Starting phenix.real_space_refine on Thu Feb 15 21:29:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwo_23057/02_2024/7kwo_23057_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwo_23057/02_2024/7kwo_23057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwo_23057/02_2024/7kwo_23057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwo_23057/02_2024/7kwo_23057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwo_23057/02_2024/7kwo_23057_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kwo_23057/02_2024/7kwo_23057_updated.pdb" } resolution = 2.9 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 Cu 1 5.60 5 S 114 5.16 5 C 8578 2.51 5 N 2277 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13469 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 9743 Classifications: {'peptide': 1200} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1142} Chain breaks: 12 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3641 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 449} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 1, ' CU': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 310 51.941 110.768 101.763 1.00 19.36 S ATOM 7122 SG CYS A2000 56.263 97.262 88.040 1.00 6.24 S Time building chain proxies: 7.55, per 1000 atoms: 0.56 Number of scatterers: 13469 At special positions: 0 Unit cell: (96.46, 135.68, 152.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 Ca 2 19.99 S 114 16.00 O 2496 8.00 N 2277 7.00 C 8578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.03 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Simple disulfide: pdb=" SG CYS V 767 " - pdb=" SG CYS V 808 " distance=2.03 Simple disulfide: pdb=" SG CYS V 776 " - pdb=" SG CYS V 804 " distance=2.25 Simple disulfide: pdb=" SG CYS V 788 " - pdb=" SG CYS V 799 " distance=2.04 Simple disulfide: pdb=" SG CYS V 792 " - pdb=" SG CYS V 827 " distance=2.03 Simple disulfide: pdb=" SG CYS V 810 " - pdb=" SG CYS V 821 " distance=2.03 Simple disulfide: pdb=" SG CYS V 829 " - pdb=" SG CYS V 851 " distance=2.03 Simple disulfide: pdb=" SG CYS V 846 " - pdb=" SG CYS V 863 " distance=2.03 Simple disulfide: pdb=" SG CYS V 849 " - pdb=" SG CYS V 858 " distance=2.03 Simple disulfide: pdb=" SG CYS V 867 " - pdb=" SG CYS V 996 " distance=2.03 Simple disulfide: pdb=" SG CYS V 889 " - pdb=" SG CYS V1031 " distance=2.03 Simple disulfide: pdb=" SG CYS V 898 " - pdb=" SG CYS V 993 " distance=2.03 Simple disulfide: pdb=" SG CYS V 914 " - pdb=" SG CYS V 921 " distance=2.03 Simple disulfide: pdb=" SG CYS V1046 " - pdb=" SG CYS V1089 " distance=2.03 Simple disulfide: pdb=" SG CYS V1060 " - pdb=" SG CYS V1084 " distance=2.04 Simple disulfide: pdb=" SG CYS V1071 " - pdb=" SG CYS V1111 " distance=2.03 Simple disulfide: pdb=" SG CYS V1091 " - pdb=" SG CYS V1097 " distance=2.03 Simple disulfide: pdb=" SG CYS V1101 " - pdb=" SG CYS V1126 " distance=2.03 Simple disulfide: pdb=" SG CYS V1130 " - pdb=" SG CYS V1173 " distance=2.03 Simple disulfide: pdb=" SG CYS V1149 " - pdb=" SG CYS V1169 " distance=2.03 Simple disulfide: pdb=" SG CYS V1153 " - pdb=" SG CYS V1165 " distance=2.03 Simple disulfide: pdb=" SG CYS V1157 " - pdb=" SG CYS V1196 " distance=2.03 Simple disulfide: pdb=" SG CYS V1177 " - pdb=" SG CYS V1190 " distance=2.03 Simple disulfide: pdb=" SG CYS V1199 " - pdb=" SG CYS V1227 " distance=2.03 Simple disulfide: pdb=" SG CYS V1222 " - pdb=" SG CYS V1237 " distance=2.03 Simple disulfide: pdb=" SG CYS V1225 " - pdb=" SG CYS V1234 " distance=2.03 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A2601 " - " ASN A 239 " " NAG A2602 " - " ASN A1810 " " NAG B 1 " - " ASN A2118 " " NAG V1701 " - " ASN V 857 " Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2604 " pdb="ZN ZN A2604 " - pdb=" ND1 HIS A 315 " pdb="ZN ZN A2604 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2604 " - pdb=" ND1 HIS A 267 " 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 33 sheets defined 9.9% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.539A pdb=" N SER A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 699 Processing helix chain 'A' and resid 1754 through 1756 No H-bonds generated for 'chain 'A' and resid 1754 through 1756' Processing helix chain 'A' and resid 1821 through 1823 No H-bonds generated for 'chain 'A' and resid 1821 through 1823' Processing helix chain 'A' and resid 1845 through 1849 Processing helix chain 'A' and resid 1885 through 1887 No H-bonds generated for 'chain 'A' and resid 1885 through 1887' Processing helix chain 'A' and resid 1891 through 1898 Processing helix chain 'A' and resid 2003 through 2008 Processing helix chain 'A' and resid 2034 through 2036 No H-bonds generated for 'chain 'A' and resid 2034 through 2036' Processing helix chain 'A' and resid 2048 through 2050 No H-bonds generated for 'chain 'A' and resid 2048 through 2050' Processing helix chain 'A' and resid 2187 through 2189 No H-bonds generated for 'chain 'A' and resid 2187 through 2189' Processing helix chain 'A' and resid 2205 through 2207 No H-bonds generated for 'chain 'A' and resid 2205 through 2207' Processing helix chain 'V' and resid 824 through 826 No H-bonds generated for 'chain 'V' and resid 824 through 826' Processing helix chain 'V' and resid 918 through 920 No H-bonds generated for 'chain 'V' and resid 918 through 920' Processing helix chain 'V' and resid 986 through 988 No H-bonds generated for 'chain 'V' and resid 986 through 988' Processing helix chain 'V' and resid 1018 through 1025 removed outlier: 3.874A pdb=" N TRP V1025 " --> pdb=" O PHE V1021 " (cutoff:3.500A) Processing helix chain 'V' and resid 1050 through 1064 removed outlier: 4.138A pdb=" N ILE V1062 " --> pdb=" O SER V1058 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU V1063 " --> pdb=" O SER V1059 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR V1064 " --> pdb=" O CYS V1060 " (cutoff:3.500A) Processing helix chain 'V' and resid 1069 through 1071 No H-bonds generated for 'chain 'V' and resid 1069 through 1071' Processing helix chain 'V' and resid 1077 through 1090 removed outlier: 3.695A pdb=" N SER V1090 " --> pdb=" O TYR V1086 " (cutoff:3.500A) Processing helix chain 'V' and resid 1098 through 1114 removed outlier: 3.651A pdb=" N HIS V1114 " --> pdb=" O VAL V1110 " (cutoff:3.500A) Processing helix chain 'V' and resid 1136 through 1138 No H-bonds generated for 'chain 'V' and resid 1136 through 1138' Processing helix chain 'V' and resid 1193 through 1195 No H-bonds generated for 'chain 'V' and resid 1193 through 1195' Processing sheet with id= A, first strand: chain 'A' and resid 46 through 53 removed outlier: 6.790A pdb=" N THR A 83 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR A 5 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 85 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU A 7 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR A 87 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA A 9 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS A 89 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLU A 11 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= C, first strand: chain 'A' and resid 230 through 234 removed outlier: 8.866A pdb=" N PHE A 195 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR A 254 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU A 197 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS A 256 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE A 199 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 258 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL A 201 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET A 260 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASP A 203 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 286 through 288 Processing sheet with id= E, first strand: chain 'A' and resid 276 through 278 Processing sheet with id= F, first strand: chain 'A' and resid 422 through 431 removed outlier: 4.349A pdb=" N TYR A 385 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR A 460 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS A 384 " --> pdb=" O THR A 460 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 462 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE A 386 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE A 464 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA A 388 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS A 466 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N GLU A 390 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 482 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 453 through 456 Processing sheet with id= H, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.503A pdb=" N SER A 674 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 626 through 630 removed outlier: 6.478A pdb=" N LEU A 705 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 629 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYS A 707 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 658 through 660 Processing sheet with id= K, first strand: chain 'A' and resid 1730 through 1737 removed outlier: 6.667A pdb=" N ASN A1770 " --> pdb=" O ARG A1696 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR A1698 " --> pdb=" O ASN A1770 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET A1772 " --> pdb=" O TYR A1698 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A1700 " --> pdb=" O MET A1772 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N THR A1774 " --> pdb=" O ILE A1700 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA A1702 " --> pdb=" O THR A1774 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG A1776 " --> pdb=" O ALA A1702 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N GLU A1704 " --> pdb=" O ARG A1776 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1763 through 1766 Processing sheet with id= M, first strand: chain 'A' and resid 1917 through 1921 Processing sheet with id= N, first strand: chain 'A' and resid 1933 through 1935 removed outlier: 8.641A pdb=" N MET A1934 " --> pdb=" O LEU A2013 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A2015 " --> pdb=" O MET A1934 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1963 through 1966 Processing sheet with id= P, first strand: chain 'A' and resid 2037 through 2039 Processing sheet with id= Q, first strand: chain 'A' and resid 2144 through 2146 removed outlier: 6.807A pdb=" N MET A2167 " --> pdb=" O HIS A2082 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE A2084 " --> pdb=" O GLU A2165 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU A2165 " --> pdb=" O ILE A2084 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR A2086 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG A2163 " --> pdb=" O THR A2086 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 2083 through 2086 Processing sheet with id= S, first strand: chain 'A' and resid 2190 through 2192 Processing sheet with id= T, first strand: chain 'A' and resid 2301 through 2303 removed outlier: 6.683A pdb=" N LEU A2324 " --> pdb=" O THR A2241 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A2243 " --> pdb=" O GLU A2322 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU A2322 " --> pdb=" O VAL A2243 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR A2245 " --> pdb=" O ARG A2320 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG A2320 " --> pdb=" O THR A2245 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 2242 through 2245 Processing sheet with id= V, first strand: chain 'A' and resid 2248 through 2250 Processing sheet with id= W, first strand: chain 'A' and resid 2256 through 2259 removed outlier: 6.454A pdb=" N SER A2312 " --> pdb=" O LYS A2258 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'V' and resid 772 through 774 Processing sheet with id= Y, first strand: chain 'V' and resid 814 through 817 Processing sheet with id= Z, first strand: chain 'V' and resid 829 through 831 Processing sheet with id= AA, first strand: chain 'V' and resid 841 through 844 removed outlier: 3.893A pdb=" N THR V 848 " --> pdb=" O THR V 859 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'V' and resid 882 through 884 removed outlier: 4.084A pdb=" N ILE V 980 " --> pdb=" O THR V 869 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU V 970 " --> pdb=" O LEU V 966 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'V' and resid 940 through 945 removed outlier: 6.344A pdb=" N GLU V 933 " --> pdb=" O LYS V 944 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL V 909 " --> pdb=" O VAL V 892 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL V 892 " --> pdb=" O VAL V 909 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASN V 911 " --> pdb=" O GLN V 890 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN V 890 " --> pdb=" O ASN V 911 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'V' and resid 1143 through 1147 Processing sheet with id= AE, first strand: chain 'V' and resid 1181 through 1184 Processing sheet with id= AF, first strand: chain 'V' and resid 1198 through 1201 Processing sheet with id= AG, first strand: chain 'V' and resid 1211 through 1214 366 hydrogen bonds defined for protein. 942 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: 6.17 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4177 1.34 - 1.46: 2433 1.46 - 1.58: 7049 1.58 - 1.70: 1 1.70 - 1.82: 158 Bond restraints: 13818 Sorted by residual: bond pdb=" OH TYS A1680 " pdb=" S TYS A1680 " ideal model delta sigma weight residual 1.679 1.596 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" CZ TYS A1680 " pdb=" OH TYS A1680 " ideal model delta sigma weight residual 1.371 1.435 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" N ASP A1676 " pdb=" CA ASP A1676 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.77e+00 bond pdb=" CA THR A2122 " pdb=" C THR A2122 " ideal model delta sigma weight residual 1.522 1.559 -0.036 1.40e-02 5.10e+03 6.67e+00 bond pdb=" N GLU V 990 " pdb=" CA GLU V 990 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.19e+00 ... (remaining 13813 not shown) Histogram of bond angle deviations from ideal: 100.14 - 107.10: 535 107.10 - 114.05: 7809 114.05 - 121.01: 5992 121.01 - 127.96: 4254 127.96 - 134.91: 149 Bond angle restraints: 18739 Sorted by residual: angle pdb=" N LYS A1967 " pdb=" CA LYS A1967 " pdb=" C LYS A1967 " ideal model delta sigma weight residual 111.96 106.39 5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" C LEU A1978 " pdb=" N TYR A1979 " pdb=" CA TYR A1979 " ideal model delta sigma weight residual 121.59 134.91 -13.32 3.54e+00 7.98e-02 1.42e+01 angle pdb=" N THR A2122 " pdb=" CA THR A2122 " pdb=" C THR A2122 " ideal model delta sigma weight residual 112.54 116.76 -4.22 1.22e+00 6.72e-01 1.20e+01 angle pdb=" N MET V 802 " pdb=" CA MET V 802 " pdb=" C MET V 802 " ideal model delta sigma weight residual 111.36 107.64 3.72 1.09e+00 8.42e-01 1.17e+01 angle pdb=" CA PHE A1677 " pdb=" C PHE A1677 " pdb=" O PHE A1677 " ideal model delta sigma weight residual 121.40 118.03 3.37 1.13e+00 7.83e-01 8.92e+00 ... (remaining 18734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 8095 21.77 - 43.54: 206 43.54 - 65.30: 28 65.30 - 87.07: 11 87.07 - 108.84: 4 Dihedral angle restraints: 8344 sinusoidal: 3465 harmonic: 4879 Sorted by residual: dihedral pdb=" CB CYS V 829 " pdb=" SG CYS V 829 " pdb=" SG CYS V 851 " pdb=" CB CYS V 851 " ideal model delta sinusoidal sigma weight residual -86.00 -127.74 41.74 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" C THR A2122 " pdb=" N THR A2122 " pdb=" CA THR A2122 " pdb=" CB THR A2122 " ideal model delta harmonic sigma weight residual -122.00 -132.02 10.02 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.87 108.84 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1787 0.068 - 0.136: 249 0.136 - 0.204: 7 0.204 - 0.272: 2 0.272 - 0.340: 1 Chirality restraints: 2046 Sorted by residual: chirality pdb=" CA THR A2122 " pdb=" N THR A2122 " pdb=" C THR A2122 " pdb=" CB THR A2122 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA VAL V 805 " pdb=" N VAL V 805 " pdb=" C VAL V 805 " pdb=" CB VAL V 805 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2043 not shown) Planarity restraints: 2389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL V 805 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C VAL V 805 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL V 805 " -0.012 2.00e-02 2.50e+03 pdb=" N SER V 806 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU V 787 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C GLU V 787 " 0.032 2.00e-02 2.50e+03 pdb=" O GLU V 787 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS V 788 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 82 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ASP A 82 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 82 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 83 " 0.010 2.00e-02 2.50e+03 ... (remaining 2386 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 162 2.61 - 3.19: 11049 3.19 - 3.76: 20616 3.76 - 4.33: 30865 4.33 - 4.90: 50060 Nonbonded interactions: 112752 Sorted by model distance: nonbonded pdb=" ND1 HIS A2005 " pdb="CU CU A2605 " model vdw 2.043 2.320 nonbonded pdb=" OE2 GLU A 389 " pdb=" OH TYR A 431 " model vdw 2.163 2.440 nonbonded pdb=" OD1 ASP A1678 " pdb=" NH1 ARG V 820 " model vdw 2.167 2.520 nonbonded pdb=" OG1 THR V1045 " pdb=" O CYS V1089 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR A1881 " pdb=" O MET A1947 " model vdw 2.198 2.440 ... (remaining 112747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 12.390 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.230 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.003 0.083 13818 Z= 0.219 Angle : 0.580 13.325 18739 Z= 0.341 Chirality : 0.046 0.340 2046 Planarity : 0.003 0.030 2385 Dihedral : 10.686 108.841 5106 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.13 % Allowed : 4.85 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1648 helix: 0.22 (0.45), residues: 143 sheet: -0.07 (0.23), residues: 494 loop : -0.38 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A2046 HIS 0.003 0.001 HIS A2082 PHE 0.014 0.001 PHE A2014 TYR 0.017 0.001 TYR A1762 ARG 0.005 0.000 ARG V 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 1.2339 time to fit residues: 188.5528 Evaluate side-chains 77 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 966 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 151 optimal weight: 7.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 311 HIS A 478 HIS A1977 ASN A2284 GLN ** V 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13818 Z= 0.274 Angle : 0.545 8.099 18739 Z= 0.280 Chirality : 0.044 0.161 2046 Planarity : 0.004 0.029 2385 Dihedral : 7.222 72.296 1936 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.75 % Allowed : 9.56 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1648 helix: 0.01 (0.43), residues: 144 sheet: -0.09 (0.24), residues: 500 loop : -0.33 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V1120 HIS 0.009 0.001 HIS A 478 PHE 0.018 0.001 PHE V1100 TYR 0.017 0.002 TYR A1762 ARG 0.006 0.000 ARG V1035 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 97 average time/residue: 1.1201 time to fit residues: 121.9186 Evaluate side-chains 84 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain V residue 1149 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1822 HIS V 847 ASN V1069 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13818 Z= 0.266 Angle : 0.531 8.474 18739 Z= 0.273 Chirality : 0.044 0.164 2046 Planarity : 0.003 0.029 2385 Dihedral : 6.319 55.047 1934 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.22 % Allowed : 10.50 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1648 helix: 0.25 (0.45), residues: 137 sheet: -0.02 (0.24), residues: 499 loop : -0.30 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V1120 HIS 0.010 0.001 HIS A 478 PHE 0.018 0.001 PHE A 501 TYR 0.017 0.001 TYR A1762 ARG 0.002 0.000 ARG A1941 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 97 average time/residue: 1.0839 time to fit residues: 118.5606 Evaluate side-chains 82 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain V residue 928 LEU Chi-restraints excluded: chain V residue 1149 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2266 GLN V1113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 13818 Z= 0.628 Angle : 0.726 8.745 18739 Z= 0.377 Chirality : 0.049 0.207 2046 Planarity : 0.005 0.056 2385 Dihedral : 6.642 57.727 1934 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 3.57 % Allowed : 10.30 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1648 helix: -0.37 (0.44), residues: 144 sheet: -0.28 (0.24), residues: 489 loop : -0.66 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A2203 HIS 0.007 0.002 HIS A 693 PHE 0.027 0.002 PHE A2101 TYR 0.028 0.003 TYR A2105 ARG 0.004 0.001 ARG A1941 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 73 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 MET cc_start: 0.6725 (mpp) cc_final: 0.6393 (mpp) outliers start: 53 outliers final: 22 residues processed: 112 average time/residue: 1.0303 time to fit residues: 130.4693 Evaluate side-chains 89 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2293 VAL Chi-restraints excluded: chain V residue 775 VAL Chi-restraints excluded: chain V residue 800 MET Chi-restraints excluded: chain V residue 802 MET Chi-restraints excluded: chain V residue 844 ILE Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 1062 ILE Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 4.9990 chunk 91 optimal weight: 0.0370 chunk 2 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 297 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2082 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13818 Z= 0.180 Angle : 0.547 10.488 18739 Z= 0.279 Chirality : 0.044 0.162 2046 Planarity : 0.003 0.029 2385 Dihedral : 5.749 55.310 1934 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.15 % Allowed : 11.91 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1648 helix: -0.05 (0.44), residues: 143 sheet: -0.11 (0.24), residues: 487 loop : -0.37 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2203 HIS 0.008 0.001 HIS V 817 PHE 0.019 0.001 PHE A 501 TYR 0.018 0.001 TYR A1976 ARG 0.002 0.000 ARG A2220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 MET cc_start: 0.6592 (mpp) cc_final: 0.6316 (mpp) REVERT: A 2238 MET cc_start: 0.6605 (mmm) cc_final: 0.6220 (mmm) outliers start: 32 outliers final: 12 residues processed: 97 average time/residue: 1.1556 time to fit residues: 125.3463 Evaluate side-chains 81 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 2038 THR Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 1149 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.0000 chunk 161 optimal weight: 0.0270 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 overall best weight: 0.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13818 Z= 0.145 Angle : 0.530 9.524 18739 Z= 0.268 Chirality : 0.044 0.192 2046 Planarity : 0.003 0.029 2385 Dihedral : 5.347 54.557 1934 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.75 % Allowed : 12.79 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1648 helix: 0.12 (0.44), residues: 144 sheet: -0.04 (0.24), residues: 494 loop : -0.31 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V1120 HIS 0.006 0.001 HIS V 817 PHE 0.017 0.001 PHE V1100 TYR 0.011 0.001 TYR A1837 ARG 0.003 0.000 ARG A2220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 MET cc_start: 0.6528 (mpp) cc_final: 0.6262 (mpp) REVERT: A 2238 MET cc_start: 0.6458 (mmm) cc_final: 0.6082 (mmm) REVERT: V 800 MET cc_start: 0.7293 (mmm) cc_final: 0.6973 (mpm) REVERT: V 1082 ASP cc_start: 0.5181 (t70) cc_final: 0.4888 (t0) outliers start: 26 outliers final: 11 residues processed: 95 average time/residue: 1.1839 time to fit residues: 125.6431 Evaluate side-chains 85 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 2038 THR Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2252 LEU Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 1062 ILE 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: 1.9990 chunk 92 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 0.0470 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13818 Z= 0.193 Angle : 0.539 10.228 18739 Z= 0.275 Chirality : 0.044 0.170 2046 Planarity : 0.003 0.029 2385 Dihedral : 5.314 54.932 1934 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.29 % Allowed : 12.79 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1648 helix: 0.16 (0.44), residues: 144 sheet: -0.04 (0.23), residues: 499 loop : -0.35 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V1120 HIS 0.005 0.001 HIS V 817 PHE 0.023 0.001 PHE A 501 TYR 0.022 0.001 TYR A1976 ARG 0.001 0.000 ARG A1897 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 74 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 MET cc_start: 0.6526 (mpp) cc_final: 0.6253 (mpp) REVERT: A 2238 MET cc_start: 0.6468 (mmm) cc_final: 0.6096 (mmm) REVERT: A 2255 MET cc_start: 0.5672 (mmm) cc_final: 0.4909 (mmm) REVERT: V 800 MET cc_start: 0.7288 (mmm) cc_final: 0.6979 (mpm) REVERT: V 1082 ASP cc_start: 0.5232 (OUTLIER) cc_final: 0.4912 (t0) outliers start: 34 outliers final: 20 residues processed: 97 average time/residue: 1.1708 time to fit residues: 127.2434 Evaluate side-chains 94 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 2038 THR Chi-restraints excluded: chain A residue 2079 MET Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2252 LEU Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 842 VAL Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 1062 ILE Chi-restraints excluded: chain V residue 1082 ASP Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1201 VAL 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: 1.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 0.0370 chunk 126 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13818 Z= 0.305 Angle : 0.584 10.887 18739 Z= 0.298 Chirality : 0.044 0.155 2046 Planarity : 0.004 0.030 2385 Dihedral : 5.548 55.912 1934 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.22 % Allowed : 13.12 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1648 helix: 0.04 (0.44), residues: 143 sheet: -0.13 (0.23), residues: 499 loop : -0.42 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V1120 HIS 0.004 0.001 HIS V 831 PHE 0.017 0.001 PHE A2014 TYR 0.029 0.002 TYR A1976 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 72 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 800 MET cc_start: 0.7301 (mmm) cc_final: 0.6973 (mpm) REVERT: V 1073 LYS cc_start: 0.7259 (mmtt) cc_final: 0.7013 (pptt) outliers start: 33 outliers final: 20 residues processed: 96 average time/residue: 1.2027 time to fit residues: 128.6492 Evaluate side-chains 92 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 2038 THR Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2252 LEU Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 842 VAL Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 1062 ILE Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13818 Z= 0.331 Angle : 0.608 11.752 18739 Z= 0.310 Chirality : 0.045 0.185 2046 Planarity : 0.004 0.036 2385 Dihedral : 5.661 56.222 1934 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.88 % Allowed : 13.39 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1648 helix: 0.04 (0.44), residues: 144 sheet: -0.21 (0.23), residues: 501 loop : -0.48 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V1120 HIS 0.004 0.001 HIS V 817 PHE 0.025 0.002 PHE A 501 TYR 0.017 0.002 TYR A2105 ARG 0.002 0.000 ARG A2052 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2255 MET cc_start: 0.5616 (mmm) cc_final: 0.4705 (mmm) REVERT: V 800 MET cc_start: 0.7290 (mmm) cc_final: 0.6971 (mpm) REVERT: V 1073 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6973 (pptt) outliers start: 28 outliers final: 24 residues processed: 93 average time/residue: 1.1933 time to fit residues: 124.1268 Evaluate side-chains 94 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 2038 THR Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2248 VAL Chi-restraints excluded: chain A residue 2252 LEU Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 802 MET Chi-restraints excluded: chain V residue 842 VAL Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 1062 ILE Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1201 VAL Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.0470 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13818 Z= 0.226 Angle : 0.584 12.110 18739 Z= 0.295 Chirality : 0.044 0.178 2046 Planarity : 0.003 0.028 2385 Dihedral : 5.522 56.582 1934 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.62 % Allowed : 13.46 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1648 helix: 0.07 (0.44), residues: 144 sheet: -0.14 (0.24), residues: 496 loop : -0.42 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V1120 HIS 0.004 0.001 HIS V 817 PHE 0.016 0.001 PHE A 679 TYR 0.042 0.001 TYR A1976 ARG 0.002 0.000 ARG A 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2255 MET cc_start: 0.5592 (mmm) cc_final: 0.4729 (mmm) REVERT: V 800 MET cc_start: 0.7256 (mmm) cc_final: 0.6945 (mpm) REVERT: V 1073 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6949 (pptt) outliers start: 24 outliers final: 21 residues processed: 89 average time/residue: 1.1872 time to fit residues: 118.3421 Evaluate side-chains 90 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 2038 THR Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain A residue 2321 MET Chi-restraints excluded: chain V residue 842 VAL Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1201 VAL Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.113806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076634 restraints weight = 29926.834| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.69 r_work: 0.3302 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13818 Z= 0.204 Angle : 0.576 11.801 18739 Z= 0.289 Chirality : 0.044 0.175 2046 Planarity : 0.003 0.030 2385 Dihedral : 5.409 56.189 1934 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.55 % Allowed : 13.86 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1648 helix: 0.14 (0.44), residues: 143 sheet: -0.11 (0.24), residues: 497 loop : -0.39 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1817 HIS 0.004 0.001 HIS V 817 PHE 0.026 0.001 PHE A 501 TYR 0.018 0.001 TYR A 636 ARG 0.002 0.000 ARG A1897 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.42 seconds wall clock time: 76 minutes 6.13 seconds (4566.13 seconds total)