average time/residue: 1.3510 time to fit residues: 157.7384 Evaluate side-chains 99 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 0.9840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 HIS A1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 7200 Z= 0.406 Angle : 0.854 28.585 9847 Z= 0.405 Chirality : 0.072 1.608 1048 Planarity : 0.006 0.049 1199 Dihedral : 16.097 71.852 1156 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.86 % Allowed : 15.14 % Favored : 80.00 % 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: -0.74 (0.28), residues: 801 helix: -0.13 (0.36), residues: 199 sheet: -0.44 (0.43), residues: 126 loop : -0.60 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1436 HIS 0.004 0.001 HIS A1156 PHE 0.030 0.003 PHE A1523 TYR 0.025 0.002 TYR A1304 ARG 0.006 0.001 ARG A1368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 0.785 Fit side-chains outliers start: 34 outliers final: 24 residues processed: 115 average time/residue: 1.3984 time to fit residues: 168.8671 Evaluate side-chains 107 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 1.6095 time to fit residues: 4.3059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 0.0010 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 GLN A1102 HIS A1270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7200 Z= 0.163 Angle : 0.709 25.737 9847 Z= 0.326 Chirality : 0.066 1.658 1048 Planarity : 0.005 0.045 1199 Dihedral : 15.820 69.794 1156 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.57 % Allowed : 15.86 % Favored : 79.57 % 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: -0.31 (0.29), residues: 801 helix: 0.44 (0.38), residues: 200 sheet: -0.30 (0.42), residues: 128 loop : -0.40 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 843 HIS 0.003 0.001 HIS A1459 PHE 0.016 0.001 PHE A1523 TYR 0.012 0.001 TYR A1304 ARG 0.001 0.000 ARG A1082 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 0.792 Fit side-chains outliers start: 32 outliers final: 21 residues processed: 110 average time/residue: 1.3761 time to fit residues: 159.3974 Evaluate side-chains 99 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 1.0029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1102 HIS A1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 7200 Z= 0.362 Angle : 0.828 28.354 9847 Z= 0.390 Chirality : 0.070 1.590 1048 Planarity : 0.006 0.047 1199 Dihedral : 15.999 72.247 1156 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.86 % Allowed : 15.43 % Favored : 79.71 % 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: -0.54 (0.29), residues: 801 helix: 0.07 (0.37), residues: 199 sheet: -0.37 (0.42), residues: 128 loop : -0.47 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1436 HIS 0.004 0.001 HIS A1156 PHE 0.027 0.002 PHE A1523 TYR 0.023 0.002 TYR A1304 ARG 0.005 0.001 ARG A1368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 0.706 Fit side-chains outliers start: 34 outliers final: 23 residues processed: 114 average time/residue: 1.4512 time to fit residues: 173.6629 Evaluate side-chains 105 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 1.6789 time to fit residues: 2.8274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1102 HIS A1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7200 Z= 0.173 Angle : 0.715 25.899 9847 Z= 0.329 Chirality : 0.067 1.650 1048 Planarity : 0.004 0.044 1199 Dihedral : 15.815 70.108 1156 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.29 % Allowed : 16.29 % Favored : 79.43 % 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: -0.18 (0.29), residues: 801 helix: 0.49 (0.38), residues: 200 sheet: -0.17 (0.42), residues: 129 loop : -0.30 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 843 HIS 0.003 0.001 HIS A1459 PHE 0.017 0.001 PHE A1523 TYR 0.013 0.001 TYR A1304 ARG 0.002 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 0.830 Fit side-chains outliers start: 30 outliers final: 21 residues processed: 106 average time/residue: 1.3564 time to fit residues: 151.5374 Evaluate side-chains 101 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 1.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 69 optimal weight: 0.0970 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1102 HIS A1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7200 Z= 0.225 Angle : 0.745 26.569 9847 Z= 0.345 Chirality : 0.067 1.635 1048 Planarity : 0.005 0.043 1199 Dihedral : 15.800 71.687 1156 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.43 % Allowed : 17.43 % Favored : 79.14 % 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: -0.20 (0.29), residues: 801 helix: 0.45 (0.38), residues: 200 sheet: -0.20 (0.42), residues: 129 loop : -0.30 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 843 HIS 0.002 0.001 HIS A1459 PHE 0.019 0.002 PHE A1523 TYR 0.018 0.001 TYR A1304 ARG 0.004 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.805 Fit side-chains outliers start: 24 outliers final: 21 residues processed: 106 average time/residue: 1.4039 time to fit residues: 156.8680 Evaluate side-chains 102 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 1.3540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1102 HIS A1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7200 Z= 0.162 Angle : 0.704 25.521 9847 Z= 0.322 Chirality : 0.066 1.651 1048 Planarity : 0.004 0.045 1199 Dihedral : 15.717 68.658 1156 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.43 % Allowed : 17.86 % Favored : 78.71 % 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: -0.04 (0.30), residues: 801 helix: 0.67 (0.39), residues: 200 sheet: -0.09 (0.42), residues: 129 loop : -0.24 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 843 HIS 0.003 0.001 HIS A1459 PHE 0.015 0.001 PHE A1523 TYR 0.012 0.001 TYR A1304 ARG 0.003 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.772 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 104 average time/residue: 1.3423 time to fit residues: 147.0032 Evaluate side-chains 101 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.0668 time to fit residues: 1.2284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.0030 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1102 HIS A1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7200 Z= 0.157 Angle : 0.702 25.473 9847 Z= 0.320 Chirality : 0.066 1.659 1048 Planarity : 0.004 0.045 1199 Dihedral : 15.671 68.192 1156 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.14 % Allowed : 18.29 % Favored : 78.57 % 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: 0.01 (0.30), residues: 801 helix: 0.74 (0.39), residues: 200 sheet: -0.05 (0.43), residues: 129 loop : -0.23 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 843 HIS 0.002 0.001 HIS A1459 PHE 0.014 0.001 PHE A1523 TYR 0.012 0.001 TYR A1304 ARG 0.003 0.000 ARG A 903 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.839 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 103 average time/residue: 1.3815 time to fit residues: 149.9365 Evaluate side-chains 98 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 1.0119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 67 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 ASN A1102 HIS A1213 GLN A1270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.196232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157907 restraints weight = 6104.798| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.42 r_work: 0.3712 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7200 Z= 0.142 Angle : 0.689 25.145 9847 Z= 0.313 Chirality : 0.066 1.660 1048 Planarity : 0.004 0.045 1199 Dihedral : 15.618 67.003 1156 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.00 % Allowed : 18.86 % Favored : 78.14 % 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: 0.07 (0.30), residues: 801 helix: 0.85 (0.39), residues: 200 sheet: -0.06 (0.43), residues: 131 loop : -0.20 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 843 HIS 0.002 0.001 HIS A1459 PHE 0.013 0.001 PHE A1523 TYR 0.010 0.001 TYR A1388 ARG 0.004 0.000 ARG A1453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3237.58 seconds wall clock time: 58 minutes 2.40 seconds (3482.40 seconds total)