Starting phenix.real_space_refine on Fri Mar 15 23:33:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/03_2024/6um2_20816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/03_2024/6um2_20816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/03_2024/6um2_20816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/03_2024/6um2_20816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/03_2024/6um2_20816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/03_2024/6um2_20816.pdb" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 107 5.16 5 C 8188 2.51 5 N 2216 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 612": "OD1" <-> "OD2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A ASP 693": "OD1" <-> "OD2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A ARG 790": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 823": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1048": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "A GLU 1102": "OE1" <-> "OE2" Residue "A TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1104": "OD1" <-> "OD2" Residue "A ARG 1112": "NH1" <-> "NH2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A TYR 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1194": "NH1" <-> "NH2" Residue "A ARG 1221": "NH1" <-> "NH2" Residue "A ASP 1240": "OD1" <-> "OD2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A ARG 1260": "NH1" <-> "NH2" Residue "A TYR 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1344": "NH1" <-> "NH2" Residue "A GLU 1363": "OE1" <-> "OE2" Residue "A ARG 1365": "NH1" <-> "NH2" Residue "A TYR 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1395": "NH1" <-> "NH2" Residue "A GLU 1410": "OE1" <-> "OE2" Residue "A GLU 1432": "OE1" <-> "OE2" Residue "A ASP 1466": "OD1" <-> "OD2" Residue "A ARG 1482": "NH1" <-> "NH2" Residue "A PHE 1621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1762": "OD1" <-> "OD2" Residue "A TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1793": "OD1" <-> "OD2" Residue "A ASP 1811": "OD1" <-> "OD2" Residue "A PHE 1834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1856": "OE1" <-> "OE2" Residue "A PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2013": "OD1" <-> "OD2" Residue "A PHE 2026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2047": "OD1" <-> "OD2" Residue "A GLU 2062": "OE1" <-> "OE2" Residue "A GLU 2102": "OE1" <-> "OE2" Residue "A PHE 2114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13094 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1638, 12632 Classifications: {'peptide': 1638} Link IDs: {'PTRANS': 88, 'TRANS': 1549} Chain breaks: 2 Chain: "B" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 364 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.63, per 1000 atoms: 0.58 Number of scatterers: 13094 At special positions: 0 Unit cell: (181.46, 126.42, 130.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 107 16.00 O 2583 8.00 N 2216 7.00 C 8188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 636 " - pdb=" SG CYS A 672 " distance=2.04 Simple disulfide: pdb=" SG CYS A 680 " - pdb=" SG CYS A 687 " distance=2.02 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 768 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 822 " distance=2.01 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 838 " distance=2.02 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS A 918 " distance=2.02 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 930 " distance=2.02 Simple disulfide: pdb=" SG CYS A 942 " - pdb=" SG CYS A 978 " distance=2.03 Simple disulfide: pdb=" SG CYS A 984 " - pdb=" SG CYS A 995 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS A1086 " distance=2.02 Simple disulfide: pdb=" SG CYS A1093 " - pdb=" SG CYS A1134 " distance=2.03 Simple disulfide: pdb=" SG CYS A1143 " - pdb=" SG CYS A1151 " distance=2.03 Simple disulfide: pdb=" SG CYS A1186 " - pdb=" SG CYS A1214 " distance=2.05 Simple disulfide: pdb=" SG CYS A1199 " - pdb=" SG CYS A1226 " distance=2.02 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1271 " distance=2.04 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1291 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1358 " distance=2.03 Simple disulfide: pdb=" SG CYS A1342 " - pdb=" SG CYS A1370 " distance=2.02 Simple disulfide: pdb=" SG CYS A1378 " - pdb=" SG CYS A1417 " distance=2.05 Simple disulfide: pdb=" SG CYS A1429 " - pdb=" SG CYS A1436 " distance=2.02 Simple disulfide: pdb=" SG CYS A1470 " - pdb=" SG CYS A1503 " distance=2.02 Simple disulfide: pdb=" SG CYS A1485 " - pdb=" SG CYS A1515 " distance=2.02 Simple disulfide: pdb=" SG CYS A1525 " - pdb=" SG CYS A1562 " distance=2.06 Simple disulfide: pdb=" SG CYS A1568 " - pdb=" SG CYS A1575 " distance=2.03 Simple disulfide: pdb=" SG CYS A1607 " - pdb=" SG CYS A1643 " distance=2.03 Simple disulfide: pdb=" SG CYS A1623 " - pdb=" SG CYS A1655 " distance=2.02 Simple disulfide: pdb=" SG CYS A1661 " - pdb=" SG CYS A1704 " distance=2.06 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1722 " distance=2.02 Simple disulfide: pdb=" SG CYS A1759 " - pdb=" SG CYS A1792 " distance=2.05 Simple disulfide: pdb=" SG CYS A1775 " - pdb=" SG CYS A1804 " distance=2.03 Simple disulfide: pdb=" SG CYS A1813 " - pdb=" SG CYS A1848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1859 " - pdb=" SG CYS A1865 " distance=2.02 Simple disulfide: pdb=" SG CYS A1902 " - pdb=" SG CYS A1984 " distance=2.04 Simple disulfide: pdb=" SG CYS A1912 " - pdb=" SG CYS A1936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1926 " - pdb=" SG CYS A1951 " distance=2.05 Simple disulfide: pdb=" SG CYS A1966 " - pdb=" SG CYS A1996 " distance=2.02 Simple disulfide: pdb=" SG CYS A2003 " - pdb=" SG CYS A2038 " distance=2.04 Simple disulfide: pdb=" SG CYS A2048 " - pdb=" SG CYS A2055 " distance=2.06 Simple disulfide: pdb=" SG CYS A2091 " - pdb=" SG CYS A2122 " distance=2.02 Simple disulfide: pdb=" SG CYS A2105 " - pdb=" SG CYS A2134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 47 " distance=2.04 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 60 " distance=2.01 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 51 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2505 " - " ASN A1030 " " NAG A2506 " - " ASN A1665 " Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 2.1 seconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 34 sheets defined 3.8% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 649 through 653 removed outlier: 3.705A pdb=" N THR A 653 " --> pdb=" O THR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 768 removed outlier: 3.562A pdb=" N CYS A 768 " --> pdb=" O SER A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 removed outlier: 4.131A pdb=" N ASP A 937 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 959 Processing helix chain 'A' and resid 1223 through 1226 Processing helix chain 'A' and resid 1825 through 1830 removed outlier: 4.296A pdb=" N SER A1828 " --> pdb=" O ASN A1825 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A1830 " --> pdb=" O SER A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1877 through 1881 removed outlier: 3.572A pdb=" N MET A1881 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2134 removed outlier: 4.249A pdb=" N CYS A2134 " --> pdb=" O ARG A2131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2131 through 2134' Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.041A pdb=" N THR B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 25 removed outlier: 3.734A pdb=" N GLY B 25 " --> pdb=" O GLY B 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 25' Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.790A pdb=" N CYS B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA2, first strand: chain 'A' and resid 548 through 549 Processing sheet with id=AA3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.770A pdb=" N GLU A 617 " --> pdb=" O THR A 607 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 607 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 619 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 605 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 631 through 632 removed outlier: 3.544A pdb=" N THR A 631 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 713 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU A 753 " --> pdb=" O THR A 757 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASN A 759 " --> pdb=" O GLN A 751 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 665 through 669 removed outlier: 3.521A pdb=" N VAL A 689 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLY A 700 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS A 687 " --> pdb=" O ASN A 698 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN A 698 " --> pdb=" O CYS A 687 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 689 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 696 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.618A pdb=" N TRP A 802 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 815 " --> pdb=" O ASP A 806 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 837 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 858 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 856 " --> pdb=" O GLN A 839 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 864 through 865 removed outlier: 4.761A pdb=" N GLY A 864 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU A 876 " --> pdb=" O GLY A 864 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA9, first strand: chain 'A' and resid 898 through 899 removed outlier: 6.462A pdb=" N HIS A 898 " --> pdb=" O TRP A 924 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER A 921 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER A 913 " --> pdb=" O SER A 921 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 943 through 946 removed outlier: 3.820A pdb=" N ILE A 944 " --> pdb=" O PHE A 953 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 953 " --> pdb=" O ILE A 944 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 964 through 965 removed outlier: 3.669A pdb=" N TYR A 964 " --> pdb=" O PHE A 975 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 975 " --> pdb=" O TYR A 964 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1019 through 1021 removed outlier: 3.821A pdb=" N GLN A1020 " --> pdb=" O THR A1028 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1115 through 1117 removed outlier: 3.502A pdb=" N TRP A1115 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A1131 " --> pdb=" O TRP A1115 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A1117 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE A1129 " --> pdb=" O ALA A1117 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A1151 " --> pdb=" O TYR A1130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1177 through 1180 removed outlier: 7.560A pdb=" N ARG A1194 " --> pdb=" O PHE A1218 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N TRP A1220 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN A1196 " --> pdb=" O TRP A1220 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR A1222 " --> pdb=" O ASN A1196 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A1198 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A1215 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN A1211 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A1217 " --> pdb=" O GLN A1209 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1230 through 1232 removed outlier: 3.601A pdb=" N TYR A1313 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A1338 " --> pdb=" O MET A1320 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A1361 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG A1365 " --> pdb=" O ALA A1348 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA A1348 " --> pdb=" O ARG A1365 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1257 through 1259 removed outlier: 3.618A pdb=" N TYR A1266 " --> pdb=" O VAL A1259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A1265 " --> pdb=" O GLU A1293 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A1267 " --> pdb=" O CYS A1291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1411 through 1414 removed outlier: 3.681A pdb=" N VAL A1444 " --> pdb=" O LEU A1437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1462 through 1464 removed outlier: 3.848A pdb=" N TYR A1505 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1508 " --> pdb=" O MET A1495 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1526 through 1528 Processing sheet with id=AC2, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AC3, first strand: chain 'A' and resid 1584 through 1585 removed outlier: 3.809A pdb=" N GLU A1602 " --> pdb=" O LYS A1585 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A1598 " --> pdb=" O THR A1591 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR A1591 " --> pdb=" O GLN A1598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1584 through 1585 removed outlier: 3.809A pdb=" N GLU A1602 " --> pdb=" O LYS A1585 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1597 " --> pdb=" O PHE A1621 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A1617 " --> pdb=" O TYR A1601 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A1618 " --> pdb=" O LEU A1645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1664 through 1665 Processing sheet with id=AC6, first strand: chain 'A' and resid 1682 through 1684 removed outlier: 6.613A pdb=" N VAL A1721 " --> pdb=" O ILE A1733 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A1723 " --> pdb=" O ILE A1731 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1731 " --> pdb=" O LYS A1723 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A1754 " --> pdb=" O ARG A1735 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A1794 " --> pdb=" O THR A1768 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N HIS A1774 " --> pdb=" O THR A1800 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1682 through 1684 removed outlier: 6.613A pdb=" N VAL A1721 " --> pdb=" O ILE A1733 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A1723 " --> pdb=" O ILE A1731 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1731 " --> pdb=" O LYS A1723 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A1754 " --> pdb=" O ARG A1735 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A1794 " --> pdb=" O THR A1768 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP A1793 " --> pdb=" O THR A1789 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR A1789 " --> pdb=" O ASP A1793 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A1795 " --> pdb=" O LEU A1787 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1837 through 1838 removed outlier: 3.861A pdb=" N HIS A1841 " --> pdb=" O ARG A1838 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1844 through 1845 Processing sheet with id=AD1, first strand: chain 'A' and resid 1882 through 1886 removed outlier: 3.825A pdb=" N SER A1960 " --> pdb=" O TYR A1896 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR A1959 " --> pdb=" O VAL A1986 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N PHE A1988 " --> pdb=" O THR A1959 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A1961 " --> pdb=" O PHE A1988 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU A1985 " --> pdb=" O GLU A1980 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU A1980 " --> pdb=" O GLU A1985 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1987 " --> pdb=" O PHE A1978 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1916 through 1918 Processing sheet with id=AD3, first strand: chain 'A' and resid 1935 through 1937 removed outlier: 3.941A pdb=" N CYS A1936 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A1949 " --> pdb=" O CYS A1936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 2025 through 2028 removed outlier: 4.056A pdb=" N PHE A2026 " --> pdb=" O TYR A2033 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2054 through 2056 removed outlier: 3.567A pdb=" N GLN A2064 " --> pdb=" O LYS A2056 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2074 through 2076 Processing sheet with id=AD7, first strand: chain 'A' and resid 2098 through 2105 removed outlier: 3.656A pdb=" N PHE A2126 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A2104 " --> pdb=" O TRP A2128 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A2130 " --> pdb=" O THR A2104 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2814 1.33 - 1.45: 3074 1.45 - 1.57: 7390 1.57 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 13397 Sorted by residual: bond pdb=" N ILE A 855 " pdb=" CA ILE A 855 " ideal model delta sigma weight residual 1.458 1.497 -0.039 9.00e-03 1.23e+04 1.86e+01 bond pdb=" N VAL A1724 " pdb=" CA VAL A1724 " ideal model delta sigma weight residual 1.460 1.492 -0.031 7.30e-03 1.88e+04 1.83e+01 bond pdb=" N ILE A 561 " pdb=" CA ILE A 561 " ideal model delta sigma weight residual 1.459 1.495 -0.037 9.10e-03 1.21e+04 1.63e+01 bond pdb=" N CYS A 636 " pdb=" CA CYS A 636 " ideal model delta sigma weight residual 1.458 1.492 -0.034 9.00e-03 1.23e+04 1.43e+01 bond pdb=" N VAL A 677 " pdb=" CA VAL A 677 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.11e-02 8.12e+03 1.37e+01 ... (remaining 13392 not shown) Histogram of bond angle deviations from ideal: 96.40 - 104.04: 214 104.04 - 111.68: 5034 111.68 - 119.33: 7048 119.33 - 126.97: 5741 126.97 - 134.62: 166 Bond angle restraints: 18203 Sorted by residual: angle pdb=" C VAL A1791 " pdb=" CA VAL A1791 " pdb=" CB VAL A1791 " ideal model delta sigma weight residual 112.02 123.50 -11.48 1.31e+00 5.83e-01 7.68e+01 angle pdb=" C ILE A 897 " pdb=" CA ILE A 897 " pdb=" CB ILE A 897 " ideal model delta sigma weight residual 110.41 119.73 -9.32 1.14e+00 7.69e-01 6.69e+01 angle pdb=" N VAL A1791 " pdb=" CA VAL A1791 " pdb=" C VAL A1791 " ideal model delta sigma weight residual 110.53 103.20 7.33 9.40e-01 1.13e+00 6.08e+01 angle pdb=" C ASN A1520 " pdb=" CA ASN A1520 " pdb=" CB ASN A1520 " ideal model delta sigma weight residual 109.72 122.63 -12.91 1.66e+00 3.63e-01 6.05e+01 angle pdb=" N VAL A1977 " pdb=" CA VAL A1977 " pdb=" C VAL A1977 " ideal model delta sigma weight residual 107.37 118.79 -11.42 1.48e+00 4.57e-01 5.95e+01 ... (remaining 18198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6975 17.18 - 34.35: 978 34.35 - 51.53: 198 51.53 - 68.71: 35 68.71 - 85.88: 13 Dihedral angle restraints: 8199 sinusoidal: 3346 harmonic: 4853 Sorted by residual: dihedral pdb=" CB CYS A2003 " pdb=" SG CYS A2003 " pdb=" SG CYS A2038 " pdb=" CB CYS A2038 " ideal model delta sinusoidal sigma weight residual -86.00 -0.12 -85.88 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CA CYS A1279 " pdb=" C CYS A1279 " pdb=" N PRO A1280 " pdb=" CA PRO A1280 " ideal model delta harmonic sigma weight residual 180.00 132.99 47.01 0 5.00e+00 4.00e-02 8.84e+01 dihedral pdb=" CB CYS A1378 " pdb=" SG CYS A1378 " pdb=" SG CYS A1417 " pdb=" CB CYS A1417 " ideal model delta sinusoidal sigma weight residual 93.00 8.91 84.09 1 1.00e+01 1.00e-02 8.61e+01 ... (remaining 8196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1871 0.154 - 0.308: 138 0.308 - 0.462: 4 0.462 - 0.616: 1 0.616 - 0.770: 2 Chirality restraints: 2016 Sorted by residual: chirality pdb=" C1 NAG A2506 " pdb=" ND2 ASN A1665 " pdb=" C2 NAG A2506 " pdb=" O5 NAG A2506 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA CYS A 942 " pdb=" N CYS A 942 " pdb=" C CYS A 942 " pdb=" CB CYS A 942 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA CYS A 775 " pdb=" N CYS A 775 " pdb=" C CYS A 775 " pdb=" CB CYS A 775 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 2013 not shown) Planarity restraints: 2375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 638 " -0.017 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C VAL A 638 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL A 638 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 639 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 897 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ILE A 897 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE A 897 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS A 898 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 914 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C LEU A 914 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU A 914 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 915 " 0.017 2.00e-02 2.50e+03 ... (remaining 2372 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.18: 5 2.18 - 2.86: 3242 2.86 - 3.54: 18148 3.54 - 4.22: 27655 4.22 - 4.90: 45297 Nonbonded interactions: 94347 Sorted by model distance: nonbonded pdb=" NZ LYS A1640 " pdb=" CG GLU B 57 " model vdw 1.505 3.520 nonbonded pdb=" CG1 VAL B 20 " pdb=" OE2 GLU B 57 " model vdw 1.764 3.460 nonbonded pdb=" NZ LYS A1640 " pdb=" CD GLU B 57 " model vdw 2.012 3.350 nonbonded pdb=" ND2 ASN A 879 " pdb=" C1 NAG A2503 " model vdw 2.033 3.550 nonbonded pdb=" O GLU A1314 " pdb=" OD1 ASN A1315 " model vdw 2.135 3.040 ... (remaining 94342 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 9.810 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.940 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 0.013 0.054 13397 Z= 0.854 Angle : 1.778 14.356 18203 Z= 1.235 Chirality : 0.092 0.770 2016 Planarity : 0.006 0.069 2373 Dihedral : 15.414 82.228 4960 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.74 % Favored : 92.90 % Rotamer: Outliers : 0.41 % Allowed : 12.32 % Favored : 87.27 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.41 % Twisted General : 0.75 % 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: -4.93 (0.16), residues: 1676 helix: -4.93 (0.36), residues: 13 sheet: -2.74 (0.24), residues: 377 loop : -3.75 (0.13), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A1400 HIS 0.012 0.002 HIS A1677 PHE 0.026 0.003 PHE A1875 TYR 0.026 0.003 TYR A1031 ARG 0.004 0.001 ARG A1190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 857 ASN cc_start: 0.7664 (m-40) cc_final: 0.7394 (m110) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.3052 time to fit residues: 38.9342 Evaluate side-chains 53 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 ASN A 759 ASN A 948 ASN A1165 GLN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 HIS ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 ASN ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1708 ASN A1946 HIS ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13397 Z= 0.237 Angle : 0.765 9.835 18203 Z= 0.408 Chirality : 0.049 0.331 2016 Planarity : 0.005 0.068 2373 Dihedral : 8.565 52.186 1983 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.90 % Favored : 89.98 % Rotamer: Outliers : 0.14 % Allowed : 6.74 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -4.48 (0.17), residues: 1676 helix: -4.29 (0.59), residues: 19 sheet: -2.41 (0.24), residues: 419 loop : -3.44 (0.14), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1400 HIS 0.011 0.001 HIS A1764 PHE 0.032 0.002 PHE A1794 TYR 0.018 0.002 TYR A1360 ARG 0.005 0.000 ARG A 790 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.2655 time to fit residues: 31.9376 Evaluate side-chains 45 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 chunk 121 optimal weight: 0.0020 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 688 GLN A 801 ASN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1747 ASN A2028 HIS ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13397 Z= 0.195 Angle : 0.707 9.645 18203 Z= 0.372 Chirality : 0.048 0.327 2016 Planarity : 0.005 0.089 2373 Dihedral : 7.574 45.067 1983 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.08 % Favored : 89.86 % Rotamer: Outliers : 0.14 % Allowed : 6.47 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -4.09 (0.18), residues: 1676 helix: -3.50 (0.98), residues: 21 sheet: -1.84 (0.26), residues: 395 loop : -3.28 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 762 HIS 0.005 0.001 HIS A1144 PHE 0.016 0.002 PHE A 747 TYR 0.018 0.001 TYR A1139 ARG 0.004 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 MET cc_start: 0.8763 (tpp) cc_final: 0.8296 (mtp) REVERT: A 926 THR cc_start: 0.7987 (m) cc_final: 0.7647 (m) outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.2635 time to fit residues: 30.6012 Evaluate side-chains 47 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 7.9990 chunk 114 optimal weight: 0.3980 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 102 optimal weight: 0.0270 chunk 152 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A1165 GLN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1766 ASN ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13397 Z= 0.165 Angle : 0.677 9.320 18203 Z= 0.354 Chirality : 0.047 0.337 2016 Planarity : 0.005 0.080 2373 Dihedral : 6.891 39.809 1983 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.67 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -3.98 (0.18), residues: 1676 helix: -3.35 (0.89), residues: 26 sheet: -1.87 (0.25), residues: 390 loop : -3.15 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1509 HIS 0.005 0.001 HIS A 668 PHE 0.014 0.001 PHE A 667 TYR 0.019 0.001 TYR A1139 ARG 0.009 0.000 ARG A1395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2999 time to fit residues: 33.7799 Evaluate side-chains 44 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 137 optimal weight: 0.0270 chunk 111 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 144 optimal weight: 0.0770 chunk 40 optimal weight: 10.0000 overall best weight: 4.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 ASN A 826 ASN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 GLN ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1702 ASN ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13397 Z= 0.402 Angle : 0.802 13.004 18203 Z= 0.419 Chirality : 0.050 0.329 2016 Planarity : 0.006 0.078 2373 Dihedral : 7.360 42.741 1983 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.96 % Favored : 85.98 % Rotamer: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.13 % 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: -4.05 (0.18), residues: 1676 helix: -3.86 (0.82), residues: 22 sheet: -1.82 (0.25), residues: 403 loop : -3.24 (0.15), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A1798 HIS 0.008 0.001 HIS A 668 PHE 0.027 0.003 PHE A1916 TYR 0.018 0.002 TYR B 59 ARG 0.005 0.001 ARG A1242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 840 MET cc_start: 0.8803 (tpp) cc_final: 0.8364 (mtp) REVERT: A 1576 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6016 (m-80) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.2740 time to fit residues: 25.7283 Evaluate side-chains 42 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.0770 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13397 Z= 0.248 Angle : 0.728 13.071 18203 Z= 0.379 Chirality : 0.048 0.323 2016 Planarity : 0.005 0.079 2373 Dihedral : 7.023 43.092 1983 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.40 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.18), residues: 1676 helix: -4.05 (0.71), residues: 22 sheet: -1.66 (0.26), residues: 402 loop : -3.18 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 762 HIS 0.005 0.001 HIS A1953 PHE 0.015 0.002 PHE A1753 TYR 0.019 0.001 TYR A1360 ARG 0.010 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 1624 ARG cc_start: 0.8027 (tpt-90) cc_final: 0.6438 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2715 time to fit residues: 28.8194 Evaluate side-chains 44 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 HIS ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 GLN A1522 HIS ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13397 Z= 0.284 Angle : 0.734 12.385 18203 Z= 0.383 Chirality : 0.048 0.318 2016 Planarity : 0.005 0.075 2373 Dihedral : 6.983 45.568 1983 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.96 % Favored : 86.04 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -3.86 (0.18), residues: 1676 helix: -3.93 (0.77), residues: 20 sheet: -1.56 (0.26), residues: 397 loop : -3.15 (0.15), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 762 HIS 0.004 0.001 HIS A1144 PHE 0.021 0.002 PHE A1380 TYR 0.017 0.002 TYR A1360 ARG 0.004 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 840 MET cc_start: 0.8920 (tpp) cc_final: 0.8482 (mtp) REVERT: A 1624 ARG cc_start: 0.8107 (tpt-90) cc_final: 0.7104 (tpt170) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2835 time to fit residues: 27.3044 Evaluate side-chains 43 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 HIS ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 13397 Z= 0.468 Angle : 0.874 16.302 18203 Z= 0.454 Chirality : 0.052 0.328 2016 Planarity : 0.006 0.074 2373 Dihedral : 7.781 53.760 1983 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.63 % Favored : 84.37 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.13 % 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: -4.12 (0.18), residues: 1676 helix: -4.80 (0.45), residues: 28 sheet: -1.84 (0.25), residues: 422 loop : -3.28 (0.15), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 924 HIS 0.009 0.002 HIS A1144 PHE 0.026 0.003 PHE A1916 TYR 0.027 0.002 TYR B 59 ARG 0.009 0.001 ARG A 728 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 840 MET cc_start: 0.9223 (tpp) cc_final: 0.8970 (tpp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2409 time to fit residues: 19.0436 Evaluate side-chains 34 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1898 ASN ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 13397 Z= 0.443 Angle : 0.862 15.613 18203 Z= 0.450 Chirality : 0.052 0.335 2016 Planarity : 0.006 0.074 2373 Dihedral : 7.847 55.947 1983 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 0.07 % Allowed : 1.10 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.13 % 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: -4.12 (0.18), residues: 1676 helix: -4.77 (0.69), residues: 15 sheet: -1.97 (0.25), residues: 421 loop : -3.26 (0.15), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 762 HIS 0.008 0.001 HIS A1144 PHE 0.023 0.003 PHE A1916 TYR 0.019 0.002 TYR B 27 ARG 0.005 0.001 ARG A 790 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.604 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.2300 time to fit residues: 19.4895 Evaluate side-chains 33 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 153 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1941 ASN ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13397 Z= 0.212 Angle : 0.721 12.058 18203 Z= 0.374 Chirality : 0.048 0.334 2016 Planarity : 0.005 0.074 2373 Dihedral : 6.981 50.331 1983 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -3.86 (0.18), residues: 1676 helix: -3.67 (1.10), residues: 13 sheet: -1.80 (0.25), residues: 413 loop : -3.08 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 762 HIS 0.004 0.001 HIS A1953 PHE 0.021 0.002 PHE A1380 TYR 0.014 0.001 TYR A1396 ARG 0.004 0.000 ARG A 731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 840 MET cc_start: 0.8979 (tpp) cc_final: 0.8299 (mtp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2308 time to fit residues: 23.6995 Evaluate side-chains 42 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 136 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 116 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 948 ASN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.099339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078731 restraints weight = 50535.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.079007 restraints weight = 55267.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079610 restraints weight = 47560.083| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13397 Z= 0.193 Angle : 0.690 11.058 18203 Z= 0.358 Chirality : 0.047 0.320 2016 Planarity : 0.005 0.069 2373 Dihedral : 6.649 46.295 1983 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -3.70 (0.19), residues: 1676 helix: -3.21 (1.27), residues: 13 sheet: -1.71 (0.26), residues: 391 loop : -2.95 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 762 HIS 0.005 0.001 HIS A1144 PHE 0.020 0.002 PHE A1380 TYR 0.017 0.001 TYR A1360 ARG 0.005 0.000 ARG A1475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.30 seconds wall clock time: 43 minutes 20.05 seconds (2600.05 seconds total)