Starting phenix.real_space_refine (version: dev) on Sat Feb 18 07:49:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2023/7xi9_33200_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2023/7xi9_33200.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2023/7xi9_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_2023/7xi9_33200_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2023/7xi9_33200_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2023/7xi9_33200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2023/7xi9_33200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2023/7xi9_33200_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xi9_33200/02_2023/7xi9_33200_updated.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.063 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 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-4877/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: 4.94, per 1000 atoms: 0.65 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: 3.44 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: 3.43 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: 3.06 Time building geometry restraints manager: 3.68 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=" C4 EIX C 18 " pdb=" N3 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=" C1' EIX C 18 " pdb=" C2' EIX C 18 " pdb=" C3' 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=" N1 EIX C 18 " pdb=" C1' EIX C 18 " pdb=" O4' 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 - 17.85: 3798 17.85 - 35.70: 436 35.70 - 53.54: 175 53.54 - 71.39: 45 71.39 - 89.24: 17 Dihedral angle restraints: 4471 sinusoidal: 1956 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=" 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 dihedral pdb=" CA TYR A 991 " pdb=" C TYR A 991 " pdb=" N ARG A 992 " pdb=" CA ARG A 992 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4468 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=" C2 EIX C 18 " 0.110 2.00e-02 2.50e+03 pdb=" C4 EIX C 18 " -0.012 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 pdb=" N1 EIX C 18 " -0.076 2.00e-02 2.50e+03 pdb=" N3 EIX C 18 " 0.013 2.00e-02 2.50e+03 pdb=" N4 EIX C 18 " -0.628 2.00e-02 2.50e+03 pdb=" O2 EIX C 18 " 0.359 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 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. 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.290 Check model and map are aligned: 0.120 Process input model: 28.510 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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= 0.524 Angle : 0.688 12.244 10397 Z= 0.357 Chirality : 0.164 5.252 1106 Planarity : 0.012 0.394 1272 Dihedral : 18.907 89.241 2853 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 % 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 *********************** 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 : 0.996 Fit side-chains outliers start: 35 outliers final: 17 residues processed: 130 average time/residue: 1.5549 time to fit residues: 211.6756 Evaluate side-chains 108 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.0661 time to fit residues: 1.1872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 7610 Z= 0.319 Angle : 0.741 26.955 10397 Z= 0.348 Chirality : 0.076 2.015 1106 Planarity : 0.005 0.076 1272 Dihedral : 15.902 88.082 1178 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 5.40 % 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 (0.26), residues: 855 helix: -1.19 (0.32), residues: 216 sheet: -0.87 (0.40), residues: 144 loop : -1.36 (0.26), residues: 495 *********************** 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 134 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 0.866 Fit side-chains outliers start: 40 outliers final: 28 residues processed: 124 average time/residue: 1.3822 time to fit residues: 180.3627 Evaluate side-chains 120 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.8695 time to fit residues: 4.8749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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: 0.8342 moved from start: 0.0764 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= 0.195 Angle : 0.688 25.241 10397 Z= 0.316 Chirality : 0.066 1.698 1106 Planarity : 0.005 0.076 1272 Dihedral : 15.761 91.524 1178 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 4.99 % 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: -1.26 (0.27), residues: 855 helix: -0.64 (0.34), residues: 219 sheet: -0.65 (0.40), residues: 144 loop : -0.93 (0.27), residues: 492 *********************** 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 138 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 101 time to evaluate : 0.864 Fit side-chains outliers start: 37 outliers final: 23 residues processed: 131 average time/residue: 1.4110 time to fit residues: 194.5109 Evaluate side-chains 121 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 1.1079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 38 optimal weight: 0.0020 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 A1493 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1084 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= 0.153 Angle : 0.660 24.897 10397 Z= 0.300 Chirality : 0.065 1.695 1106 Planarity : 0.005 0.074 1272 Dihedral : 15.581 93.919 1178 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 4.72 % 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: -0.77 (0.28), residues: 855 helix: -0.23 (0.35), residues: 220 sheet: -0.28 (0.44), residues: 127 loop : -0.64 (0.27), residues: 508 *********************** 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 136 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 0.968 Fit side-chains outliers start: 35 outliers final: 20 residues processed: 131 average time/residue: 1.4714 time to fit residues: 203.5409 Evaluate side-chains 117 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.8070 time to fit residues: 2.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.0170 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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: 0.8323 moved from start: 0.1193 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= 0.190 Angle : 0.674 24.952 10397 Z= 0.306 Chirality : 0.065 1.687 1106 Planarity : 0.005 0.072 1272 Dihedral : 15.567 92.337 1178 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 4.45 % 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: -0.60 (0.28), residues: 855 helix: -0.11 (0.35), residues: 220 sheet: -0.09 (0.44), residues: 122 loop : -0.54 (0.27), residues: 513 *********************** 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 128 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 0.916 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 123 average time/residue: 1.5161 time to fit residues: 195.9405 Evaluate side-chains 113 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.4673 time to fit residues: 2.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8330 moved from start: 0.1183 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= 0.206 Angle : 0.685 24.911 10397 Z= 0.311 Chirality : 0.065 1.683 1106 Planarity : 0.005 0.073 1272 Dihedral : 15.575 91.687 1178 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.28), residues: 855 helix: -0.11 (0.35), residues: 220 sheet: -0.15 (0.44), residues: 130 loop : -0.36 (0.28), residues: 505 *********************** 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 118 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.876 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 114 average time/residue: 1.4803 time to fit residues: 177.4280 Evaluate side-chains 113 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.9047 time to fit residues: 3.0882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.8346 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 7610 Z= 0.244 Angle : 0.702 24.953 10397 Z= 0.321 Chirality : 0.066 1.678 1106 Planarity : 0.005 0.074 1272 Dihedral : 15.612 90.321 1178 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 3.78 % 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: -0.45 (0.28), residues: 855 helix: -0.16 (0.35), residues: 220 sheet: -0.12 (0.43), residues: 135 loop : -0.33 (0.28), residues: 500 *********************** 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 120 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.866 Fit side-chains outliers start: 28 outliers final: 23 residues processed: 115 average time/residue: 1.4971 time to fit residues: 180.7642 Evaluate side-chains 115 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.1028 time to fit residues: 1.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 0.0050 chunk 66 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A 788 ASN A1464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1265 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= 0.192 Angle : 0.680 24.755 10397 Z= 0.309 Chirality : 0.065 1.674 1106 Planarity : 0.005 0.073 1272 Dihedral : 15.537 92.592 1178 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 3.91 % 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: -0.32 (0.29), residues: 855 helix: -0.00 (0.35), residues: 220 sheet: -0.10 (0.43), residues: 135 loop : -0.24 (0.28), residues: 500 *********************** 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 121 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.953 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 116 average time/residue: 1.4983 time to fit residues: 182.7072 Evaluate side-chains 112 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 1.0568 time to fit residues: 2.1773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.8299 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 7610 Z= 0.158 Angle : 0.661 24.533 10397 Z= 0.299 Chirality : 0.064 1.678 1106 Planarity : 0.005 0.072 1272 Dihedral : 15.393 93.911 1178 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 2.97 % 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: -0.14 (0.29), residues: 855 helix: 0.21 (0.36), residues: 214 sheet: 0.04 (0.45), residues: 122 loop : -0.18 (0.28), residues: 519 *********************** 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 111 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.893 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 1.5050 time to fit residues: 174.0236 Evaluate side-chains 107 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.1201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 7610 Z= 0.328 Angle : 0.746 25.179 10397 Z= 0.345 Chirality : 0.067 1.665 1106 Planarity : 0.005 0.075 1272 Dihedral : 15.623 87.967 1178 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 2.97 % 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: -0.45 (0.28), residues: 855 helix: -0.14 (0.35), residues: 217 sheet: -0.13 (0.42), residues: 137 loop : -0.33 (0.28), residues: 501 ********************** 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 112 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.876 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 109 average time/residue: 1.5461 time to fit residues: 176.9289 Evaluate side-chains 109 residues out of total 747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 1.3230 time to fit residues: 3.8925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 8 optimal weight: 0.0030 chunk 12 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.167909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137363 restraints weight = 7563.253| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.40 r_work: 0.3516 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1328 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= 0.219 Angle : 0.695 24.602 10397 Z= 0.318 Chirality : 0.065 1.676 1106 Planarity : 0.005 0.075 1272 Dihedral : 15.558 91.552 1178 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 2.56 % 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: -0.33 (0.28), residues: 855 helix: -0.07 (0.35), residues: 220 sheet: -0.07 (0.43), residues: 137 loop : -0.23 (0.28), residues: 498 =============================================================================== Job complete usr+sys time: 3485.82 seconds wall clock time: 62 minutes 52.71 seconds (3772.71 seconds total)