Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:58:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/12_2022/6um2_20816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/12_2022/6um2_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_20816/12_2022/6um2_20816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/12_2022/6um2_20816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/12_2022/6um2_20816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um2_20816/12_2022/6um2_20816.pdb" } resolution = 4.32 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= 0.001 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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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 chiralities: 7 Time building chain proxies: 7.60, 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: 5.02 Conformation dependent library (CDL) restraints added in 2.0 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: 1.35 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: 7.04 Time building geometry restraints manager: 5.60 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: 6890 17.18 - 34.35: 976 34.35 - 51.53: 188 51.53 - 68.71: 27 68.71 - 85.88: 13 Dihedral angle restraints: 8094 sinusoidal: 3241 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 8091 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 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. 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: 2.860 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: 0.020 Extract box with map and model: 10.250 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.110 Process input model: 38.730 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 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= 0.851 Angle : 1.776 14.356 18203 Z= 1.239 Chirality : 0.092 0.770 2016 Planarity : 0.006 0.069 2373 Dihedral : 15.318 82.228 4855 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 % 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 *********************** 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 : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.3013 time to fit residues: 38.9285 Evaluate side-chains 52 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1131 time to fit residues: 2.6578 ------------------------------------------------------------------------------- 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 ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 13397 Z= 0.234 Angle : 0.769 9.617 18203 Z= 0.410 Chirality : 0.049 0.368 2016 Planarity : 0.005 0.070 2373 Dihedral : 7.900 42.908 1878 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.02 % Favored : 89.86 % Rotamer Outliers : 0.07 % 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: -4.50 (0.17), residues: 1676 helix: -4.44 (0.62), residues: 21 sheet: -2.38 (0.24), residues: 425 loop : -3.46 (0.14), residues: 1230 *********************** 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 76 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.2676 time to fit residues: 30.9006 Evaluate side-chains 47 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7956 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** 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 A1946 HIS A2028 HIS ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2386 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= 0.212 Angle : 0.715 9.930 18203 Z= 0.377 Chirality : 0.048 0.342 2016 Planarity : 0.005 0.076 2373 Dihedral : 7.167 39.307 1878 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.08 % Favored : 89.86 % Rotamer Outliers : 0.14 % 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: -4.13 (0.18), residues: 1676 helix: -3.44 (0.94), residues: 19 sheet: -1.88 (0.25), residues: 395 loop : -3.31 (0.15), residues: 1262 *********************** 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 73 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.2436 time to fit residues: 28.2574 Evaluate side-chains 44 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1036 time to fit residues: 2.2336 ------------------------------------------------------------------------------- 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: 9.9990 chunk 114 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 161 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 144 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 HIS A1165 GLN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 GLN ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1708 ASN ** 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: 0.6611 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 13397 Z= 0.167 Angle : 0.678 9.224 18203 Z= 0.356 Chirality : 0.047 0.375 2016 Planarity : 0.005 0.092 2373 Dihedral : 6.699 39.723 1878 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.31 % Favored : 90.63 % Rotamer Outliers : 0.07 % 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: -3.97 (0.18), residues: 1676 helix: -3.38 (0.92), residues: 20 sheet: -1.78 (0.26), residues: 380 loop : -3.18 (0.15), residues: 1276 *********************** 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 80 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.2737 time to fit residues: 32.8429 Evaluate side-chains 49 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1192 time to fit residues: 2.3197 ------------------------------------------------------------------------------- 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: 7.9990 chunk 91 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A1702 ASN ** A1708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1766 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: 0.6860 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 13397 Z= 0.427 Angle : 0.843 14.051 18203 Z= 0.441 Chirality : 0.051 0.371 2016 Planarity : 0.006 0.088 2373 Dihedral : 7.467 41.462 1878 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.44 % Favored : 85.44 % Rotamer Outliers : 0.14 % 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: -4.08 (0.18), residues: 1676 helix: -4.43 (0.62), residues: 22 sheet: -1.80 (0.26), residues: 392 loop : -3.26 (0.15), residues: 1262 *********************** 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 64 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.474 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.2844 time to fit residues: 27.2815 Evaluate side-chains 41 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1136 time to fit residues: 2.3130 ------------------------------------------------------------------------------- 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: 3.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 13397 Z= 0.373 Angle : 0.798 15.107 18203 Z= 0.418 Chirality : 0.050 0.355 2016 Planarity : 0.006 0.075 2373 Dihedral : 7.363 38.926 1878 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.31 % Favored : 86.63 % Rotamer Outliers : 0.00 % 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: -4.12 (0.18), residues: 1676 helix: -4.61 (0.49), residues: 26 sheet: -1.88 (0.25), residues: 412 loop : -3.27 (0.15), residues: 1238 *********************** 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 55 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.627 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2647 time to fit residues: 23.2779 Evaluate side-chains 37 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1777 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 13397 Z= 0.290 Angle : 0.742 12.749 18203 Z= 0.389 Chirality : 0.049 0.343 2016 Planarity : 0.005 0.079 2373 Dihedral : 7.059 38.987 1878 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.20 % Favored : 85.80 % Rotamer Outliers : 0.00 % 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: -4.05 (0.18), residues: 1676 helix: -4.50 (0.54), residues: 22 sheet: -1.90 (0.25), residues: 412 loop : -3.20 (0.15), residues: 1242 *********************** 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 54 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.504 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2380 time to fit residues: 21.2411 Evaluate side-chains 37 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0913 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** ** A1705 GLN ** 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: 0.6787 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 13397 Z= 0.270 Angle : 0.728 13.131 18203 Z= 0.380 Chirality : 0.048 0.340 2016 Planarity : 0.005 0.071 2373 Dihedral : 6.885 38.640 1878 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer Outliers : 0.00 % 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: -3.92 (0.18), residues: 1676 helix: -4.06 (0.68), residues: 20 sheet: -1.83 (0.26), residues: 405 loop : -3.11 (0.15), residues: 1251 *********************** 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 55 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.293 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2424 time to fit residues: 21.9458 Evaluate side-chains 39 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0756 ------------------------------------------------------------------------------- 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: 10.0000 chunk 140 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** A1705 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3656 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= 0.207 Angle : 0.704 11.751 18203 Z= 0.367 Chirality : 0.048 0.331 2016 Planarity : 0.005 0.073 2373 Dihedral : 6.610 38.224 1878 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer Outliers : 0.00 % 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: -3.81 (0.19), residues: 1676 helix: -3.95 (0.79), residues: 22 sheet: -1.79 (0.26), residues: 403 loop : -3.01 (0.16), residues: 1251 *********************** 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 60 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2425 time to fit residues: 23.7538 Evaluate side-chains 41 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0072 > 50: distance: 11 - 15: 33.934 distance: 16 - 17: 12.893 distance: 17 - 18: 25.833 distance: 17 - 26: 14.185 distance: 18 - 66: 55.456 distance: 20 - 22: 39.233 distance: 23 - 25: 39.154 distance: 28 - 33: 37.751 distance: 33 - 34: 40.689 distance: 33 - 58: 58.687 distance: 35 - 36: 38.939 distance: 35 - 43: 40.325 distance: 36 - 55: 56.800 distance: 38 - 39: 30.669 distance: 38 - 40: 56.250 distance: 39 - 41: 14.507 distance: 41 - 42: 41.567 distance: 44 - 45: 40.774 distance: 44 - 47: 39.565 distance: 45 - 46: 7.728 distance: 45 - 51: 32.147 distance: 47 - 48: 40.095 distance: 48 - 50: 39.543 distance: 51 - 52: 39.285 distance: 52 - 53: 40.816 distance: 55 - 56: 39.000 distance: 56 - 57: 36.255 distance: 57 - 58: 3.956 distance: 57 - 60: 3.512 distance: 61 - 64: 56.404 distance: 64 - 65: 39.510 distance: 66 - 67: 15.732 distance: 67 - 68: 43.121 distance: 67 - 70: 60.983 distance: 71 - 72: 14.650 distance: 72 - 74: 14.433 distance: 74 - 76: 11.190 distance: 75 - 76: 9.395 distance: 76 - 77: 30.370 distance: 79 - 80: 40.636 distance: 79 - 82: 39.813 distance: 80 - 90: 12.506 distance: 83 - 84: 44.389 distance: 84 - 86: 19.516 distance: 85 - 87: 39.961 distance: 87 - 88: 40.068 distance: 90 - 91: 29.973 distance: 91 - 94: 5.800 distance: 92 - 93: 38.805 distance: 92 - 98: 34.037 distance: 94 - 95: 6.591 distance: 94 - 96: 39.933 distance: 95 - 97: 39.647