Starting phenix.real_space_refine on Fri Jan 19 21:08:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6f_11672/01_2024/7a6f_11672_updated.pdb" } resolution = 3.5 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 8193 2.51 5 N 2092 2.21 5 O 2316 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A ARG 798": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A GLU 889": "OE1" <-> "OE2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A GLU 1039": "OE1" <-> "OE2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A GLU 1119": "OE1" <-> "OE2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "A GLU 1159": "OE1" <-> "OE2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A ARG 1233": "NH1" <-> "NH2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 154": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12655 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 302 Unusual residues: {'CLR': 8, 'ZQU': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 7.03, per 1000 atoms: 0.56 Number of scatterers: 12655 At special positions: 0 Unit cell: (103.32, 208.32, 100.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 F 4 9.00 O 2316 8.00 N 2092 7.00 C 8193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.65 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.09 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 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.3 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 12 sheets defined 43.4% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 45 through 61 removed outlier: 3.552A pdb=" N VAL A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.649A pdb=" N GLU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 156 removed outlier: 3.560A pdb=" N ALA A 140 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 188 through 210 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.635A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 270 through 322 removed outlier: 3.969A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 350 through 370 removed outlier: 4.631A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.822A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 484 through 491 removed outlier: 5.392A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 563 through 576 removed outlier: 4.274A pdb=" N ALA A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 708 through 740 removed outlier: 4.933A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 4.460A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 798 removed outlier: 3.895A pdb=" N ARG A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 811 through 851 removed outlier: 3.569A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 863 removed outlier: 3.883A pdb=" N ALA A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 879 Processing helix chain 'A' and resid 888 through 902 removed outlier: 3.570A pdb=" N GLY A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.790A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 910 " --> pdb=" O THR A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 966 removed outlier: 3.932A pdb=" N MET A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 923 " --> pdb=" O MET A 919 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.528A pdb=" N HIS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 939 " --> pdb=" O ALA A 935 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 943 " --> pdb=" O GLY A 939 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 953 " --> pdb=" O MET A 949 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA A 954 " --> pdb=" O TYR A 950 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 992 removed outlier: 3.979A pdb=" N PHE A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 4.116A pdb=" N VAL A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN A1081 " --> pdb=" O SER A1077 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1082 " --> pdb=" O THR A1078 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1083 " --> pdb=" O VAL A1079 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1076 through 1083' Processing helix chain 'A' and resid 1108 through 1112 Processing helix chain 'A' and resid 1127 through 1133 Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1156 through 1160 removed outlier: 3.674A pdb=" N SER A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1156 through 1160' Processing helix chain 'A' and resid 1178 through 1190 removed outlier: 3.929A pdb=" N ARG A1183 " --> pdb=" O GLY A1179 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A1184 " --> pdb=" O GLN A1180 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1219 removed outlier: 3.718A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1259 No H-bonds generated for 'chain 'A' and resid 1257 through 1259' Processing helix chain 'A' and resid 1266 through 1270 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'A' and resid 414 through 417 removed outlier: 3.828A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 608 removed outlier: 6.243A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR A 582 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N LEU A 425 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 584 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1058 through 1060 Processing sheet with id= D, first strand: chain 'A' and resid 1066 through 1068 removed outlier: 3.713A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1040 through 1042 removed outlier: 3.525A pdb=" N LEU A1056 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE A1042 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN A1054 " --> pdb=" O PHE A1042 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 18 through 24 Processing sheet with id= G, first strand: chain 'B' and resid 38 through 44 Processing sheet with id= H, first strand: chain 'B' and resid 151 through 155 Processing sheet with id= I, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'C' and resid 92 through 98 removed outlier: 5.818A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU C 45 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.632A pdb=" N LYS C 149 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 144 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.882A pdb=" N ILE C 199 " --> pdb=" O ILE C 216 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1626 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: 5.04 Time building geometry restraints manager: 5.88 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: 3945 1.34 - 1.46: 2864 1.46 - 1.58: 6030 1.58 - 1.71: 15 1.71 - 1.83: 83 Bond restraints: 12937 Sorted by residual: bond pdb=" C21 ZQU A1301 " pdb=" N02 ZQU A1301 " ideal model delta sigma weight residual 1.487 1.295 0.192 2.00e-02 2.50e+03 9.18e+01 bond pdb=" C21 ZQU A1302 " pdb=" N02 ZQU A1302 " ideal model delta sigma weight residual 1.487 1.301 0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" C07 ZQU A1301 " pdb=" C13 ZQU A1301 " ideal model delta sigma weight residual 1.398 1.557 -0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" C04 ZQU A1302 " pdb=" C09 ZQU A1302 " ideal model delta sigma weight residual 1.400 1.557 -0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C04 ZQU A1301 " pdb=" C09 ZQU A1301 " ideal model delta sigma weight residual 1.400 1.557 -0.157 2.00e-02 2.50e+03 6.13e+01 ... (remaining 12932 not shown) Histogram of bond angle deviations from ideal: 59.69 - 75.74: 6 75.74 - 91.79: 0 91.79 - 107.84: 534 107.84 - 123.89: 16638 123.89 - 139.94: 395 Bond angle restraints: 17573 Sorted by residual: angle pdb=" C03 ZQU A1301 " pdb=" C01 ZQU A1301 " pdb=" C04 ZQU A1301 " ideal model delta sigma weight residual 58.20 139.94 -81.74 3.00e+00 1.11e-01 7.42e+02 angle pdb=" C03 ZQU A1302 " pdb=" C01 ZQU A1302 " pdb=" C04 ZQU A1302 " ideal model delta sigma weight residual 58.20 138.12 -79.92 3.00e+00 1.11e-01 7.10e+02 angle pdb=" C01 ZQU A1301 " pdb=" C04 ZQU A1301 " pdb=" C07 ZQU A1301 " ideal model delta sigma weight residual 110.79 131.41 -20.62 3.00e+00 1.11e-01 4.73e+01 angle pdb=" C01 ZQU A1302 " pdb=" C04 ZQU A1302 " pdb=" C07 ZQU A1302 " ideal model delta sigma weight residual 110.79 130.42 -19.63 3.00e+00 1.11e-01 4.28e+01 angle pdb=" C01 ZQU A1301 " pdb=" C04 ZQU A1301 " pdb=" C09 ZQU A1301 " ideal model delta sigma weight residual 124.30 105.10 19.20 3.00e+00 1.11e-01 4.10e+01 ... (remaining 17568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 7699 33.37 - 66.75: 337 66.75 - 100.12: 16 100.12 - 133.50: 4 133.50 - 166.87: 2 Dihedral angle restraints: 8058 sinusoidal: 3472 harmonic: 4586 Sorted by residual: dihedral pdb=" CA ALA C 104 " pdb=" C ALA C 104 " pdb=" N TRP C 105 " pdb=" CA TRP C 105 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PHE A1123 " pdb=" C PHE A1123 " pdb=" N ASP A1124 " pdb=" CA ASP A1124 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA TYR A 853 " pdb=" C TYR A 853 " pdb=" N GLY A 854 " pdb=" CA GLY A 854 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 8055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.069: 2028 1.069 - 2.139: 0 2.139 - 3.208: 0 3.208 - 4.278: 0 4.278 - 5.347: 2 Chirality restraints: 2030 Sorted by residual: chirality pdb=" C06 ZQU A1302 " pdb=" C07 ZQU A1302 " pdb=" C08 ZQU A1302 " pdb=" N01 ZQU A1302 " both_signs ideal model delta sigma weight residual False 2.75 -2.60 5.35 2.00e-01 2.50e+01 7.15e+02 chirality pdb=" C06 ZQU A1301 " pdb=" C07 ZQU A1301 " pdb=" C08 ZQU A1301 " pdb=" N01 ZQU A1301 " both_signs ideal model delta sigma weight residual False 2.75 -2.52 5.27 2.00e-01 2.50e+01 6.93e+02 chirality pdb=" C01 ZQU A1302 " pdb=" C02 ZQU A1302 " pdb=" C03 ZQU A1302 " pdb=" C04 ZQU A1302 " both_signs ideal model delta sigma weight residual True 1.33 -2.08 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 2027 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 428 " 0.020 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ASN A 428 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN A 428 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 429 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1119 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A1120 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1120 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1120 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 222 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO A 223 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.031 5.00e-02 4.00e+02 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 14 2.25 - 2.92: 5763 2.92 - 3.58: 17871 3.58 - 4.24: 28352 4.24 - 4.90: 48350 Nonbonded interactions: 100350 Sorted by model distance: nonbonded pdb=" CD1 LEU A 425 " pdb=" CE1 PHE A 601 " model vdw 1.592 3.760 nonbonded pdb=" O SER A1020 " pdb=" CD GLN A1107 " model vdw 2.062 3.270 nonbonded pdb=" CB ALA A 58 " pdb=" OE1 GLN A 132 " model vdw 2.122 3.460 nonbonded pdb=" N ASP A 744 " pdb=" OD1 ASP A 744 " model vdw 2.163 2.520 nonbonded pdb=" O THR A 898 " pdb=" CG2 ILE A 901 " model vdw 2.172 3.460 ... (remaining 100345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 12.170 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 38.780 Find NCS groups from input model: 0.450 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 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 : 0.012 0.192 12937 Z= 0.745 Angle : 1.435 81.737 17573 Z= 0.704 Chirality : 0.180 5.347 2030 Planarity : 0.005 0.071 2162 Dihedral : 17.534 166.873 5103 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 33.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 1.50 % Allowed : 28.39 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -4.13 (0.18), residues: 1584 helix: -2.25 (0.16), residues: 705 sheet: -2.59 (0.30), residues: 264 loop : -3.22 (0.20), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 708 HIS 0.005 0.001 HIS A 166 PHE 0.030 0.002 PHE B 94 TYR 0.019 0.002 TYR A 310 ARG 0.007 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 105 MET cc_start: 0.7287 (ttt) cc_final: 0.6590 (tpp) REVERT: A 276 ARG cc_start: 0.6823 (mtp180) cc_final: 0.6617 (mtp180) REVERT: A 616 MET cc_start: 0.3092 (mtt) cc_final: 0.2580 (mtm) REVERT: A 628 MET cc_start: 0.1775 (tpp) cc_final: 0.1492 (ttt) REVERT: A 1133 TYR cc_start: 0.6890 (t80) cc_final: 0.6648 (t80) REVERT: C 154 GLU cc_start: 0.6801 (tp30) cc_final: 0.6565 (tp30) outliers start: 20 outliers final: 11 residues processed: 144 average time/residue: 0.2812 time to fit residues: 57.1709 Evaluate side-chains 114 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 117 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 0.4980 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 280 ASN A 347 GLN A 750 GLN A 809 ASN A 842 ASN A 990 GLN A1112 HIS A1180 GLN A1254 HIS A1274 GLN B 43 GLN B 212 ASN C 39 GLN C 170 HIS C 202 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12937 Z= 0.197 Angle : 0.766 17.624 17573 Z= 0.359 Chirality : 0.052 0.751 2030 Planarity : 0.004 0.054 2162 Dihedral : 11.118 158.595 2295 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 6.59 % Allowed : 25.32 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1584 helix: -0.37 (0.18), residues: 701 sheet: -1.89 (0.32), residues: 253 loop : -2.49 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 708 HIS 0.006 0.001 HIS C 205 PHE 0.016 0.001 PHE A1042 TYR 0.018 0.002 TYR B 145 ARG 0.005 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 108 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 105 MET cc_start: 0.7188 (ttt) cc_final: 0.6554 (tpp) REVERT: A 227 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7532 (tt) REVERT: A 616 MET cc_start: 0.3069 (mtt) cc_final: 0.2556 (mtm) REVERT: A 913 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: A 1133 TYR cc_start: 0.6806 (t80) cc_final: 0.6561 (t80) REVERT: C 62 ASP cc_start: 0.7504 (m-30) cc_final: 0.7170 (m-30) outliers start: 88 outliers final: 50 residues processed: 186 average time/residue: 0.2273 time to fit residues: 63.7592 Evaluate side-chains 150 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 98 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1204 SER Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 97 optimal weight: 0.0670 chunk 39 optimal weight: 0.3980 chunk 143 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 0.0050 chunk 115 optimal weight: 2.9990 overall best weight: 0.1530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN A 936 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 12937 Z= 0.163 Angle : 0.691 17.029 17573 Z= 0.319 Chirality : 0.050 0.750 2030 Planarity : 0.003 0.054 2162 Dihedral : 10.683 159.012 2281 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.39 % Allowed : 26.67 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1584 helix: 0.47 (0.19), residues: 721 sheet: -1.34 (0.32), residues: 253 loop : -2.12 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 708 HIS 0.007 0.001 HIS C 205 PHE 0.013 0.001 PHE C 172 TYR 0.020 0.001 TYR A 950 ARG 0.004 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 103 time to evaluate : 1.310 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 111 MET cc_start: 0.6539 (mmm) cc_final: 0.6007 (mmm) REVERT: A 616 MET cc_start: 0.2581 (mtt) cc_final: 0.2320 (mtm) REVERT: A 913 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5576 (pm20) REVERT: A 946 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: B 193 ARG cc_start: 0.6533 (ttm170) cc_final: 0.5405 (ttp-170) REVERT: C 62 ASP cc_start: 0.7466 (m-30) cc_final: 0.6979 (m-30) outliers start: 72 outliers final: 44 residues processed: 165 average time/residue: 0.2365 time to fit residues: 58.6356 Evaluate side-chains 135 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 89 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 946 GLN Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 96 optimal weight: 0.0870 chunk 144 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12937 Z= 0.144 Angle : 0.653 16.888 17573 Z= 0.299 Chirality : 0.049 0.755 2030 Planarity : 0.003 0.051 2162 Dihedral : 10.331 159.027 2279 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.02 % Allowed : 27.12 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.62 (0.21), residues: 1584 helix: 0.94 (0.20), residues: 722 sheet: -0.98 (0.32), residues: 253 loop : -1.80 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 708 HIS 0.006 0.001 HIS C 205 PHE 0.014 0.001 PHE A 944 TYR 0.012 0.001 TYR A 950 ARG 0.003 0.000 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 97 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 111 MET cc_start: 0.6363 (mmm) cc_final: 0.5968 (mmm) REVERT: A 197 MET cc_start: 0.8149 (tpp) cc_final: 0.7636 (tpt) REVERT: A 699 ARG cc_start: 0.6853 (ptt90) cc_final: 0.6440 (mmp-170) REVERT: A 826 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7169 (pttm) REVERT: A 913 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5250 (pm20) REVERT: A 1133 TYR cc_start: 0.6390 (t80) cc_final: 0.6170 (t80) REVERT: B 193 ARG cc_start: 0.6664 (ttm170) cc_final: 0.5435 (ttp-170) REVERT: C 44 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7238 (mtp85) REVERT: C 62 ASP cc_start: 0.7407 (m-30) cc_final: 0.7176 (m-30) REVERT: C 113 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7751 (t) outliers start: 67 outliers final: 42 residues processed: 154 average time/residue: 0.2548 time to fit residues: 57.9579 Evaluate side-chains 139 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 38 optimal weight: 30.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12937 Z= 0.254 Angle : 0.709 18.082 17573 Z= 0.328 Chirality : 0.052 0.829 2030 Planarity : 0.003 0.045 2162 Dihedral : 10.430 159.099 2277 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.07 % Allowed : 27.34 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.70 (0.21), residues: 1584 helix: 0.77 (0.19), residues: 719 sheet: -1.01 (0.31), residues: 269 loop : -1.68 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 708 HIS 0.004 0.001 HIS C 205 PHE 0.015 0.002 PHE A 200 TYR 0.016 0.001 TYR C 95 ARG 0.002 0.000 ARG A1110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 98 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. REVERT: A 913 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5346 (pm20) REVERT: A 946 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: A 1133 TYR cc_start: 0.6487 (t80) cc_final: 0.6271 (t80) REVERT: C 44 ARG cc_start: 0.7590 (mtp85) cc_final: 0.7349 (mtp85) REVERT: C 62 ASP cc_start: 0.7449 (m-30) cc_final: 0.7244 (m-30) outliers start: 81 outliers final: 65 residues processed: 171 average time/residue: 0.2302 time to fit residues: 59.3983 Evaluate side-chains 157 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 90 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 946 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 37 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12937 Z= 0.176 Angle : 0.666 17.113 17573 Z= 0.304 Chirality : 0.050 0.767 2030 Planarity : 0.003 0.043 2162 Dihedral : 10.312 159.005 2277 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.24 % Allowed : 28.46 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1584 helix: 1.03 (0.19), residues: 714 sheet: -0.77 (0.32), residues: 257 loop : -1.56 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 708 HIS 0.004 0.001 HIS C 205 PHE 0.015 0.001 PHE C 172 TYR 0.015 0.001 TYR C 151 ARG 0.002 0.000 ARG A1110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 90 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 826 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7226 (pttm) REVERT: C 44 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7303 (mtp85) outliers start: 70 outliers final: 57 residues processed: 153 average time/residue: 0.2483 time to fit residues: 56.3024 Evaluate side-chains 145 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 87 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12937 Z= 0.204 Angle : 0.677 17.526 17573 Z= 0.308 Chirality : 0.050 0.795 2030 Planarity : 0.003 0.041 2162 Dihedral : 10.302 159.076 2277 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.62 % Allowed : 28.46 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1584 helix: 0.96 (0.19), residues: 717 sheet: -0.67 (0.32), residues: 257 loop : -1.49 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 708 HIS 0.004 0.001 HIS C 205 PHE 0.013 0.001 PHE A 200 TYR 0.013 0.001 TYR C 95 ARG 0.002 0.000 ARG A1110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 92 time to evaluate : 1.391 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 44 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7335 (mtp85) outliers start: 75 outliers final: 60 residues processed: 155 average time/residue: 0.2424 time to fit residues: 56.5679 Evaluate side-chains 150 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 90 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12937 Z= 0.250 Angle : 0.698 17.627 17573 Z= 0.321 Chirality : 0.051 0.801 2030 Planarity : 0.003 0.040 2162 Dihedral : 10.369 159.034 2277 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.44 % Allowed : 28.16 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1584 helix: 0.89 (0.19), residues: 715 sheet: -0.61 (0.32), residues: 257 loop : -1.45 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 708 HIS 0.004 0.001 HIS A 383 PHE 0.016 0.001 PHE B 94 TYR 0.015 0.001 TYR C 151 ARG 0.003 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 93 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 913 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5311 (pm20) REVERT: C 44 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7354 (mtp85) outliers start: 86 outliers final: 73 residues processed: 170 average time/residue: 0.2388 time to fit residues: 60.7969 Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 93 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 150 optimal weight: 0.0470 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12937 Z= 0.190 Angle : 0.667 17.143 17573 Z= 0.304 Chirality : 0.050 0.772 2030 Planarity : 0.003 0.040 2162 Dihedral : 10.291 159.011 2277 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.47 % Allowed : 29.21 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.21 (0.21), residues: 1584 helix: 1.08 (0.19), residues: 719 sheet: -0.55 (0.32), residues: 257 loop : -1.41 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 708 HIS 0.004 0.001 HIS C 205 PHE 0.014 0.001 PHE A 512 TYR 0.011 0.001 TYR A 130 ARG 0.002 0.000 ARG A1110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 94 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 44 ARG cc_start: 0.7569 (mtp85) cc_final: 0.7337 (mtp85) outliers start: 73 outliers final: 66 residues processed: 159 average time/residue: 0.2463 time to fit residues: 58.3940 Evaluate side-chains 159 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 93 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12937 Z= 0.182 Angle : 0.665 17.247 17573 Z= 0.303 Chirality : 0.050 0.778 2030 Planarity : 0.003 0.040 2162 Dihedral : 10.261 159.024 2277 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.02 % Allowed : 29.59 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.15 (0.21), residues: 1584 helix: 1.12 (0.19), residues: 720 sheet: -0.48 (0.33), residues: 257 loop : -1.39 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 160 HIS 0.004 0.001 HIS C 205 PHE 0.016 0.001 PHE A 512 TYR 0.015 0.001 TYR C 151 ARG 0.002 0.000 ARG A1110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 91 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 44 ARG cc_start: 0.7554 (mtp85) cc_final: 0.7318 (mtp85) outliers start: 67 outliers final: 63 residues processed: 151 average time/residue: 0.2792 time to fit residues: 63.0764 Evaluate side-chains 152 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 89 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 992 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 30.0000 chunk 115 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 704 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 = 0.4550 r_free = 0.4550 target = 0.218508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.187167 restraints weight = 16719.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179686 restraints weight = 42260.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174454 restraints weight = 27122.919| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12937 Z= 0.154 Angle : 0.646 16.852 17573 Z= 0.293 Chirality : 0.049 0.755 2030 Planarity : 0.003 0.040 2162 Dihedral : 10.174 158.958 2277 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.34 % Allowed : 30.26 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.02 (0.22), residues: 1584 helix: 1.29 (0.20), residues: 720 sheet: -0.42 (0.33), residues: 257 loop : -1.33 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 160 HIS 0.004 0.000 HIS C 205 PHE 0.017 0.001 PHE A 512 TYR 0.021 0.001 TYR A 363 ARG 0.002 0.000 ARG A1110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.61 seconds wall clock time: 46 minutes 27.94 seconds (2787.94 seconds total)