Starting phenix.real_space_refine on Thu Feb 15 09:06:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2024/6roh_4972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2024/6roh_4972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2024/6roh_4972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2024/6roh_4972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2024/6roh_4972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2024/6roh_4972_updated.pdb" } resolution = 2.8 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= 0.004 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: 8 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 48 5.16 5 Be 1 3.05 5 C 7580 2.51 5 N 1917 2.21 5 O 2207 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 183": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 606": "OD1" <-> "OD2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 704": "NH1" <-> "NH2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 784": "OD1" <-> "OD2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A ASP 815": "OD1" <-> "OD2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A ASP 889": "OD1" <-> "OD2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A TYR 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1228": "NH1" <-> "NH2" Residue "A ARG 1264": "NH1" <-> "NH2" Residue "A GLU 1282": "OE1" <-> "OE2" Residue "A GLU 1286": "OE1" <-> "OE2" Residue "A ASP 1293": "OD1" <-> "OD2" Residue "A ARG 1298": "NH1" <-> "NH2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11758 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8895 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 30, 'TRANS': 1081} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2738 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 20, 'TRANS': 316} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'PSF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.66, per 1000 atoms: 0.57 Number of scatterers: 11758 At special positions: 0 Unit cell: (74.313, 96.93, 173.397, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 2207 8.00 N 1917 7.00 C 7580 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 503 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.2 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 9 sheets defined 34.5% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 211 through 222 removed outlier: 4.431A pdb=" N LEU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.679A pdb=" N LEU A 218 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 219 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 222 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.658A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 269 removed outlier: 3.587A pdb=" N THR A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.758A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.903A pdb=" N THR A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 511 through 525 removed outlier: 3.508A pdb=" N LEU A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 618 through 630 Proline residue: A 621 - end of helix removed outlier: 4.149A pdb=" N ASP A 625 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 627 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A 628 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.510A pdb=" N VAL A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.767A pdb=" N ARG A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 removed outlier: 3.747A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.533A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 880 removed outlier: 3.759A pdb=" N GLU A 870 " --> pdb=" O ARG A 866 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 892 No H-bonds generated for 'chain 'A' and resid 890 through 892' Processing helix chain 'A' and resid 899 through 904 removed outlier: 3.546A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 918 removed outlier: 3.591A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.969A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 958 No H-bonds generated for 'chain 'A' and resid 956 through 958' Processing helix chain 'A' and resid 960 through 963 No H-bonds generated for 'chain 'A' and resid 960 through 963' Processing helix chain 'A' and resid 990 through 998 removed outlier: 3.533A pdb=" N LYS A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 995 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 996 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 997 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 998 " --> pdb=" O LYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 removed outlier: 3.667A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1023 No H-bonds generated for 'chain 'A' and resid 1020 through 1023' Processing helix chain 'A' and resid 1025 through 1031 removed outlier: 3.690A pdb=" N VAL A1030 " --> pdb=" O GLN A1026 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A1031 " --> pdb=" O PHE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1051 removed outlier: 3.969A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 3.558A pdb=" N GLY A1062 " --> pdb=" O PRO A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.640A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1070 through 1075' Processing helix chain 'A' and resid 1077 through 1084 removed outlier: 3.596A pdb=" N LYS A1081 " --> pdb=" O GLN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1114 removed outlier: 3.629A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1153 removed outlier: 3.685A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1179 Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1203 through 1208 Processing helix chain 'A' and resid 1212 through 1216 Processing helix chain 'A' and resid 1218 through 1229 Processing helix chain 'A' and resid 1254 through 1257 No H-bonds generated for 'chain 'A' and resid 1254 through 1257' Processing helix chain 'A' and resid 1260 through 1262 No H-bonds generated for 'chain 'A' and resid 1260 through 1262' Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.821A pdb=" N LYS C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 267 through 273 removed outlier: 3.749A pdb=" N VAL C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 345 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.814A pdb=" N LEU C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 355' Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 283 through 288 removed outlier: 3.612A pdb=" N SER A 288 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.570A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1266 through 1268 removed outlier: 6.540A pdb=" N ALA A 923 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE A 897 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 925 " --> pdb=" O ILE A 897 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 948 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE A 557 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 950 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N SER A 559 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 952 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 967 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY A 953 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 969 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 985 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.942A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 694 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 671 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 680 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE A 669 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 637 through 640 Processing sheet with id= G, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.532A pdb=" N PHE A 419 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 321 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 417 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.013A pdb=" N LEU C 73 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 137 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 110 through 113 removed outlier: 3.638A pdb=" N GLY C 296 " --> pdb=" O ILE C 129 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 858 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: 3.82 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3276 1.33 - 1.46: 2850 1.46 - 1.58: 5813 1.58 - 1.71: 2 1.71 - 1.83: 77 Bond restraints: 12018 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.527 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O2 PSF A2101 " pdb=" P PSF A2101 " ideal model delta sigma weight residual 1.637 1.701 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.35e-02 5.49e+03 5.59e+00 bond pdb=" CA BFD A 560 " pdb=" C BFD A 560 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.52e+00 ... (remaining 12013 not shown) Histogram of bond angle deviations from ideal: 95.99 - 103.83: 138 103.83 - 111.68: 5293 111.68 - 119.52: 4887 119.52 - 127.37: 5848 127.37 - 135.21: 117 Bond angle restraints: 16283 Sorted by residual: angle pdb=" N ILE A1174 " pdb=" CA ILE A1174 " pdb=" C ILE A1174 " ideal model delta sigma weight residual 111.90 107.86 4.04 8.10e-01 1.52e+00 2.48e+01 angle pdb=" C ASP A 784 " pdb=" N ASN A 785 " pdb=" CA ASN A 785 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C CYS C 176 " pdb=" N SER C 177 " pdb=" CA SER C 177 " ideal model delta sigma weight residual 119.78 125.42 -5.64 1.24e+00 6.50e-01 2.07e+01 angle pdb=" CA CYS C 176 " pdb=" CB CYS C 176 " pdb=" SG CYS C 176 " ideal model delta sigma weight residual 114.40 123.44 -9.04 2.30e+00 1.89e-01 1.55e+01 angle pdb=" C PRO A 240 " pdb=" N HIS A 241 " pdb=" CA HIS A 241 " ideal model delta sigma weight residual 123.47 129.36 -5.89 1.53e+00 4.27e-01 1.48e+01 ... (remaining 16278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 6782 22.53 - 45.06: 416 45.06 - 67.59: 50 67.59 - 90.12: 18 90.12 - 112.65: 7 Dihedral angle restraints: 7273 sinusoidal: 3025 harmonic: 4248 Sorted by residual: dihedral pdb=" CA LEU A1114 " pdb=" C LEU A1114 " pdb=" N ILE A1115 " pdb=" CA ILE A1115 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR C 320 " pdb=" C THR C 320 " pdb=" N THR C 321 " pdb=" CA THR C 321 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU A 490 " pdb=" C LEU A 490 " pdb=" N PHE A 491 " pdb=" CA PHE A 491 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1427 0.059 - 0.118: 351 0.118 - 0.177: 63 0.177 - 0.236: 13 0.236 - 0.295: 1 Chirality restraints: 1855 Sorted by residual: chirality pdb=" C5 BMA D 4 " pdb=" C4 BMA D 4 " pdb=" C6 BMA D 4 " pdb=" O5 BMA D 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU A 480 " pdb=" CB LEU A 480 " pdb=" CD1 LEU A 480 " pdb=" CD2 LEU A 480 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1852 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 111 " 0.026 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" CG TRP C 111 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP C 111 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 111 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 111 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 111 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 111 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 111 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 111 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A1058 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 977 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C MET A 977 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A 977 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 978 " 0.016 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 20 2.35 - 2.99: 5561 2.99 - 3.62: 16880 3.62 - 4.26: 28513 4.26 - 4.90: 46273 Nonbonded interactions: 97247 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A2102 " model vdw 1.709 2.120 nonbonded pdb="MG MG A2102 " pdb=" O HOH A2201 " model vdw 1.742 2.170 nonbonded pdb="MG MG A2102 " pdb=" O HOH A2202 " model vdw 1.906 2.170 nonbonded pdb=" O THR A 562 " pdb=" O HOH A2201 " model vdw 1.909 2.440 nonbonded pdb=" O THR A 562 " pdb="MG MG A2102 " model vdw 2.042 2.170 ... (remaining 97242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 4.140 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 34.280 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.006 0.210 12018 Z= 0.399 Angle : 0.893 10.208 16283 Z= 0.502 Chirality : 0.055 0.295 1855 Planarity : 0.006 0.073 2039 Dihedral : 14.973 112.654 4527 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.17), residues: 1440 helix: -4.68 (0.08), residues: 565 sheet: -1.21 (0.33), residues: 234 loop : -2.22 (0.20), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP C 111 HIS 0.010 0.001 HIS A 634 PHE 0.028 0.002 PHE A1094 TYR 0.018 0.002 TYR C 141 ARG 0.006 0.001 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 SER cc_start: 0.7218 (p) cc_final: 0.6902 (p) REVERT: A 263 MET cc_start: 0.6907 (mtt) cc_final: 0.6519 (mmp) REVERT: A 291 HIS cc_start: 0.6491 (t70) cc_final: 0.6291 (t70) REVERT: A 335 GLU cc_start: 0.7569 (tt0) cc_final: 0.7328 (tt0) REVERT: A 356 LYS cc_start: 0.7472 (mmtm) cc_final: 0.7268 (mtpt) REVERT: A 400 MET cc_start: 0.7561 (ttt) cc_final: 0.7156 (tpt) REVERT: A 469 MET cc_start: 0.8151 (ttm) cc_final: 0.7885 (mtp) REVERT: A 520 TYR cc_start: 0.6702 (t80) cc_final: 0.6416 (t80) REVERT: A 535 LYS cc_start: 0.8221 (tttm) cc_final: 0.7594 (ttmm) REVERT: A 540 THR cc_start: 0.8626 (t) cc_final: 0.8351 (m) REVERT: A 571 GLU cc_start: 0.7089 (tt0) cc_final: 0.6641 (mt-10) REVERT: A 604 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7562 (mtpp) REVERT: A 724 ASP cc_start: 0.8116 (p0) cc_final: 0.7845 (p0) REVERT: A 838 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.7162 (mtt90) REVERT: A 856 MET cc_start: 0.8409 (ttt) cc_final: 0.8168 (ttm) REVERT: A 871 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7532 (mtp180) REVERT: A 881 ASN cc_start: 0.7158 (t0) cc_final: 0.6082 (p0) REVERT: A 1156 GLN cc_start: 0.8369 (tt0) cc_final: 0.7814 (tt0) REVERT: A 1269 MET cc_start: 0.7130 (mmm) cc_final: 0.6799 (mmp) REVERT: A 1285 GLN cc_start: 0.7973 (pm20) cc_final: 0.7503 (pm20) REVERT: A 1296 GLN cc_start: 0.7576 (tt0) cc_final: 0.7130 (tt0) REVERT: C 114 THR cc_start: 0.8177 (m) cc_final: 0.7802 (m) REVERT: C 124 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7616 (mt-10) REVERT: C 135 LYS cc_start: 0.8146 (mttt) cc_final: 0.7495 (ttpp) REVERT: C 197 MET cc_start: 0.8891 (ttt) cc_final: 0.8654 (ttt) REVERT: C 229 HIS cc_start: 0.7194 (m90) cc_final: 0.6638 (m-70) REVERT: C 250 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8164 (tttt) REVERT: C 295 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7598 (tptt) outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 1.2227 time to fit residues: 298.0935 Evaluate side-chains 131 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 877 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 466 ASN A 580 HIS A 649 GLN A 694 ASN A 839 GLN A 862 ASN A 891 ASN A1019 ASN A1038 GLN A1050 ASN C 30 GLN C 37 GLN C 121 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12018 Z= 0.266 Angle : 0.617 10.163 16283 Z= 0.320 Chirality : 0.045 0.185 1855 Planarity : 0.005 0.048 2039 Dihedral : 9.401 79.943 1741 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.42 % Allowed : 12.51 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.19), residues: 1440 helix: -3.24 (0.15), residues: 572 sheet: -0.81 (0.33), residues: 232 loop : -1.66 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 111 HIS 0.009 0.001 HIS A 634 PHE 0.017 0.002 PHE C 311 TYR 0.016 0.001 TYR C 188 ARG 0.005 0.000 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.5722 (p90) REVERT: A 263 MET cc_start: 0.6904 (mtt) cc_final: 0.6531 (mmp) REVERT: A 335 GLU cc_start: 0.7450 (tt0) cc_final: 0.7194 (tt0) REVERT: A 342 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7161 (mt-10) REVERT: A 356 LYS cc_start: 0.7534 (mmtm) cc_final: 0.7117 (mtmm) REVERT: A 385 THR cc_start: 0.8020 (m) cc_final: 0.7702 (t) REVERT: A 401 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7424 (mt) REVERT: A 469 MET cc_start: 0.8163 (ttm) cc_final: 0.7945 (ttt) REVERT: A 490 LEU cc_start: 0.5980 (pp) cc_final: 0.5704 (mp) REVERT: A 535 LYS cc_start: 0.8192 (tttm) cc_final: 0.7566 (ttmm) REVERT: A 555 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 571 GLU cc_start: 0.6939 (tt0) cc_final: 0.6433 (mt-10) REVERT: A 610 LYS cc_start: 0.8250 (mttp) cc_final: 0.7700 (tmmt) REVERT: A 838 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.6716 (mmt-90) REVERT: A 1296 GLN cc_start: 0.7651 (tt0) cc_final: 0.7183 (tt0) REVERT: C 37 GLN cc_start: 0.8290 (mt0) cc_final: 0.7818 (mt0) REVERT: C 135 LYS cc_start: 0.8193 (mttt) cc_final: 0.7615 (ttpp) REVERT: C 152 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8034 (ttt180) REVERT: C 197 MET cc_start: 0.9023 (ttt) cc_final: 0.8780 (ttt) REVERT: C 229 HIS cc_start: 0.7236 (m90) cc_final: 0.6717 (m-70) REVERT: C 295 LYS cc_start: 0.8300 (ttpt) cc_final: 0.7698 (tptt) outliers start: 31 outliers final: 12 residues processed: 158 average time/residue: 1.1409 time to fit residues: 197.4484 Evaluate side-chains 135 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS A1254 GLN A1258 ASN C 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12018 Z= 0.250 Angle : 0.571 8.458 16283 Z= 0.295 Chirality : 0.044 0.180 1855 Planarity : 0.004 0.038 2039 Dihedral : 7.765 65.318 1739 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.28 % Allowed : 15.25 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.20), residues: 1440 helix: -2.29 (0.19), residues: 576 sheet: -0.62 (0.34), residues: 232 loop : -1.28 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 111 HIS 0.008 0.001 HIS A1131 PHE 0.016 0.001 PHE A1094 TYR 0.015 0.001 TYR C 141 ARG 0.004 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.5633 (p90) REVERT: A 216 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7748 (tttt) REVERT: A 263 MET cc_start: 0.6889 (mtt) cc_final: 0.6376 (mmp) REVERT: A 342 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7240 (mt-10) REVERT: A 351 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7220 (mmm160) REVERT: A 385 THR cc_start: 0.8045 (m) cc_final: 0.7697 (t) REVERT: A 391 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6824 (mtp85) REVERT: A 401 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7756 (mt) REVERT: A 469 MET cc_start: 0.8127 (ttm) cc_final: 0.7895 (ttt) REVERT: A 535 LYS cc_start: 0.8239 (tttm) cc_final: 0.7625 (ttmm) REVERT: A 549 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7486 (pp20) REVERT: A 555 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 571 GLU cc_start: 0.6915 (tt0) cc_final: 0.6610 (mt-10) REVERT: A 668 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7399 (ttmm) REVERT: A 689 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: A 697 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: A 812 LYS cc_start: 0.8375 (mmmm) cc_final: 0.7866 (mptp) REVERT: A 838 ARG cc_start: 0.7335 (mtm-85) cc_final: 0.6766 (mmt-90) REVERT: A 944 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7995 (mptt) REVERT: A 1296 GLN cc_start: 0.7696 (tt0) cc_final: 0.7222 (tt0) REVERT: C 37 GLN cc_start: 0.8224 (mt0) cc_final: 0.7820 (mt0) REVERT: C 47 PRO cc_start: 0.6667 (Cg_exo) cc_final: 0.6412 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8222 (mttt) cc_final: 0.7616 (ttpp) REVERT: C 152 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8375 (ttt180) REVERT: C 197 MET cc_start: 0.9063 (ttt) cc_final: 0.8819 (ttt) REVERT: C 229 HIS cc_start: 0.7236 (m90) cc_final: 0.6724 (m-70) REVERT: C 295 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7685 (tptt) outliers start: 42 outliers final: 18 residues processed: 165 average time/residue: 1.2137 time to fit residues: 218.2572 Evaluate side-chains 153 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1093 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 374 GLN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12018 Z= 0.257 Angle : 0.579 10.906 16283 Z= 0.294 Chirality : 0.045 0.261 1855 Planarity : 0.003 0.036 2039 Dihedral : 7.119 67.404 1739 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.52 % Allowed : 15.95 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.21), residues: 1440 helix: -1.88 (0.20), residues: 582 sheet: -0.48 (0.34), residues: 232 loop : -1.13 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 111 HIS 0.007 0.001 HIS A 634 PHE 0.019 0.002 PHE A 491 TYR 0.015 0.001 TYR C 141 ARG 0.003 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.5578 (p90) REVERT: A 216 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7733 (tttt) REVERT: A 263 MET cc_start: 0.6811 (mtt) cc_final: 0.6334 (mmp) REVERT: A 342 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 351 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7217 (mmm160) REVERT: A 385 THR cc_start: 0.8050 (m) cc_final: 0.7716 (t) REVERT: A 391 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6593 (mtp85) REVERT: A 401 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7911 (mt) REVERT: A 469 MET cc_start: 0.8162 (ttm) cc_final: 0.7905 (ttt) REVERT: A 535 LYS cc_start: 0.8182 (tttm) cc_final: 0.7625 (ttmm) REVERT: A 549 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7616 (pp20) REVERT: A 555 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7446 (mt-10) REVERT: A 571 GLU cc_start: 0.6920 (tt0) cc_final: 0.6610 (mt-10) REVERT: A 577 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6729 (tp) REVERT: A 610 LYS cc_start: 0.7965 (mttm) cc_final: 0.7549 (mmtp) REVERT: A 668 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7408 (ttmm) REVERT: A 689 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: A 697 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7016 (mm-30) REVERT: A 748 ASP cc_start: 0.7435 (m-30) cc_final: 0.7118 (t0) REVERT: A 812 LYS cc_start: 0.8374 (mmmm) cc_final: 0.7867 (mptp) REVERT: A 838 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.6730 (mmt-90) REVERT: A 1296 GLN cc_start: 0.7706 (tt0) cc_final: 0.7258 (tt0) REVERT: C 37 GLN cc_start: 0.8285 (mt0) cc_final: 0.7860 (mt0) REVERT: C 47 PRO cc_start: 0.6629 (Cg_exo) cc_final: 0.6358 (Cg_endo) REVERT: C 113 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8303 (tt) REVERT: C 114 THR cc_start: 0.7853 (m) cc_final: 0.7627 (m) REVERT: C 135 LYS cc_start: 0.8173 (mttt) cc_final: 0.7562 (ttpp) REVERT: C 152 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8362 (ttt180) REVERT: C 197 MET cc_start: 0.9076 (ttt) cc_final: 0.8832 (ttt) REVERT: C 229 HIS cc_start: 0.7223 (m90) cc_final: 0.6746 (m-70) REVERT: C 295 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7701 (tptt) outliers start: 45 outliers final: 24 residues processed: 162 average time/residue: 1.1515 time to fit residues: 204.8493 Evaluate side-chains 152 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 0.0870 chunk 96 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12018 Z= 0.151 Angle : 0.521 13.968 16283 Z= 0.262 Chirality : 0.043 0.251 1855 Planarity : 0.003 0.039 2039 Dihedral : 6.734 75.082 1739 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.89 % Allowed : 16.97 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1440 helix: -1.47 (0.21), residues: 579 sheet: -0.37 (0.34), residues: 232 loop : -1.00 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.004 0.001 HIS A 634 PHE 0.015 0.001 PHE A1094 TYR 0.014 0.001 TYR C 141 ARG 0.002 0.000 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.5400 (p90) REVERT: A 216 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7689 (tttt) REVERT: A 263 MET cc_start: 0.6841 (mtt) cc_final: 0.6480 (mtp) REVERT: A 342 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: A 385 THR cc_start: 0.7973 (m) cc_final: 0.7639 (t) REVERT: A 391 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6558 (mtp85) REVERT: A 401 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7902 (mt) REVERT: A 469 MET cc_start: 0.8146 (ttm) cc_final: 0.7885 (ttt) REVERT: A 535 LYS cc_start: 0.8177 (tttm) cc_final: 0.7598 (ttmm) REVERT: A 540 THR cc_start: 0.8613 (t) cc_final: 0.8253 (m) REVERT: A 549 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7615 (pp20) REVERT: A 555 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 571 GLU cc_start: 0.6915 (tt0) cc_final: 0.6607 (mt-10) REVERT: A 577 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6744 (tp) REVERT: A 668 LYS cc_start: 0.7604 (ttmt) cc_final: 0.7389 (ttmm) REVERT: A 689 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: A 697 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: A 748 ASP cc_start: 0.7392 (m-30) cc_final: 0.7097 (t0) REVERT: A 812 LYS cc_start: 0.8342 (mmmm) cc_final: 0.7829 (mptp) REVERT: A 838 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.6730 (mmp80) REVERT: A 944 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7999 (mptt) REVERT: A 1296 GLN cc_start: 0.7718 (tt0) cc_final: 0.7276 (tt0) REVERT: C 47 PRO cc_start: 0.6565 (Cg_exo) cc_final: 0.6297 (Cg_endo) REVERT: C 51 PHE cc_start: 0.7106 (t80) cc_final: 0.6780 (t80) REVERT: C 114 THR cc_start: 0.7852 (m) cc_final: 0.7598 (m) REVERT: C 135 LYS cc_start: 0.8196 (mttt) cc_final: 0.7507 (ttpp) REVERT: C 197 MET cc_start: 0.9051 (ttt) cc_final: 0.8809 (ttt) REVERT: C 229 HIS cc_start: 0.7190 (m90) cc_final: 0.6694 (m-70) REVERT: C 295 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7683 (tptt) outliers start: 37 outliers final: 16 residues processed: 155 average time/residue: 1.1789 time to fit residues: 200.3880 Evaluate side-chains 154 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 320 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.0570 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 773 ASN A 800 ASN C 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12018 Z= 0.307 Angle : 0.591 10.624 16283 Z= 0.300 Chirality : 0.046 0.298 1855 Planarity : 0.004 0.034 2039 Dihedral : 6.811 75.860 1739 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.60 % Allowed : 16.97 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1440 helix: -1.48 (0.21), residues: 582 sheet: -0.33 (0.34), residues: 232 loop : -1.01 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 111 HIS 0.009 0.001 HIS A1131 PHE 0.021 0.002 PHE A 491 TYR 0.016 0.002 TYR C 141 ARG 0.003 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.5319 (p90) REVERT: A 216 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7609 (tttt) REVERT: A 263 MET cc_start: 0.6814 (mtt) cc_final: 0.6458 (mtp) REVERT: A 342 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 351 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7218 (mmm160) REVERT: A 385 THR cc_start: 0.8019 (m) cc_final: 0.7676 (t) REVERT: A 391 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6836 (mtp85) REVERT: A 401 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8007 (mt) REVERT: A 469 MET cc_start: 0.8153 (ttm) cc_final: 0.7895 (ttt) REVERT: A 535 LYS cc_start: 0.8257 (tttm) cc_final: 0.7560 (ttmm) REVERT: A 571 GLU cc_start: 0.6928 (tt0) cc_final: 0.6605 (mt-10) REVERT: A 577 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6737 (tp) REVERT: A 610 LYS cc_start: 0.7899 (mttp) cc_final: 0.7509 (mmtp) REVERT: A 689 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: A 697 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: A 748 ASP cc_start: 0.7372 (m-30) cc_final: 0.7078 (t0) REVERT: A 812 LYS cc_start: 0.8407 (mmmm) cc_final: 0.7909 (mptp) REVERT: A 838 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6719 (mmt-90) REVERT: A 944 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7998 (mptt) REVERT: A 1190 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7658 (mtm180) REVERT: A 1296 GLN cc_start: 0.7750 (tt0) cc_final: 0.7305 (tt0) REVERT: C 47 PRO cc_start: 0.6446 (Cg_exo) cc_final: 0.6191 (Cg_endo) REVERT: C 114 THR cc_start: 0.7862 (m) cc_final: 0.7566 (m) REVERT: C 135 LYS cc_start: 0.8227 (mttt) cc_final: 0.7529 (ttpp) REVERT: C 174 THR cc_start: 0.8552 (t) cc_final: 0.8323 (t) REVERT: C 197 MET cc_start: 0.9087 (ttt) cc_final: 0.8846 (ttt) REVERT: C 229 HIS cc_start: 0.7179 (m90) cc_final: 0.6675 (m-70) REVERT: C 295 LYS cc_start: 0.8305 (ttpt) cc_final: 0.7677 (tptt) outliers start: 46 outliers final: 29 residues processed: 165 average time/residue: 1.1129 time to fit residues: 201.1090 Evaluate side-chains 160 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1093 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 317 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 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 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12018 Z= 0.195 Angle : 0.539 14.237 16283 Z= 0.271 Chirality : 0.044 0.300 1855 Planarity : 0.003 0.038 2039 Dihedral : 6.628 81.116 1739 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.44 % Allowed : 17.67 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.22), residues: 1440 helix: -1.23 (0.21), residues: 582 sheet: -0.29 (0.34), residues: 232 loop : -0.91 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 PHE 0.016 0.001 PHE A1094 TYR 0.014 0.001 TYR C 141 ARG 0.002 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.5225 (p90) REVERT: A 216 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7567 (tttt) REVERT: A 263 MET cc_start: 0.6737 (mtt) cc_final: 0.6407 (mtp) REVERT: A 342 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 351 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7363 (mmm160) REVERT: A 385 THR cc_start: 0.8019 (m) cc_final: 0.7676 (t) REVERT: A 391 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6807 (mtp85) REVERT: A 401 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8049 (mt) REVERT: A 469 MET cc_start: 0.8135 (ttm) cc_final: 0.7878 (ttt) REVERT: A 535 LYS cc_start: 0.8144 (tttm) cc_final: 0.7531 (ttmm) REVERT: A 540 THR cc_start: 0.8671 (t) cc_final: 0.8258 (m) REVERT: A 571 GLU cc_start: 0.6915 (tt0) cc_final: 0.6602 (mt-10) REVERT: A 577 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6696 (tp) REVERT: A 610 LYS cc_start: 0.7910 (mttp) cc_final: 0.7486 (mmtp) REVERT: A 689 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: A 697 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: A 748 ASP cc_start: 0.7362 (m-30) cc_final: 0.7079 (t0) REVERT: A 761 MET cc_start: 0.7447 (ptt) cc_final: 0.7033 (ptm) REVERT: A 812 LYS cc_start: 0.8364 (mmmm) cc_final: 0.7867 (mptp) REVERT: A 838 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.6700 (mmt-90) REVERT: A 944 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7998 (mptt) REVERT: A 1296 GLN cc_start: 0.7719 (tt0) cc_final: 0.7263 (tt0) REVERT: A 1304 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6198 (tt) REVERT: C 47 PRO cc_start: 0.6478 (Cg_exo) cc_final: 0.6220 (Cg_endo) REVERT: C 114 THR cc_start: 0.7851 (m) cc_final: 0.7562 (m) REVERT: C 135 LYS cc_start: 0.8217 (mttt) cc_final: 0.7521 (ttpp) REVERT: C 174 THR cc_start: 0.8410 (t) cc_final: 0.8186 (t) REVERT: C 197 MET cc_start: 0.9063 (ttt) cc_final: 0.8831 (ttt) REVERT: C 229 HIS cc_start: 0.7160 (m90) cc_final: 0.6707 (m-70) REVERT: C 295 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7673 (tptt) outliers start: 44 outliers final: 26 residues processed: 162 average time/residue: 1.0863 time to fit residues: 194.2697 Evaluate side-chains 162 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 317 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 773 ASN C 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12018 Z= 0.356 Angle : 0.623 10.895 16283 Z= 0.317 Chirality : 0.047 0.320 1855 Planarity : 0.004 0.033 2039 Dihedral : 6.829 79.195 1739 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.67 % Allowed : 17.83 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1440 helix: -1.45 (0.20), residues: 589 sheet: 0.01 (0.36), residues: 210 loop : -1.00 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 111 HIS 0.010 0.001 HIS A 634 PHE 0.021 0.002 PHE A 491 TYR 0.017 0.002 TYR C 141 ARG 0.003 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.5317 (p90) REVERT: A 216 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7622 (tttt) REVERT: A 263 MET cc_start: 0.6807 (mtt) cc_final: 0.6484 (mtp) REVERT: A 342 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 351 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7206 (mmm160) REVERT: A 385 THR cc_start: 0.8060 (m) cc_final: 0.7698 (t) REVERT: A 391 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6753 (mtp85) REVERT: A 401 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8099 (mt) REVERT: A 469 MET cc_start: 0.8140 (ttm) cc_final: 0.7883 (ttt) REVERT: A 535 LYS cc_start: 0.8167 (tttm) cc_final: 0.7497 (ttmm) REVERT: A 571 GLU cc_start: 0.6906 (tt0) cc_final: 0.6599 (mt-10) REVERT: A 577 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6785 (tp) REVERT: A 610 LYS cc_start: 0.7911 (mttp) cc_final: 0.7504 (mmtp) REVERT: A 689 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: A 697 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7007 (mm-30) REVERT: A 748 ASP cc_start: 0.7342 (m-30) cc_final: 0.7047 (t0) REVERT: A 761 MET cc_start: 0.7476 (ptt) cc_final: 0.7042 (ptm) REVERT: A 812 LYS cc_start: 0.8398 (mmmm) cc_final: 0.7904 (mptp) REVERT: A 838 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.6797 (mmt-90) REVERT: A 1193 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: A 1287 LYS cc_start: 0.7143 (pttt) cc_final: 0.6813 (pttp) REVERT: A 1296 GLN cc_start: 0.7738 (tt0) cc_final: 0.7279 (tt0) REVERT: A 1304 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6216 (tt) REVERT: C 47 PRO cc_start: 0.6473 (Cg_exo) cc_final: 0.6224 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8186 (mttt) cc_final: 0.7515 (ttpp) REVERT: C 174 THR cc_start: 0.8551 (t) cc_final: 0.8325 (t) REVERT: C 197 MET cc_start: 0.9093 (ttt) cc_final: 0.8856 (ttt) REVERT: C 229 HIS cc_start: 0.7209 (m90) cc_final: 0.6750 (m-70) REVERT: C 295 LYS cc_start: 0.8308 (ttpt) cc_final: 0.7679 (tptt) outliers start: 47 outliers final: 27 residues processed: 162 average time/residue: 1.1660 time to fit residues: 206.6556 Evaluate side-chains 160 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 317 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12018 Z= 0.194 Angle : 0.552 15.303 16283 Z= 0.276 Chirality : 0.044 0.282 1855 Planarity : 0.003 0.037 2039 Dihedral : 6.619 85.435 1739 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.74 % Allowed : 18.84 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1440 helix: -1.16 (0.21), residues: 588 sheet: -0.06 (0.35), residues: 220 loop : -0.87 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 PHE 0.016 0.001 PHE A1094 TYR 0.013 0.001 TYR C 141 ARG 0.001 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.5207 (p90) REVERT: A 216 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7563 (tttt) REVERT: A 263 MET cc_start: 0.6782 (mtt) cc_final: 0.6447 (mtp) REVERT: A 342 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 385 THR cc_start: 0.8018 (m) cc_final: 0.7683 (t) REVERT: A 391 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6727 (mtp85) REVERT: A 453 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7320 (p) REVERT: A 469 MET cc_start: 0.8132 (ttm) cc_final: 0.7874 (ttt) REVERT: A 535 LYS cc_start: 0.8097 (tttm) cc_final: 0.7483 (ttmm) REVERT: A 571 GLU cc_start: 0.6831 (tt0) cc_final: 0.6545 (mt-10) REVERT: A 577 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6717 (tp) REVERT: A 610 LYS cc_start: 0.7921 (mttp) cc_final: 0.7499 (mmtp) REVERT: A 689 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: A 697 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 748 ASP cc_start: 0.7333 (m-30) cc_final: 0.7038 (t0) REVERT: A 761 MET cc_start: 0.7483 (ptt) cc_final: 0.7066 (ptm) REVERT: A 812 LYS cc_start: 0.8367 (mmmm) cc_final: 0.7866 (mptp) REVERT: A 838 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.6705 (mmt-90) REVERT: A 889 ASP cc_start: 0.6808 (t0) cc_final: 0.6455 (t0) REVERT: A 1296 GLN cc_start: 0.7675 (tt0) cc_final: 0.7226 (tt0) REVERT: C 47 PRO cc_start: 0.6420 (Cg_exo) cc_final: 0.6175 (Cg_endo) REVERT: C 114 THR cc_start: 0.7852 (m) cc_final: 0.7562 (m) REVERT: C 135 LYS cc_start: 0.8223 (mttt) cc_final: 0.7522 (ttpp) REVERT: C 174 THR cc_start: 0.8417 (t) cc_final: 0.8196 (t) REVERT: C 197 MET cc_start: 0.9065 (ttt) cc_final: 0.8829 (ttt) REVERT: C 229 HIS cc_start: 0.7197 (m90) cc_final: 0.6744 (m-70) REVERT: C 295 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7665 (tptt) outliers start: 35 outliers final: 23 residues processed: 161 average time/residue: 1.1020 time to fit residues: 194.8901 Evaluate side-chains 154 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 317 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS C 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12018 Z= 0.272 Angle : 0.592 15.062 16283 Z= 0.296 Chirality : 0.045 0.306 1855 Planarity : 0.003 0.036 2039 Dihedral : 6.676 87.912 1739 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.50 % Allowed : 19.08 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1440 helix: -1.17 (0.21), residues: 582 sheet: 0.07 (0.36), residues: 210 loop : -0.88 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.008 0.001 HIS A 634 PHE 0.018 0.002 PHE A1094 TYR 0.019 0.001 TYR A 382 ARG 0.003 0.000 ARG C 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.5203 (p90) REVERT: A 216 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7589 (tttt) REVERT: A 263 MET cc_start: 0.6869 (mtt) cc_final: 0.6530 (mtp) REVERT: A 342 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 385 THR cc_start: 0.8054 (m) cc_final: 0.7714 (t) REVERT: A 391 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6665 (mtp85) REVERT: A 469 MET cc_start: 0.8134 (ttm) cc_final: 0.7878 (ttt) REVERT: A 535 LYS cc_start: 0.8127 (tttm) cc_final: 0.7526 (ttmm) REVERT: A 549 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7582 (pp20) REVERT: A 571 GLU cc_start: 0.6848 (tt0) cc_final: 0.6549 (mt-10) REVERT: A 577 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6787 (tp) REVERT: A 610 LYS cc_start: 0.7914 (mttp) cc_final: 0.7497 (mmtp) REVERT: A 689 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: A 697 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: A 748 ASP cc_start: 0.7346 (m-30) cc_final: 0.7045 (t0) REVERT: A 761 MET cc_start: 0.7583 (ptt) cc_final: 0.7292 (ptm) REVERT: A 812 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7892 (mptp) REVERT: A 838 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6801 (mmt-90) REVERT: A 889 ASP cc_start: 0.6893 (t0) cc_final: 0.6516 (t0) REVERT: A 1193 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: A 1287 LYS cc_start: 0.7119 (pttt) cc_final: 0.6787 (pttp) REVERT: A 1296 GLN cc_start: 0.7712 (tt0) cc_final: 0.7253 (tt0) REVERT: C 47 PRO cc_start: 0.6429 (Cg_exo) cc_final: 0.6187 (Cg_endo) REVERT: C 114 THR cc_start: 0.7857 (m) cc_final: 0.7559 (m) REVERT: C 135 LYS cc_start: 0.8232 (mttt) cc_final: 0.7545 (ttpp) REVERT: C 174 THR cc_start: 0.8452 (t) cc_final: 0.8224 (t) REVERT: C 197 MET cc_start: 0.9082 (ttt) cc_final: 0.8848 (ttt) REVERT: C 229 HIS cc_start: 0.7186 (m90) cc_final: 0.6726 (m-70) REVERT: C 295 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7665 (tptt) outliers start: 32 outliers final: 21 residues processed: 152 average time/residue: 1.0576 time to fit residues: 177.8186 Evaluate side-chains 153 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 317 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 47 optimal weight: 0.0060 chunk 117 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A1000 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121270 restraints weight = 13446.699| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.08 r_work: 0.3212 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12018 Z= 0.175 Angle : 0.545 15.251 16283 Z= 0.272 Chirality : 0.043 0.269 1855 Planarity : 0.004 0.088 2039 Dihedral : 6.413 85.217 1739 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.27 % Allowed : 19.70 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1440 helix: -0.94 (0.22), residues: 582 sheet: 0.13 (0.36), residues: 210 loop : -0.82 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1134 HIS 0.005 0.001 HIS A 634 PHE 0.025 0.001 PHE A 491 TYR 0.024 0.001 TYR A 382 ARG 0.007 0.000 ARG A1264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.94 seconds wall clock time: 76 minutes 24.74 seconds (4584.74 seconds total)