Starting phenix.real_space_refine on Thu Mar 14 15:28:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uox_20834/03_2024/6uox_20834_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uox_20834/03_2024/6uox_20834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uox_20834/03_2024/6uox_20834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uox_20834/03_2024/6uox_20834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uox_20834/03_2024/6uox_20834_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uox_20834/03_2024/6uox_20834_updated.pdb" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 1 7.06 5 S 68 5.16 5 Cl 2 4.86 5 C 5882 2.51 5 N 1468 2.21 5 O 1717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A TYR 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8909 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1161, 8907 Classifications: {'peptide': 1161} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 62, 'TRANS': 1098} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 124 Conformer: "B" Number of residues, atoms: 1161, 8907 Classifications: {'peptide': 1161} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 62, 'TRANS': 1098} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 124 bond proxies already assigned to first conformer: 9126 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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 162 Unusual residues: {'NAG': 8, 'QDG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.92, per 1000 atoms: 0.98 Number of scatterers: 9138 At special positions: 0 Unit cell: (112.86, 145.2, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 1 34.99 Cl 2 17.00 S 68 16.00 O 1717 8.00 N 1468 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1301 " - " ASN A 452 " " NAG A1302 " - " ASN A 459 " " NAG A1305 " - " ASN A 524 " " NAG A1309 " - " ASN A 598 " " NAG A1310 " - " ASN A 916 " " NAG A1311 " - " ASN A 931 " " NAG A1312 " - " ASN A 961 " " NAG A1313 " - " ASN A 968 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 7 sheets defined 44.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.890A pdb=" N ASP A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 58 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 59 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 62 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.837A pdb=" N ASP A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.692A pdb=" N LEU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.671A pdb=" N LEU A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 271 through 283 removed outlier: 4.227A pdb=" N PHE A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 281 " --> pdb=" O MET A 277 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.606A pdb=" N ARG A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.743A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.939A pdb=" N TYR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 451 removed outlier: 5.235A pdb=" N GLN A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 578 through 592 removed outlier: 3.659A pdb=" N TRP A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.882A pdb=" N GLU A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 637 removed outlier: 3.775A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 678 removed outlier: 3.624A pdb=" N ALA A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 710 Proline residue: A 691 - end of helix removed outlier: 3.589A pdb=" N LEU A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 701 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 702 " --> pdb=" O GLY A 698 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 704 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 747 Proline residue: A 733 - end of helix removed outlier: 3.993A pdb=" N LEU A 737 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 742 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 775 removed outlier: 4.170A pdb=" N LEU A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.596A pdb=" N LEU A 782 " --> pdb=" O CYS A 778 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 829 removed outlier: 3.587A pdb=" N SER A 824 " --> pdb=" O PHE A 820 " (cutoff:3.500A) Proline residue: A 827 - end of helix Processing helix chain 'A' and resid 837 through 851 removed outlier: 3.959A pdb=" N PHE A 842 " --> pdb=" O VAL A 838 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 879 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 919 through 928 removed outlier: 4.137A pdb=" N GLN A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 950 removed outlier: 3.569A pdb=" N PHE A 947 " --> pdb=" O ILE A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 994 through 1003 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1048 through 1069 removed outlier: 3.742A pdb=" N ILE A1052 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A1057 " --> pdb=" O ASP A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1117 removed outlier: 3.730A pdb=" N ILE A1094 " --> pdb=" O TYR A1091 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE A1095 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A1096 " --> pdb=" O THR A1093 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP A1097 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR A1098 " --> pdb=" O ILE A1095 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU A1102 " --> pdb=" O ILE A1099 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A1106 " --> pdb=" O GLY A1103 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL A1112 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR A1113 " --> pdb=" O PHE A1110 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A1117 " --> pdb=" O MET A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1145 removed outlier: 3.713A pdb=" N ILE A1126 " --> pdb=" O TRP A1122 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET A1127 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A1143 " --> pdb=" O PHE A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 4.117A pdb=" N ASN A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A1160 " --> pdb=" O ASN A1156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS A1161 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1176 removed outlier: 4.279A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A1174 " --> pdb=" O HIS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1193 removed outlier: 3.959A pdb=" N GLU A1188 " --> pdb=" O VAL A1184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A1189 " --> pdb=" O GLU A1185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1201 Processing helix chain 'A' and resid 1203 through 1215 removed outlier: 3.609A pdb=" N ILE A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A1211 " --> pdb=" O PHE A1207 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A1212 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1213 " --> pdb=" O GLY A1209 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A1215 " --> pdb=" O VAL A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1223 No H-bonds generated for 'chain 'A' and resid 1220 through 1223' Processing helix chain 'A' and resid 1227 through 1241 removed outlier: 4.152A pdb=" N LEU A1235 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1248 removed outlier: 3.515A pdb=" N LEU A1247 " --> pdb=" O PHE A1243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 206 through 210 removed outlier: 6.315A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 600 through 605 Processing sheet with id= D, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= E, first strand: chain 'A' and resid 455 through 457 Processing sheet with id= F, first strand: chain 'A' and resid 958 through 960 Processing sheet with id= G, first strand: chain 'A' and resid 1025 through 1027 291 hydrogen bonds defined for protein. 798 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: 2.42 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2778 1.34 - 1.49: 2650 1.49 - 1.64: 3838 1.64 - 1.79: 23 1.79 - 1.94: 76 Bond restraints: 9365 Sorted by residual: bond pdb=" C17 QDG A1314 " pdb=" C49 QDG A1314 " ideal model delta sigma weight residual 1.536 1.211 0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C09 QDG A1314 " pdb=" O16 QDG A1314 " ideal model delta sigma weight residual 1.396 1.197 0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C45 QDG A1314 " pdb=" N44 QDG A1314 " ideal model delta sigma weight residual 1.283 1.445 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C17 QDG A1314 " pdb=" O16 QDG A1314 " ideal model delta sigma weight residual 1.419 1.557 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C40 QDG A1314 " pdb=" N39 QDG A1314 " ideal model delta sigma weight residual 1.453 1.333 0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 9360 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.86: 309 106.86 - 113.67: 4841 113.67 - 120.48: 3999 120.48 - 127.29: 3526 127.29 - 134.10: 93 Bond angle restraints: 12768 Sorted by residual: angle pdb=" N PRO A 132 " pdb=" CA PRO A 132 " pdb=" CB PRO A 132 " ideal model delta sigma weight residual 103.25 110.45 -7.20 1.05e+00 9.07e-01 4.70e+01 angle pdb=" N PRO A 433 " pdb=" CA PRO A 433 " pdb=" C PRO A 433 " ideal model delta sigma weight residual 110.70 118.24 -7.54 1.22e+00 6.72e-01 3.82e+01 angle pdb=" N ASP A 552 " pdb=" CA ASP A 552 " pdb=" C ASP A 552 " ideal model delta sigma weight residual 110.80 121.94 -11.14 2.13e+00 2.20e-01 2.74e+01 angle pdb=" N TYR A 571 " pdb=" CA TYR A 571 " pdb=" C TYR A 571 " ideal model delta sigma weight residual 111.33 117.17 -5.84 1.21e+00 6.83e-01 2.33e+01 angle pdb=" N ILE A 962 " pdb=" CA ILE A 962 " pdb=" C ILE A 962 " ideal model delta sigma weight residual 111.90 115.78 -3.88 8.10e-01 1.52e+00 2.29e+01 ... (remaining 12763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 5458 22.32 - 44.65: 197 44.65 - 66.97: 43 66.97 - 89.29: 20 89.29 - 111.61: 13 Dihedral angle restraints: 5731 sinusoidal: 2355 harmonic: 3376 Sorted by residual: dihedral pdb=" CB CYS A 468 " pdb=" SG CYS A 468 " pdb=" SG CYS A 479 " pdb=" CB CYS A 479 " ideal model delta sinusoidal sigma weight residual -86.00 -176.29 90.29 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 957 " pdb=" SG CYS A 957 " pdb=" SG CYS A 979 " pdb=" CB CYS A 979 " ideal model delta sinusoidal sigma weight residual 93.00 173.40 -80.40 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 914 " pdb=" CB CYS A 914 " ideal model delta sinusoidal sigma weight residual 93.00 162.63 -69.63 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 5728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1408 0.139 - 0.277: 68 0.277 - 0.415: 5 0.415 - 0.554: 4 0.554 - 0.692: 2 Chirality restraints: 1487 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.05e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.12e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 478 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 1484 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 253 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 254 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 89 " -0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO A 90 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 254 " 0.032 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO A 255 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 255 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 255 " 0.027 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 3675 2.95 - 3.44: 9343 3.44 - 3.92: 14191 3.92 - 4.41: 15301 4.41 - 4.90: 25071 Nonbonded interactions: 67581 Sorted by model distance: nonbonded pdb=" OG SER A 849 " pdb=" O VAL A1136 " model vdw 2.461 2.440 nonbonded pdb=" OG1 THR A 454 " pdb=" OG1 THR A 461 " model vdw 2.494 2.440 nonbonded pdb=" O ALA A1062 " pdb=" OG1 THR A1066 " model vdw 2.496 2.440 nonbonded pdb=" O TYR A 932 " pdb=" NZ LYS A1057 " model vdw 2.507 2.520 nonbonded pdb=" OG SER A 608 " pdb=" OH TYR A 871 " model vdw 2.545 2.440 ... (remaining 67576 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.260 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 29.680 Find NCS groups from input model: 0.240 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.010 0.325 9365 Z= 0.703 Angle : 1.179 11.140 12768 Z= 0.752 Chirality : 0.076 0.692 1487 Planarity : 0.005 0.081 1622 Dihedral : 14.585 111.613 3512 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -4.01 (0.20), residues: 1153 helix: -2.78 (0.16), residues: 549 sheet: -2.22 (0.54), residues: 90 loop : -2.48 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1145 HIS 0.004 0.001 HIS A 897 PHE 0.017 0.002 PHE A1139 TYR 0.015 0.002 TYR A 899 ARG 0.006 0.000 ARG A1227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8849 (m-30) cc_final: 0.8550 (t0) REVERT: A 85 ASP cc_start: 0.8768 (t70) cc_final: 0.8266 (t0) REVERT: A 103 ASN cc_start: 0.9530 (m110) cc_final: 0.9082 (m110) REVERT: A 106 ASN cc_start: 0.8784 (m-40) cc_final: 0.8504 (m-40) REVERT: A 108 PHE cc_start: 0.8783 (m-80) cc_final: 0.8501 (m-80) REVERT: A 355 PHE cc_start: 0.9111 (t80) cc_final: 0.8778 (t80) REVERT: A 364 CYS cc_start: 0.8516 (m) cc_final: 0.8145 (m) REVERT: A 406 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8226 (mt-10) REVERT: A 593 ASN cc_start: 0.8958 (m-40) cc_final: 0.8434 (p0) REVERT: A 634 TYR cc_start: 0.8639 (t80) cc_final: 0.8419 (t80) REVERT: A 663 ILE cc_start: 0.9179 (mt) cc_final: 0.8893 (mt) REVERT: A 689 VAL cc_start: 0.8739 (t) cc_final: 0.8266 (t) REVERT: A 730 GLU cc_start: 0.9401 (tp30) cc_final: 0.8841 (tm-30) REVERT: A 735 MET cc_start: 0.8544 (ttp) cc_final: 0.7998 (ttp) REVERT: A 834 MET cc_start: 0.7817 (mtt) cc_final: 0.7404 (mmm) REVERT: A 864 LEU cc_start: 0.8463 (mt) cc_final: 0.8200 (pp) REVERT: A 872 MET cc_start: 0.8546 (mmm) cc_final: 0.7980 (mmm) REVERT: A 922 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8480 (tp-100) REVERT: A 930 ASP cc_start: 0.8554 (p0) cc_final: 0.7879 (t0) REVERT: A 933 THR cc_start: 0.8749 (t) cc_final: 0.8470 (t) REVERT: A 1122 TRP cc_start: 0.7946 (m100) cc_final: 0.7449 (m-10) REVERT: A 1150 ASN cc_start: 0.8223 (p0) cc_final: 0.7741 (p0) REVERT: A 1156 ASN cc_start: 0.8981 (t0) cc_final: 0.8777 (t0) REVERT: A 1179 MET cc_start: 0.7488 (mpp) cc_final: 0.7224 (mmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2013 time to fit residues: 60.4604 Evaluate side-chains 118 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 447 GLN A 578 GLN A 988 GLN A1042 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9365 Z= 0.190 Angle : 0.681 8.355 12768 Z= 0.332 Chirality : 0.048 0.362 1487 Planarity : 0.005 0.078 1622 Dihedral : 13.102 88.938 1547 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -3.04 (0.22), residues: 1153 helix: -1.72 (0.19), residues: 553 sheet: -2.34 (0.47), residues: 110 loop : -2.15 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 583 HIS 0.004 0.001 HIS A 398 PHE 0.032 0.002 PHE A 937 TYR 0.015 0.001 TYR A1085 ARG 0.006 0.000 ARG A 958 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8832 (m-30) cc_final: 0.8554 (t0) REVERT: A 106 ASN cc_start: 0.8807 (m-40) cc_final: 0.8387 (m-40) REVERT: A 108 PHE cc_start: 0.8582 (m-80) cc_final: 0.8377 (m-80) REVERT: A 110 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 194 PHE cc_start: 0.9045 (m-10) cc_final: 0.8777 (m-80) REVERT: A 355 PHE cc_start: 0.8939 (t80) cc_final: 0.8650 (t80) REVERT: A 364 CYS cc_start: 0.8431 (m) cc_final: 0.8085 (m) REVERT: A 406 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7887 (mt-10) REVERT: A 514 LEU cc_start: 0.9230 (mt) cc_final: 0.8900 (tp) REVERT: A 586 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8809 (mt-10) REVERT: A 593 ASN cc_start: 0.8991 (m-40) cc_final: 0.8509 (p0) REVERT: A 634 TYR cc_start: 0.8648 (t80) cc_final: 0.8409 (t80) REVERT: A 676 SER cc_start: 0.8983 (m) cc_final: 0.8694 (t) REVERT: A 730 GLU cc_start: 0.9411 (tp30) cc_final: 0.8835 (tm-30) REVERT: A 742 GLU cc_start: 0.7972 (pp20) cc_final: 0.7763 (pp20) REVERT: A 774 LEU cc_start: 0.9281 (tp) cc_final: 0.9045 (tp) REVERT: A 834 MET cc_start: 0.7916 (mtt) cc_final: 0.7659 (mmm) REVERT: A 930 ASP cc_start: 0.8507 (p0) cc_final: 0.7906 (t0) REVERT: A 935 ILE cc_start: 0.8089 (mt) cc_final: 0.7648 (mt) REVERT: A 1001 MET cc_start: 0.8979 (mpp) cc_final: 0.8667 (ptp) REVERT: A 1150 ASN cc_start: 0.8061 (p0) cc_final: 0.7647 (p0) REVERT: A 1156 ASN cc_start: 0.8872 (t0) cc_final: 0.8488 (t0) REVERT: A 1175 PHE cc_start: 0.7900 (t80) cc_final: 0.7380 (t80) REVERT: A 1194 MET cc_start: 0.8514 (mtp) cc_final: 0.8299 (mtm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1762 time to fit residues: 38.7543 Evaluate side-chains 106 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 29 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9365 Z= 0.174 Angle : 0.649 10.006 12768 Z= 0.311 Chirality : 0.045 0.325 1487 Planarity : 0.004 0.075 1622 Dihedral : 10.925 85.978 1547 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -2.62 (0.23), residues: 1153 helix: -1.23 (0.20), residues: 547 sheet: -2.23 (0.46), residues: 110 loop : -2.08 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1143 HIS 0.008 0.001 HIS A1042 PHE 0.044 0.001 PHE A 632 TYR 0.014 0.001 TYR A 875 ARG 0.007 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8844 (m-30) cc_final: 0.8553 (t0) REVERT: A 106 ASN cc_start: 0.8741 (m-40) cc_final: 0.8528 (m-40) REVERT: A 194 PHE cc_start: 0.9044 (m-10) cc_final: 0.8796 (m-80) REVERT: A 355 PHE cc_start: 0.8928 (t80) cc_final: 0.8650 (t80) REVERT: A 364 CYS cc_start: 0.8432 (m) cc_final: 0.8091 (m) REVERT: A 406 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7889 (mt-10) REVERT: A 514 LEU cc_start: 0.9249 (mt) cc_final: 0.8931 (tp) REVERT: A 586 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8960 (tt0) REVERT: A 593 ASN cc_start: 0.8977 (m-40) cc_final: 0.8473 (p0) REVERT: A 676 SER cc_start: 0.9043 (m) cc_final: 0.8749 (t) REVERT: A 730 GLU cc_start: 0.9394 (tp30) cc_final: 0.8847 (tm-30) REVERT: A 742 GLU cc_start: 0.7931 (pp20) cc_final: 0.7648 (pp20) REVERT: A 834 MET cc_start: 0.7915 (mtt) cc_final: 0.7612 (mmm) REVERT: A 872 MET cc_start: 0.8241 (mmm) cc_final: 0.7945 (mmm) REVERT: A 930 ASP cc_start: 0.8472 (p0) cc_final: 0.8022 (t0) REVERT: A 935 ILE cc_start: 0.8176 (mt) cc_final: 0.7803 (mt) REVERT: A 945 ASP cc_start: 0.8881 (t70) cc_final: 0.8599 (t70) REVERT: A 1063 SER cc_start: 0.9531 (t) cc_final: 0.9148 (p) REVERT: A 1150 ASN cc_start: 0.8036 (p0) cc_final: 0.7636 (p0) REVERT: A 1156 ASN cc_start: 0.8841 (t0) cc_final: 0.8457 (t0) REVERT: A 1175 PHE cc_start: 0.7885 (t80) cc_final: 0.7384 (t80) REVERT: A 1194 MET cc_start: 0.8506 (mtp) cc_final: 0.8107 (ttm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1797 time to fit residues: 38.3710 Evaluate side-chains 104 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 0.0870 chunk 30 optimal weight: 8.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9365 Z= 0.168 Angle : 0.616 8.578 12768 Z= 0.295 Chirality : 0.044 0.327 1487 Planarity : 0.004 0.076 1622 Dihedral : 9.429 88.188 1547 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -2.29 (0.23), residues: 1153 helix: -0.99 (0.21), residues: 552 sheet: -2.13 (0.47), residues: 110 loop : -1.86 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 544 HIS 0.006 0.001 HIS A1042 PHE 0.018 0.001 PHE A1243 TYR 0.011 0.001 TYR A 875 ARG 0.004 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8833 (m-30) cc_final: 0.8527 (t0) REVERT: A 108 PHE cc_start: 0.8447 (m-10) cc_final: 0.8172 (m-80) REVERT: A 194 PHE cc_start: 0.9041 (m-10) cc_final: 0.8775 (m-80) REVERT: A 355 PHE cc_start: 0.8930 (t80) cc_final: 0.8656 (t80) REVERT: A 364 CYS cc_start: 0.8443 (m) cc_final: 0.8109 (m) REVERT: A 406 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7882 (mt-10) REVERT: A 514 LEU cc_start: 0.9249 (mt) cc_final: 0.8923 (tp) REVERT: A 586 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8955 (tt0) REVERT: A 593 ASN cc_start: 0.8952 (m-40) cc_final: 0.8473 (p0) REVERT: A 632 PHE cc_start: 0.8083 (m-80) cc_final: 0.7687 (m-80) REVERT: A 676 SER cc_start: 0.9100 (m) cc_final: 0.8819 (t) REVERT: A 730 GLU cc_start: 0.9390 (tp30) cc_final: 0.8841 (tm-30) REVERT: A 742 GLU cc_start: 0.7868 (pp20) cc_final: 0.7643 (pp20) REVERT: A 834 MET cc_start: 0.7832 (mtt) cc_final: 0.7626 (mmm) REVERT: A 872 MET cc_start: 0.8256 (mmm) cc_final: 0.7992 (mmm) REVERT: A 930 ASP cc_start: 0.8448 (p0) cc_final: 0.8059 (t0) REVERT: A 945 ASP cc_start: 0.8916 (t70) cc_final: 0.8606 (t70) REVERT: A 1063 SER cc_start: 0.9529 (t) cc_final: 0.9146 (p) REVERT: A 1150 ASN cc_start: 0.8090 (p0) cc_final: 0.7674 (p0) REVERT: A 1156 ASN cc_start: 0.8861 (t0) cc_final: 0.8468 (t0) REVERT: A 1166 GLU cc_start: 0.8299 (tp30) cc_final: 0.7856 (tp30) REVERT: A 1175 PHE cc_start: 0.7881 (t80) cc_final: 0.7388 (t80) REVERT: A 1194 MET cc_start: 0.8509 (mtp) cc_final: 0.8130 (ttm) REVERT: A 1225 TYR cc_start: 0.8886 (m-80) cc_final: 0.8548 (m-80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1723 time to fit residues: 35.4446 Evaluate side-chains 108 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 991 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9365 Z= 0.182 Angle : 0.611 7.427 12768 Z= 0.293 Chirality : 0.043 0.325 1487 Planarity : 0.004 0.073 1622 Dihedral : 8.218 88.307 1547 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.99 (0.24), residues: 1153 helix: -0.73 (0.21), residues: 554 sheet: -2.18 (0.48), residues: 100 loop : -1.71 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1143 HIS 0.007 0.001 HIS A1042 PHE 0.016 0.001 PHE A1243 TYR 0.011 0.001 TYR A 102 ARG 0.005 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8866 (m-30) cc_final: 0.8562 (t0) REVERT: A 194 PHE cc_start: 0.9063 (m-10) cc_final: 0.8802 (m-80) REVERT: A 355 PHE cc_start: 0.8942 (t80) cc_final: 0.8695 (t80) REVERT: A 364 CYS cc_start: 0.8444 (m) cc_final: 0.8120 (m) REVERT: A 406 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7952 (mt-10) REVERT: A 481 ILE cc_start: 0.8883 (mt) cc_final: 0.8623 (mt) REVERT: A 514 LEU cc_start: 0.9259 (mt) cc_final: 0.8929 (tp) REVERT: A 531 ASP cc_start: 0.8260 (t0) cc_final: 0.7906 (t0) REVERT: A 586 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8862 (mt-10) REVERT: A 593 ASN cc_start: 0.8956 (m-40) cc_final: 0.8458 (p0) REVERT: A 632 PHE cc_start: 0.8071 (m-80) cc_final: 0.7671 (m-80) REVERT: A 676 SER cc_start: 0.9089 (m) cc_final: 0.8815 (t) REVERT: A 730 GLU cc_start: 0.9393 (tp30) cc_final: 0.8848 (tm-30) REVERT: A 834 MET cc_start: 0.7844 (mtt) cc_final: 0.7613 (mmm) REVERT: A 872 MET cc_start: 0.8238 (mmm) cc_final: 0.7588 (mmm) REVERT: A 930 ASP cc_start: 0.8476 (p0) cc_final: 0.8085 (t0) REVERT: A 945 ASP cc_start: 0.8957 (t70) cc_final: 0.8636 (t70) REVERT: A 1001 MET cc_start: 0.9062 (mpp) cc_final: 0.8743 (ptp) REVERT: A 1063 SER cc_start: 0.9529 (t) cc_final: 0.9142 (p) REVERT: A 1150 ASN cc_start: 0.8130 (p0) cc_final: 0.7712 (p0) REVERT: A 1156 ASN cc_start: 0.8883 (t0) cc_final: 0.8517 (t0) REVERT: A 1166 GLU cc_start: 0.8307 (tp30) cc_final: 0.7828 (tp30) REVERT: A 1175 PHE cc_start: 0.7925 (t80) cc_final: 0.7575 (t80) REVERT: A 1194 MET cc_start: 0.8533 (mtp) cc_final: 0.8169 (ttm) REVERT: A 1225 TYR cc_start: 0.8874 (m-80) cc_final: 0.8478 (m-80) REVERT: A 1250 TYR cc_start: 0.7671 (t80) cc_final: 0.7444 (t80) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1684 time to fit residues: 35.7741 Evaluate side-chains 108 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9365 Z= 0.342 Angle : 0.711 9.107 12768 Z= 0.350 Chirality : 0.047 0.327 1487 Planarity : 0.005 0.074 1622 Dihedral : 8.026 86.012 1547 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -2.15 (0.24), residues: 1153 helix: -0.84 (0.21), residues: 566 sheet: -2.48 (0.47), residues: 90 loop : -1.81 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 381 HIS 0.008 0.002 HIS A1042 PHE 0.018 0.002 PHE A 590 TYR 0.014 0.002 TYR A1088 ARG 0.007 0.001 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8919 (m-30) cc_final: 0.8655 (t70) REVERT: A 194 PHE cc_start: 0.9121 (m-10) cc_final: 0.8846 (m-80) REVERT: A 364 CYS cc_start: 0.8461 (m) cc_final: 0.8115 (m) REVERT: A 415 THR cc_start: 0.8761 (m) cc_final: 0.8559 (m) REVERT: A 514 LEU cc_start: 0.9267 (mt) cc_final: 0.8931 (tp) REVERT: A 531 ASP cc_start: 0.8328 (t0) cc_final: 0.7974 (t0) REVERT: A 586 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8975 (tt0) REVERT: A 593 ASN cc_start: 0.9050 (m-40) cc_final: 0.8503 (p0) REVERT: A 632 PHE cc_start: 0.8102 (m-80) cc_final: 0.7683 (m-80) REVERT: A 676 SER cc_start: 0.9092 (m) cc_final: 0.8758 (t) REVERT: A 730 GLU cc_start: 0.9445 (tp30) cc_final: 0.8836 (tm-30) REVERT: A 770 ILE cc_start: 0.8631 (tp) cc_final: 0.8428 (tt) REVERT: A 785 LEU cc_start: 0.9363 (tt) cc_final: 0.9086 (mm) REVERT: A 834 MET cc_start: 0.7968 (mtt) cc_final: 0.7677 (mmm) REVERT: A 875 TYR cc_start: 0.9125 (t80) cc_final: 0.8592 (t80) REVERT: A 930 ASP cc_start: 0.8565 (p0) cc_final: 0.8032 (t0) REVERT: A 937 PHE cc_start: 0.8253 (m-80) cc_final: 0.8013 (m-10) REVERT: A 1150 ASN cc_start: 0.8462 (p0) cc_final: 0.7952 (p0) REVERT: A 1156 ASN cc_start: 0.8964 (t0) cc_final: 0.8585 (t0) REVERT: A 1166 GLU cc_start: 0.8440 (tp30) cc_final: 0.8016 (tp30) REVERT: A 1175 PHE cc_start: 0.8019 (t80) cc_final: 0.7674 (t80) REVERT: A 1250 TYR cc_start: 0.7690 (t80) cc_final: 0.7457 (t80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1683 time to fit residues: 32.7420 Evaluate side-chains 98 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9365 Z= 0.223 Angle : 0.628 9.668 12768 Z= 0.307 Chirality : 0.044 0.323 1487 Planarity : 0.004 0.073 1622 Dihedral : 7.712 88.568 1547 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -2.05 (0.24), residues: 1153 helix: -0.69 (0.21), residues: 557 sheet: -2.40 (0.48), residues: 90 loop : -1.84 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 583 HIS 0.007 0.001 HIS A1042 PHE 0.025 0.002 PHE A 746 TYR 0.011 0.001 TYR A1037 ARG 0.004 0.001 ARG A1173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8908 (m-30) cc_final: 0.8650 (t0) REVERT: A 194 PHE cc_start: 0.9111 (m-10) cc_final: 0.8865 (m-80) REVERT: A 364 CYS cc_start: 0.8389 (m) cc_final: 0.8088 (m) REVERT: A 514 LEU cc_start: 0.9263 (mt) cc_final: 0.8929 (tp) REVERT: A 531 ASP cc_start: 0.8226 (t0) cc_final: 0.7881 (t0) REVERT: A 586 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8900 (mt-10) REVERT: A 593 ASN cc_start: 0.9026 (m-40) cc_final: 0.8487 (p0) REVERT: A 676 SER cc_start: 0.9113 (m) cc_final: 0.8797 (t) REVERT: A 730 GLU cc_start: 0.9423 (tp30) cc_final: 0.8830 (tm-30) REVERT: A 770 ILE cc_start: 0.8581 (tp) cc_final: 0.8353 (tt) REVERT: A 834 MET cc_start: 0.7639 (mtt) cc_final: 0.7401 (mmm) REVERT: A 930 ASP cc_start: 0.8545 (p0) cc_final: 0.8041 (t0) REVERT: A 945 ASP cc_start: 0.8991 (t70) cc_final: 0.8655 (t70) REVERT: A 1001 MET cc_start: 0.9064 (mpp) cc_final: 0.8824 (ptp) REVERT: A 1150 ASN cc_start: 0.8323 (p0) cc_final: 0.7864 (p0) REVERT: A 1156 ASN cc_start: 0.8902 (t0) cc_final: 0.8534 (t0) REVERT: A 1166 GLU cc_start: 0.8401 (tp30) cc_final: 0.7915 (tp30) REVERT: A 1175 PHE cc_start: 0.7883 (t80) cc_final: 0.7214 (t80) REVERT: A 1225 TYR cc_start: 0.8943 (m-80) cc_final: 0.8545 (m-80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1650 time to fit residues: 33.2684 Evaluate side-chains 106 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 0.0770 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.0050 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9365 Z= 0.157 Angle : 0.607 10.633 12768 Z= 0.292 Chirality : 0.043 0.308 1487 Planarity : 0.004 0.073 1622 Dihedral : 7.329 83.886 1547 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -1.84 (0.24), residues: 1153 helix: -0.56 (0.21), residues: 556 sheet: -2.07 (0.52), residues: 90 loop : -1.72 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 544 HIS 0.007 0.001 HIS A1042 PHE 0.029 0.001 PHE A 632 TYR 0.014 0.001 TYR A1250 ARG 0.004 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8897 (m-30) cc_final: 0.8647 (t0) REVERT: A 194 PHE cc_start: 0.9094 (m-10) cc_final: 0.8800 (m-80) REVERT: A 364 CYS cc_start: 0.8340 (m) cc_final: 0.8051 (m) REVERT: A 514 LEU cc_start: 0.9261 (mt) cc_final: 0.8917 (tp) REVERT: A 531 ASP cc_start: 0.8165 (t0) cc_final: 0.7827 (t0) REVERT: A 586 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8871 (mt-10) REVERT: A 593 ASN cc_start: 0.8968 (m-40) cc_final: 0.8452 (p0) REVERT: A 634 TYR cc_start: 0.8614 (t80) cc_final: 0.8409 (t80) REVERT: A 676 SER cc_start: 0.9094 (m) cc_final: 0.8776 (p) REVERT: A 730 GLU cc_start: 0.9390 (tp30) cc_final: 0.8866 (tm-30) REVERT: A 770 ILE cc_start: 0.8581 (tp) cc_final: 0.8358 (tt) REVERT: A 785 LEU cc_start: 0.9351 (tt) cc_final: 0.9118 (mm) REVERT: A 834 MET cc_start: 0.7663 (mtt) cc_final: 0.7407 (mmm) REVERT: A 930 ASP cc_start: 0.8451 (p0) cc_final: 0.8043 (t0) REVERT: A 945 ASP cc_start: 0.8953 (t70) cc_final: 0.8602 (t0) REVERT: A 1001 MET cc_start: 0.9014 (mpp) cc_final: 0.8759 (ptp) REVERT: A 1063 SER cc_start: 0.9530 (t) cc_final: 0.9161 (p) REVERT: A 1150 ASN cc_start: 0.8163 (p0) cc_final: 0.7725 (p0) REVERT: A 1156 ASN cc_start: 0.8918 (t0) cc_final: 0.8461 (t0) REVERT: A 1166 GLU cc_start: 0.8336 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1175 PHE cc_start: 0.7823 (t80) cc_final: 0.7093 (t80) REVERT: A 1194 MET cc_start: 0.7582 (pmm) cc_final: 0.7248 (pmm) REVERT: A 1225 TYR cc_start: 0.8835 (m-80) cc_final: 0.8519 (m-80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1672 time to fit residues: 34.6076 Evaluate side-chains 106 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.0770 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9365 Z= 0.226 Angle : 0.637 9.433 12768 Z= 0.311 Chirality : 0.044 0.307 1487 Planarity : 0.004 0.073 1622 Dihedral : 7.289 83.572 1547 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -1.83 (0.24), residues: 1153 helix: -0.51 (0.21), residues: 560 sheet: -2.23 (0.50), residues: 90 loop : -1.74 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 583 HIS 0.007 0.001 HIS A1042 PHE 0.026 0.002 PHE A 632 TYR 0.018 0.001 TYR A1250 ARG 0.006 0.001 ARG A1032 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.095 Fit side-chains REVERT: A 57 ASP cc_start: 0.8917 (m-30) cc_final: 0.8669 (t70) REVERT: A 194 PHE cc_start: 0.9083 (m-10) cc_final: 0.8839 (m-80) REVERT: A 364 CYS cc_start: 0.8378 (m) cc_final: 0.8059 (m) REVERT: A 514 LEU cc_start: 0.9275 (mt) cc_final: 0.8924 (tp) REVERT: A 531 ASP cc_start: 0.8176 (t0) cc_final: 0.7843 (t0) REVERT: A 586 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8906 (mt-10) REVERT: A 593 ASN cc_start: 0.9007 (m-40) cc_final: 0.8472 (p0) REVERT: A 676 SER cc_start: 0.9117 (m) cc_final: 0.8794 (p) REVERT: A 730 GLU cc_start: 0.9401 (tp30) cc_final: 0.8863 (tm-30) REVERT: A 770 ILE cc_start: 0.8589 (tp) cc_final: 0.8346 (tt) REVERT: A 772 PHE cc_start: 0.7928 (t80) cc_final: 0.7647 (t80) REVERT: A 773 LEU cc_start: 0.9041 (mp) cc_final: 0.8756 (mp) REVERT: A 785 LEU cc_start: 0.9346 (tt) cc_final: 0.9103 (mm) REVERT: A 834 MET cc_start: 0.7729 (mtt) cc_final: 0.7462 (mmm) REVERT: A 930 ASP cc_start: 0.8485 (p0) cc_final: 0.8083 (t0) REVERT: A 1001 MET cc_start: 0.9061 (mpp) cc_final: 0.8843 (ptp) REVERT: A 1063 SER cc_start: 0.9554 (t) cc_final: 0.9181 (p) REVERT: A 1150 ASN cc_start: 0.8255 (p0) cc_final: 0.7830 (p0) REVERT: A 1156 ASN cc_start: 0.8921 (t0) cc_final: 0.8519 (t0) REVERT: A 1166 GLU cc_start: 0.8476 (tp30) cc_final: 0.8020 (tp30) REVERT: A 1175 PHE cc_start: 0.7892 (t80) cc_final: 0.7397 (t80) REVERT: A 1194 MET cc_start: 0.7565 (pmm) cc_final: 0.7350 (pmm) REVERT: A 1225 TYR cc_start: 0.8910 (m-80) cc_final: 0.8535 (m-80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1675 time to fit residues: 33.8075 Evaluate side-chains 102 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9365 Z= 0.213 Angle : 0.630 9.502 12768 Z= 0.306 Chirality : 0.044 0.306 1487 Planarity : 0.004 0.073 1622 Dihedral : 7.248 83.101 1547 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.82 (0.24), residues: 1153 helix: -0.49 (0.21), residues: 557 sheet: -2.15 (0.50), residues: 90 loop : -1.77 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 583 HIS 0.007 0.001 HIS A1042 PHE 0.022 0.001 PHE A1243 TYR 0.016 0.001 TYR A1250 ARG 0.004 0.000 ARG A 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.070 Fit side-chains REVERT: A 57 ASP cc_start: 0.8927 (m-30) cc_final: 0.8659 (t0) REVERT: A 194 PHE cc_start: 0.9089 (m-10) cc_final: 0.8841 (m-80) REVERT: A 514 LEU cc_start: 0.9274 (mt) cc_final: 0.8917 (tp) REVERT: A 531 ASP cc_start: 0.8178 (t0) cc_final: 0.7854 (t0) REVERT: A 586 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8906 (mt-10) REVERT: A 593 ASN cc_start: 0.9001 (m-40) cc_final: 0.8464 (p0) REVERT: A 632 PHE cc_start: 0.8072 (m-10) cc_final: 0.7739 (m-80) REVERT: A 676 SER cc_start: 0.9119 (m) cc_final: 0.8788 (p) REVERT: A 730 GLU cc_start: 0.9404 (tp30) cc_final: 0.8868 (tm-30) REVERT: A 770 ILE cc_start: 0.8604 (tp) cc_final: 0.8352 (tt) REVERT: A 773 LEU cc_start: 0.9015 (mp) cc_final: 0.8761 (mp) REVERT: A 834 MET cc_start: 0.7738 (mtt) cc_final: 0.7388 (mmm) REVERT: A 930 ASP cc_start: 0.8484 (p0) cc_final: 0.8090 (t0) REVERT: A 945 ASP cc_start: 0.8994 (t70) cc_final: 0.8647 (t70) REVERT: A 1001 MET cc_start: 0.9045 (mpp) cc_final: 0.8817 (ptp) REVERT: A 1063 SER cc_start: 0.9547 (t) cc_final: 0.9174 (p) REVERT: A 1150 ASN cc_start: 0.8237 (p0) cc_final: 0.7808 (p0) REVERT: A 1156 ASN cc_start: 0.8963 (t0) cc_final: 0.8492 (t0) REVERT: A 1166 GLU cc_start: 0.8426 (tp30) cc_final: 0.7927 (tp30) REVERT: A 1175 PHE cc_start: 0.7903 (t80) cc_final: 0.7403 (t80) REVERT: A 1194 MET cc_start: 0.7572 (pmm) cc_final: 0.7276 (pmm) REVERT: A 1225 TYR cc_start: 0.8868 (m-80) cc_final: 0.8501 (m-80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1693 time to fit residues: 32.5807 Evaluate side-chains 102 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1137 ASN A1239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.087296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067052 restraints weight = 30358.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.069057 restraints weight = 16871.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070384 restraints weight = 11444.897| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9365 Z= 0.252 Angle : 0.640 9.159 12768 Z= 0.313 Chirality : 0.044 0.307 1487 Planarity : 0.004 0.073 1622 Dihedral : 7.280 84.104 1547 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.94 (0.24), residues: 1153 helix: -0.66 (0.21), residues: 566 sheet: -2.43 (0.47), residues: 100 loop : -1.67 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 583 HIS 0.007 0.001 HIS A1042 PHE 0.022 0.002 PHE A1243 TYR 0.019 0.001 TYR A1250 ARG 0.004 0.001 ARG A 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1925.85 seconds wall clock time: 35 minutes 33.06 seconds (2133.06 seconds total)