Starting phenix.real_space_refine on Tue Feb 13 20:15:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2024/7xi9_33200_updated.pdb" } resolution = 2.52 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= 0.063 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 4 6.06 5 P 22 5.49 5 S 52 5.16 5 C 4590 2.51 5 N 1312 2.21 5 O 1639 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 GLU 657": "OE1" <-> "OE2" Residue "A ASP 768": "OD1" <-> "OD2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A GLU 906": "OE1" <-> "OE2" Residue "A GLU 912": "OE1" <-> "OE2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ARG 1017": "NH1" <-> "NH2" Residue "A ASP 1046": "OD1" <-> "OD2" Residue "A ASP 1052": "OD1" <-> "OD2" Residue "A ARG 1059": "NH1" <-> "NH2" Residue "A GLU 1066": "OE1" <-> "OE2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A ASP 1162": "OD1" <-> "OD2" Residue "A GLU 1202": "OE1" <-> "OE2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1259": "NH1" <-> "NH2" Residue "A GLU 1329": "OE1" <-> "OE2" Residue "A ARG 1337": "NH1" <-> "NH2" Residue "A GLU 1385": "OE1" <-> "OE2" Residue "A GLU 1391": "OE1" <-> "OE2" Residue "A ARG 1398": "NH1" <-> "NH2" Residue "A ARG 1410": "NH1" <-> "NH2" Residue "A ARG 1456": "NH1" <-> "NH2" Residue "A ASP 1461": "OD1" <-> "OD2" Residue "A ARG 1516": "NH1" <-> "NH2" Residue "A GLU 1518": "OE1" <-> "OE2" 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-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6868 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 814} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 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: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 233 Unusual residues: {' ZN': 4} Classifications: {'peptide': 1, 'undetermined': 4, 'water': 203} Link IDs: {None: 207} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} 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 5830 SG CYS A1476 21.257 33.173 22.278 1.00 54.16 S ATOM 5842 SG CYS A1478 20.341 32.058 25.990 1.00 61.94 S ATOM 5887 SG CYS A1485 22.216 31.111 25.329 1.00 62.81 S ATOM 1016 SG CYS A 820 25.371 42.691 86.769 1.00 54.46 S ATOM 1497 SG CYS A 893 27.733 41.503 89.094 1.00 58.40 S ATOM 1516 SG CYS A 896 25.816 44.812 89.557 1.00 55.08 S ATOM 228 SG CYS A 653 28.209 17.646 58.993 1.00 64.71 S ATOM 245 SG CYS A 656 24.928 19.164 58.940 1.00 62.09 S ATOM 267 SG CYS A 659 25.620 18.008 62.290 1.00 64.16 S ATOM 488 SG CYS A 691 26.224 15.560 59.358 1.00 77.33 S ATOM 307 SG CYS A 664 14.026 19.266 70.395 1.00 87.82 S ATOM 326 SG CYS A 667 14.069 16.287 71.030 1.00 93.09 S ATOM 342 SG CYS A 670 16.697 19.004 72.106 1.00 91.79 S ATOM 448 SG CYS A 686 16.949 18.768 68.937 1.00 86.87 S Time building chain proxies: 5.09, per 1000 atoms: 0.67 Number of scatterers: 7620 At special positions: 0 Unit cell: (76.36, 97.94, 111.22, 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 4 29.99 S 52 16.00 P 22 15.00 F 1 9.00 O 1639 8.00 N 1312 7.00 C 4590 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: 3.15 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 896 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 820 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 691 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 653 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 659 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 656 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 667 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 686 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 664 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 670 " Number of angles added : 18 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1618 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 11 sheets defined 23.8% alpha, 16.3% beta 7 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 4.30 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 658 through 660 No H-bonds generated for 'chain 'A' and resid 658 through 660' Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' 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 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' 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 1157 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: 3.941A pdb=" N LEU A1247 " --> pdb=" O PHE A1243 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A1249 " --> pdb=" O ASN A1245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A1250 " --> pdb=" O SER A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1271 No H-bonds generated for 'chain 'A' and resid 1269 through 1271' Processing helix chain 'A' and resid 1278 through 1290 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 1368 through 1371 No H-bonds generated for 'chain 'A' and resid 1368 through 1371' Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1419 through 1427 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: 5.202A pdb=" N ASN A1505 " --> pdb=" O PRO A1501 " (cutoff:3.500A) removed outlier: 6.743A 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: 3.669A pdb=" N CYS A1595 " --> pdb=" O GLU A1591 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 828 through 832 removed outlier: 6.646A pdb=" N SER A 764 " --> pdb=" O HIS A 829 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS A 831 " --> pdb=" O CYS A 762 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS A 762 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 6.300A 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: 6.517A pdb=" N PHE A 864 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU A 816 " --> pdb=" O PHE A 864 " (cutoff:3.500A) removed outlier: 8.899A 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: 6.740A pdb=" N LEU A 922 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP A 916 " --> pdb=" O ARG A 920 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ARG A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 999 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A1017 " --> pdb=" O LYS A 997 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE A 999 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 6.949A 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: 4.166A 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 removed outlier: 8.439A pdb=" N LEU A1042 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR A1084 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TRP A1044 " --> pdb=" O TYR A1084 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N LEU A1086 " --> pdb=" O TRP A1044 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR A1061 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE A1085 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU A1063 " --> pdb=" O PHE A1085 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLU A1087 " --> pdb=" O GLU A1063 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= I, first strand: chain 'A' and resid 1293 through 1300 removed outlier: 7.549A pdb=" N ASP A1143 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA A1166 " --> pdb=" O ASP A1143 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A1185 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1343 through 1345 Processing sheet with id= K, first strand: chain 'A' and resid 1385 through 1387 169 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 3.38 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: 1166 1.31 - 1.43: 2189 1.43 - 1.56: 4135 1.56 - 1.69: 47 1.69 - 1.81: 73 Bond restraints: 7610 Sorted by residual: bond pdb=" C2' 5CM B 6 " pdb=" C1' 5CM B 6 " ideal model delta sigma weight residual 1.521 1.267 0.254 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 1.263 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C2 EIX C 18 " pdb=" N3 EIX C 18 " ideal model delta sigma weight residual 1.526 1.330 0.196 2.00e-02 2.50e+03 9.63e+01 bond pdb=" C4' EIX C 18 " pdb=" O4' EIX C 18 " ideal model delta sigma weight residual 1.613 1.431 0.182 2.00e-02 2.50e+03 8.28e+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 8.18e+01 ... (remaining 7605 not shown) Histogram of bond angle deviations from ideal: 89.53 - 98.42: 2 98.42 - 107.32: 470 107.32 - 116.21: 4721 116.21 - 125.11: 5000 125.11 - 134.01: 204 Bond angle restraints: 10397 Sorted by residual: angle pdb=" CG SAH A1705 " pdb=" SD SAH A1705 " pdb=" C5' SAH A1705 " ideal model delta sigma weight residual 101.77 89.53 12.24 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C4 EIX C 18 " pdb=" C5 EIX C 18 " pdb=" C6 EIX C 18 " ideal model delta sigma weight residual 119.72 108.16 11.56 3.00e+00 1.11e-01 1.49e+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 94.66 10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O SAH A1705 " pdb=" C SAH A1705 " pdb=" OXT SAH A1705 " ideal model delta sigma weight residual 126.79 117.56 9.23 3.00e+00 1.11e-01 9.47e+00 angle pdb=" O4' EIX C 18 " pdb=" C1' EIX C 18 " pdb=" N1 EIX C 18 " ideal model delta sigma weight residual 110.14 119.32 -9.18 3.00e+00 1.11e-01 9.36e+00 ... (remaining 10392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.95: 4221 32.95 - 65.90: 261 65.90 - 98.85: 24 98.85 - 131.80: 0 131.80 - 164.75: 1 Dihedral angle restraints: 4507 sinusoidal: 1992 harmonic: 2515 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 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+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 72.07 164.75 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA GLN A 687 " pdb=" C GLN A 687 " pdb=" N GLU A 688 " pdb=" CA GLU A 688 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 4504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.050: 1105 1.050 - 2.101: 0 2.101 - 3.151: 0 3.151 - 4.202: 0 4.202 - 5.252: 1 Chirality restraints: 1106 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 -2.61 5.25 2.00e-01 2.50e+01 6.90e+02 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 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB ILE A1408 " pdb=" CA ILE A1408 " pdb=" CG1 ILE A1408 " pdb=" CG2 ILE A1408 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 1103 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' EIX C 18 " -0.616 2.00e-02 2.50e+03 3.94e-01 3.50e+03 pdb=" N1 EIX C 18 " -0.076 2.00e-02 2.50e+03 pdb=" C2 EIX C 18 " 0.110 2.00e-02 2.50e+03 pdb=" O2 EIX C 18 " 0.359 2.00e-02 2.50e+03 pdb=" N3 EIX C 18 " 0.013 2.00e-02 2.50e+03 pdb=" C4 EIX C 18 " -0.012 2.00e-02 2.50e+03 pdb=" N4 EIX C 18 " -0.628 2.00e-02 2.50e+03 pdb=" C5 EIX C 18 " 0.666 2.00e-02 2.50e+03 pdb=" C6 EIX C 18 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1031 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO A1032 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1032 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1032 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A1541 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A1542 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1542 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1542 " -0.027 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1207 2.76 - 3.29: 7010 3.29 - 3.83: 13934 3.83 - 4.36: 17933 4.36 - 4.90: 27744 Nonbonded interactions: 67828 Sorted by model distance: nonbonded pdb=" OG SER A1230 " pdb=" OP1 EIX C 18 " model vdw 2.221 2.440 nonbonded pdb=" O VAL A1272 " pdb=" OG SER A1277 " model vdw 2.230 2.440 nonbonded pdb=" O CYS A1148 " pdb=" OH TYR A1563 " model vdw 2.255 2.440 nonbonded pdb=" O THR A1163 " pdb=" OG SER A1184 " model vdw 2.261 2.440 nonbonded pdb=" OG SER A 977 " pdb=" OP1 DT C 15 " model vdw 2.267 2.440 ... (remaining 67823 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: 0.910 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: 3.950 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 29.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 0.254 7610 Z= 0.515 Angle : 0.688 12.244 10397 Z= 0.357 Chirality : 0.164 5.252 1106 Planarity : 0.012 0.394 1272 Dihedral : 19.274 164.751 2889 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.72 % Allowed : 16.06 % Favored : 79.22 % 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: -2.68 (0.25), residues: 855 helix: -2.06 (0.29), residues: 218 sheet: -1.17 (0.40), residues: 144 loop : -1.84 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 843 HIS 0.002 0.001 HIS A1509 PHE 0.014 0.002 PHE A1523 TYR 0.021 0.002 TYR A1388 ARG 0.006 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 0.905 Fit side-chains REVERT: A 934 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7567 (mtm180) REVERT: A 978 ASP cc_start: 0.7281 (m-30) cc_final: 0.6751 (t0) REVERT: A 1097 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: A 1564 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7300 (mmp-170) REVERT: A 1609 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5298 (pmtt) outliers start: 35 outliers final: 17 residues processed: 130 average time/residue: 1.5080 time to fit residues: 205.2732 Evaluate side-chains 111 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 LYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1342 SER Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1477 SER Chi-restraints excluded: chain A residue 1543 GLU Chi-restraints excluded: chain A residue 1609 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1156 HIS A1157 GLN A1192 ASN A1213 GLN A1267 ASN A1464 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7610 Z= 0.347 Angle : 0.762 29.875 10397 Z= 0.357 Chirality : 0.073 1.882 1106 Planarity : 0.006 0.077 1272 Dihedral : 17.206 87.360 1247 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.59 % Allowed : 18.08 % Favored : 77.33 % 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: -1.85 (0.26), residues: 855 helix: -1.22 (0.32), residues: 216 sheet: -0.84 (0.41), residues: 139 loop : -1.34 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 868 HIS 0.003 0.001 HIS A1102 PHE 0.017 0.002 PHE A 946 TYR 0.023 0.002 TYR A1388 ARG 0.003 0.000 ARG A1546 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 0.877 Fit side-chains REVERT: A 934 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7559 (mtm180) REVERT: A 978 ASP cc_start: 0.7301 (m-30) cc_final: 0.6788 (t0) REVERT: A 1097 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: A 1451 MET cc_start: 0.7683 (mmt) cc_final: 0.7480 (tpt) REVERT: A 1564 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.7284 (mmp-170) outliers start: 34 outliers final: 20 residues processed: 118 average time/residue: 1.5019 time to fit residues: 185.8668 Evaluate side-chains 113 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1352 SER Chi-restraints excluded: chain A residue 1438 ASP Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1483 LYS Chi-restraints excluded: chain A residue 1543 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7610 Z= 0.232 Angle : 0.707 25.458 10397 Z= 0.327 Chirality : 0.066 1.675 1106 Planarity : 0.005 0.079 1272 Dihedral : 16.777 90.092 1229 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.59 % Allowed : 18.76 % Favored : 76.65 % 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: -1.31 (0.27), residues: 855 helix: -0.69 (0.34), residues: 219 sheet: -0.66 (0.40), residues: 144 loop : -0.97 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 843 HIS 0.003 0.001 HIS A1102 PHE 0.013 0.002 PHE A1523 TYR 0.018 0.001 TYR A1388 ARG 0.002 0.000 ARG A1368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 0.902 Fit side-chains REVERT: A 657 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 671 LYS cc_start: 0.7304 (mttm) cc_final: 0.7001 (mtpp) REVERT: A 934 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7517 (mtm180) REVERT: A 978 ASP cc_start: 0.7279 (m-30) cc_final: 0.6766 (t0) REVERT: A 1063 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6906 (mm-30) REVERT: A 1097 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: A 1609 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5284 (pmtt) outliers start: 34 outliers final: 15 residues processed: 123 average time/residue: 1.5515 time to fit residues: 200.0037 Evaluate side-chains 113 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1352 SER Chi-restraints excluded: chain A residue 1483 LYS Chi-restraints excluded: chain A residue 1543 GLU Chi-restraints excluded: chain A residue 1609 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1379 ASN A1493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7610 Z= 0.178 Angle : 0.675 25.034 10397 Z= 0.308 Chirality : 0.065 1.679 1106 Planarity : 0.005 0.075 1272 Dihedral : 16.337 92.116 1222 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.24 % Allowed : 20.65 % Favored : 76.11 % 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: -0.90 (0.28), residues: 855 helix: -0.34 (0.35), residues: 220 sheet: -0.59 (0.40), residues: 146 loop : -0.65 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 843 HIS 0.003 0.000 HIS A1102 PHE 0.011 0.001 PHE A1523 TYR 0.016 0.001 TYR A1388 ARG 0.002 0.000 ARG A1564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.866 Fit side-chains REVERT: A 657 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 833 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7791 (ttmt) REVERT: A 934 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7466 (mtm180) REVERT: A 978 ASP cc_start: 0.7222 (m-30) cc_final: 0.6713 (t0) REVERT: A 1063 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6757 (mm-30) REVERT: A 1097 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: A 1609 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5261 (pmtt) outliers start: 24 outliers final: 12 residues processed: 118 average time/residue: 1.6368 time to fit residues: 202.6837 Evaluate side-chains 112 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1408 ILE Chi-restraints excluded: chain A residue 1483 LYS Chi-restraints excluded: chain A residue 1543 GLU Chi-restraints excluded: chain A residue 1609 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.0770 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1379 ASN A1464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7610 Z= 0.150 Angle : 0.658 24.811 10397 Z= 0.298 Chirality : 0.064 1.660 1106 Planarity : 0.005 0.072 1272 Dihedral : 16.162 93.576 1222 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.64 % Allowed : 20.65 % Favored : 75.71 % 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: -0.53 (0.28), residues: 855 helix: -0.08 (0.35), residues: 220 sheet: -0.06 (0.45), residues: 120 loop : -0.49 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1498 HIS 0.003 0.000 HIS A1102 PHE 0.009 0.001 PHE A1523 TYR 0.014 0.001 TYR A1388 ARG 0.004 0.000 ARG A1207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.792 Fit side-chains REVERT: A 657 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 672 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.5570 (m-30) REVERT: A 833 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7778 (ttpt) REVERT: A 917 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6270 (mm) REVERT: A 934 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7475 (mtm180) REVERT: A 978 ASP cc_start: 0.7187 (m-30) cc_final: 0.6678 (t0) REVERT: A 1063 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6772 (mm-30) REVERT: A 1609 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5239 (pmtt) outliers start: 27 outliers final: 9 residues processed: 119 average time/residue: 1.5841 time to fit residues: 197.6316 Evaluate side-chains 103 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1408 ILE Chi-restraints excluded: chain A residue 1483 LYS Chi-restraints excluded: chain A residue 1543 GLU Chi-restraints excluded: chain A residue 1609 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7610 Z= 0.145 Angle : 0.653 24.757 10397 Z= 0.295 Chirality : 0.064 1.654 1106 Planarity : 0.004 0.069 1272 Dihedral : 15.911 93.029 1218 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.10 % Allowed : 21.19 % Favored : 75.71 % 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: -0.31 (0.29), residues: 855 helix: 0.07 (0.35), residues: 220 sheet: 0.00 (0.46), residues: 120 loop : -0.30 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1498 HIS 0.003 0.000 HIS A1102 PHE 0.008 0.001 PHE A1523 TYR 0.013 0.001 TYR A1388 ARG 0.002 0.000 ARG A1207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.852 Fit side-chains REVERT: A 657 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 672 ASP cc_start: 0.6603 (OUTLIER) cc_final: 0.5550 (m-30) REVERT: A 821 GLU cc_start: 0.8127 (pt0) cc_final: 0.7815 (pt0) REVERT: A 833 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7752 (ttpt) REVERT: A 934 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7409 (mtm180) REVERT: A 967 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: A 978 ASP cc_start: 0.7184 (m-30) cc_final: 0.6680 (t70) REVERT: A 1017 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: A 1063 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6705 (mm-30) REVERT: A 1453 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7406 (tpp-160) REVERT: A 1609 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5254 (pmtt) outliers start: 23 outliers final: 11 residues processed: 112 average time/residue: 1.6041 time to fit residues: 188.2226 Evaluate side-chains 106 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 861 LYS Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 967 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1453 ARG Chi-restraints excluded: chain A residue 1543 GLU Chi-restraints excluded: chain A residue 1609 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7610 Z= 0.243 Angle : 0.699 25.119 10397 Z= 0.319 Chirality : 0.065 1.645 1106 Planarity : 0.005 0.068 1272 Dihedral : 16.095 89.409 1218 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.91 % Allowed : 20.65 % Favored : 75.44 % 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: -0.40 (0.28), residues: 855 helix: -0.12 (0.35), residues: 220 sheet: -0.13 (0.42), residues: 137 loop : -0.28 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 868 HIS 0.003 0.001 HIS A1102 PHE 0.014 0.001 PHE A 946 TYR 0.017 0.001 TYR A1388 ARG 0.002 0.000 ARG A1207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.909 Fit side-chains REVERT: A 657 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 672 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.5540 (m-30) REVERT: A 833 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7820 (ttmt) REVERT: A 934 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7456 (mtm180) REVERT: A 978 ASP cc_start: 0.7222 (m-30) cc_final: 0.6708 (t0) REVERT: A 1063 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6749 (mm-30) REVERT: A 1609 LYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5208 (pmtt) outliers start: 29 outliers final: 16 residues processed: 115 average time/residue: 1.5522 time to fit residues: 186.9232 Evaluate side-chains 111 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1352 SER Chi-restraints excluded: chain A residue 1408 ILE Chi-restraints excluded: chain A residue 1543 GLU Chi-restraints excluded: chain A residue 1609 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7610 Z= 0.173 Angle : 0.668 24.691 10397 Z= 0.303 Chirality : 0.064 1.654 1106 Planarity : 0.005 0.071 1272 Dihedral : 16.001 92.241 1218 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.97 % Allowed : 21.59 % Favored : 75.44 % 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: -0.24 (0.29), residues: 855 helix: 0.00 (0.35), residues: 220 sheet: 0.09 (0.44), residues: 125 loop : -0.21 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 868 HIS 0.003 0.000 HIS A1102 PHE 0.010 0.001 PHE A1523 TYR 0.013 0.001 TYR A1388 ARG 0.002 0.000 ARG A1207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.768 Fit side-chains REVERT: A 657 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 672 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.5465 (m-30) REVERT: A 833 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7818 (ttmt) REVERT: A 861 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.6132 (tttp) REVERT: A 934 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7449 (mtm180) REVERT: A 978 ASP cc_start: 0.7198 (m-30) cc_final: 0.6686 (t70) REVERT: A 1063 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6770 (mm-30) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 1.5203 time to fit residues: 172.0035 Evaluate side-chains 108 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 861 LYS Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1352 SER Chi-restraints excluded: chain A residue 1408 ILE Chi-restraints excluded: chain A residue 1543 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1406 GLN A1464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7610 Z= 0.212 Angle : 0.685 24.888 10397 Z= 0.312 Chirality : 0.065 1.647 1106 Planarity : 0.005 0.070 1272 Dihedral : 16.043 90.771 1218 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.56 % Allowed : 21.86 % Favored : 75.57 % 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: -0.30 (0.28), residues: 855 helix: -0.05 (0.35), residues: 220 sheet: 0.05 (0.44), residues: 127 loop : -0.24 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 868 HIS 0.003 0.001 HIS A1102 PHE 0.012 0.001 PHE A 946 TYR 0.015 0.001 TYR A1388 ARG 0.002 0.000 ARG A1207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.931 Fit side-chains REVERT: A 657 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7537 (tm-30) REVERT: A 672 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.5473 (m-30) REVERT: A 833 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7833 (ttmt) REVERT: A 861 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.6119 (tttp) REVERT: A 934 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7462 (mtm180) REVERT: A 978 ASP cc_start: 0.7229 (m-30) cc_final: 0.6719 (t0) REVERT: A 1063 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6770 (mm-30) outliers start: 19 outliers final: 14 residues processed: 110 average time/residue: 1.5358 time to fit residues: 177.1717 Evaluate side-chains 109 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 861 LYS Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 967 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1352 SER Chi-restraints excluded: chain A residue 1408 ILE Chi-restraints excluded: chain A residue 1543 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7610 Z= 0.229 Angle : 0.695 24.913 10397 Z= 0.318 Chirality : 0.065 1.647 1106 Planarity : 0.005 0.072 1272 Dihedral : 16.092 90.390 1218 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.70 % Allowed : 21.73 % Favored : 75.57 % 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: -0.30 (0.28), residues: 855 helix: -0.09 (0.35), residues: 220 sheet: 0.01 (0.42), residues: 135 loop : -0.22 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 868 HIS 0.003 0.001 HIS A1102 PHE 0.013 0.001 PHE A 946 TYR 0.016 0.001 TYR A1388 ARG 0.002 0.000 ARG A1207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.877 Fit side-chains REVERT: A 672 ASP cc_start: 0.6550 (OUTLIER) cc_final: 0.5453 (m-30) REVERT: A 833 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7840 (ttmt) REVERT: A 861 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6135 (tttp) REVERT: A 934 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7474 (mtm180) REVERT: A 978 ASP cc_start: 0.7225 (m-30) cc_final: 0.6711 (t0) REVERT: A 1063 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 1609 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5222 (pmtt) outliers start: 20 outliers final: 15 residues processed: 109 average time/residue: 1.5035 time to fit residues: 171.9261 Evaluate side-chains 112 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 861 LYS Chi-restraints excluded: chain A residue 895 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 967 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1309 THR Chi-restraints excluded: chain A residue 1352 SER Chi-restraints excluded: chain A residue 1408 ILE Chi-restraints excluded: chain A residue 1543 GLU Chi-restraints excluded: chain A residue 1609 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 8 optimal weight: 0.0030 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A1464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136252 restraints weight = 7584.422| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.38 r_work: 0.3502 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7610 Z= 0.278 Angle : 0.718 24.993 10397 Z= 0.331 Chirality : 0.066 1.647 1106 Planarity : 0.005 0.072 1272 Dihedral : 16.225 88.825 1218 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.70 % Allowed : 21.73 % Favored : 75.57 % 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: -0.39 (0.28), residues: 855 helix: -0.22 (0.35), residues: 220 sheet: 0.01 (0.42), residues: 135 loop : -0.26 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 868 HIS 0.003 0.001 HIS A1102 PHE 0.016 0.002 PHE A 946 TYR 0.017 0.002 TYR A1388 ARG 0.002 0.000 ARG A1234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3557.99 seconds wall clock time: 63 minutes 33.79 seconds (3813.79 seconds total)