Starting phenix.real_space_refine on Fri Mar 15 12:22:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/03_2024/7oh5_12894_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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 Al 1 5.89 5 P 4 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 7484 2.51 5 N 1870 2.21 5 O 2190 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ARG 1117": "NH1" <-> "NH2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" 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: 11603 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2878 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 22, 'TRANS': 332} 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: 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: "E" 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: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Unusual residues: {' MG': 2, '2Y5': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 6.29, per 1000 atoms: 0.54 Number of scatterers: 11603 At special positions: 0 Unit cell: (81.4648, 105.182, 169.117, 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 4 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 2190 8.00 N 1870 7.00 C 7484 6.00 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=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.19 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=1, symmetry=0 Links applied BETA1-3 " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 501 " - " ASN C 237 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.1 seconds 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 10 sheets defined 39.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 190 through 193 No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.329A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.628A pdb=" N GLN A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 279 removed outlier: 3.635A pdb=" N LYS A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.892A pdb=" N LYS A 364 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.870A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 488 through 505 removed outlier: 4.271A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 525 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 613 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 653 through 663 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: 3.809A pdb=" N ARG A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 780 removed outlier: 4.365A pdb=" N GLU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 866 through 881 removed outlier: 3.576A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 899 through 904 removed outlier: 3.634A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 918 removed outlier: 3.593A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 3.871A pdb=" N ALA A 935 " --> pdb=" O PRO A 931 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 991 through 996 removed outlier: 3.668A pdb=" N LYS A 995 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 996 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1023 removed outlier: 3.615A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1028 No H-bonds generated for 'chain 'A' and resid 1025 through 1028' Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.681A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1043 through 1047' Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.617A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.602A 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 1085 removed outlier: 3.700A pdb=" N GLY A1083 " --> pdb=" O TYR A1080 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A1085 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1115 removed outlier: 3.566A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1153 removed outlier: 4.251A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1164 removed outlier: 3.602A pdb=" N ILE A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1186 Proline residue: A1177 - end of helix removed outlier: 3.573A pdb=" N SER A1181 " --> pdb=" O PRO A1177 " (cutoff:3.500A) Proline residue: A1184 - end of helix Processing helix chain 'A' and resid 1190 through 1192 No H-bonds generated for 'chain 'A' and resid 1190 through 1192' Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1205 through 1229 removed outlier: 3.640A pdb=" N LEU A1209 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 5.013A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1244 removed outlier: 3.501A pdb=" N ILE A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A1240 " --> pdb=" O HIS A1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 46 through 68 Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 80 through 83 No H-bonds generated for 'chain 'C' and resid 80 through 83' 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 removed outlier: 3.757A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' 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 225 through 230 Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 331 through 356 removed outlier: 3.604A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) 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: 3.700A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 307 through 311 removed outlier: 6.960A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 385 through 388 removed outlier: 3.530A pdb=" N MET A 386 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.382A pdb=" N TYR A 556 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 952 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 558 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS A 830 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER A 559 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TRP A 832 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 580 through 582 removed outlier: 7.161A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 706 " --> pdb=" O CYS A 696 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 637 through 640 removed outlier: 3.815A pdb=" N ILE A 637 " --> pdb=" O GLN A 649 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 667 through 669 Processing sheet with id= I, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.504A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 110 through 115 395 hydrogen bonds defined for protein. 1128 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: 4.01 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1870 1.31 - 1.44: 3233 1.44 - 1.56: 6673 1.56 - 1.69: 8 1.69 - 1.82: 81 Bond restraints: 11865 Sorted by residual: bond pdb=" C3' ADP A1504 " pdb=" C4' ADP A1504 " ideal model delta sigma weight residual 1.524 1.277 0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C1' ADP A1504 " pdb=" C2' ADP A1504 " ideal model delta sigma weight residual 1.524 1.285 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C6 ADP A1504 " pdb=" N6 ADP A1504 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C4' ADP A1504 " pdb=" O4' ADP A1504 " ideal model delta sigma weight residual 1.426 1.562 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C2' ADP A1504 " pdb=" C3' ADP A1504 " ideal model delta sigma weight residual 1.524 1.654 -0.130 2.00e-02 2.50e+03 4.21e+01 ... (remaining 11860 not shown) Histogram of bond angle deviations from ideal: 89.56 - 107.56: 403 107.56 - 125.55: 15510 125.55 - 143.55: 176 143.55 - 161.54: 0 161.54 - 179.54: 2 Bond angle restraints: 16091 Sorted by residual: angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 178.82 -70.14 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.54 -69.91 3.00e+00 1.11e-01 5.43e+02 angle pdb=" C21 2Y5 A1505 " pdb=" C22 2Y5 A1505 " pdb=" C23 2Y5 A1505 " ideal model delta sigma weight residual 85.82 119.68 -33.86 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C18 2Y5 A1505 " pdb=" C19 2Y5 A1505 " pdb=" C20 2Y5 A1505 " ideal model delta sigma weight residual 152.65 119.78 32.87 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C24 2Y5 A1505 " pdb=" C25 2Y5 A1505 " pdb=" C26 2Y5 A1505 " ideal model delta sigma weight residual 152.70 120.06 32.64 3.00e+00 1.11e-01 1.18e+02 ... (remaining 16086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.44: 7043 30.44 - 60.87: 102 60.87 - 91.31: 21 91.31 - 121.74: 13 121.74 - 152.18: 2 Dihedral angle restraints: 7181 sinusoidal: 3018 harmonic: 4163 Sorted by residual: dihedral pdb=" C1 2Y5 A1505 " pdb=" O1 2Y5 A1505 " pdb=" P1 2Y5 A1505 " pdb=" O13 2Y5 A1505 " ideal model delta sinusoidal sigma weight residual 64.28 -143.54 -152.18 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C24 2Y5 A1505 " pdb=" C25 2Y5 A1505 " pdb=" C26 2Y5 A1505 " pdb=" C27 2Y5 A1505 " ideal model delta sinusoidal sigma weight residual -30.76 -174.00 143.24 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C2' ADP A1504 " pdb=" C1' ADP A1504 " pdb=" N9 ADP A1504 " pdb=" C4 ADP A1504 " ideal model delta sinusoidal sigma weight residual 91.55 164.92 -73.38 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 7178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1565 0.054 - 0.108: 240 0.108 - 0.162: 36 0.162 - 0.216: 1 0.216 - 0.270: 2 Chirality restraints: 1844 Sorted by residual: chirality pdb=" C5 BMA E 4 " pdb=" C4 BMA E 4 " pdb=" C6 BMA E 4 " pdb=" O5 BMA E 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 237 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1841 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1056 " 0.029 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A1057 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1183 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A1184 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A1184 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1184 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A1058 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " -0.020 5.00e-02 4.00e+02 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.30: 17 2.30 - 2.95: 5117 2.95 - 3.60: 16026 3.60 - 4.25: 26883 4.25 - 4.90: 44742 Nonbonded interactions: 92785 Sorted by model distance: nonbonded pdb=" OD1 ASP A 560 " pdb=" F1 ALF A1502 " model vdw 1.656 2.390 nonbonded pdb=" OD1 ASP A 560 " pdb="AL ALF A1502 " model vdw 1.714 2.760 nonbonded pdb=" F4 ALF A1502 " pdb="MG MG A1503 " model vdw 1.726 2.120 nonbonded pdb=" O THR A 562 " pdb="MG MG A1503 " model vdw 2.030 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 2.031 2.170 ... (remaining 92780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.820 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: 0.090 Process input model: 33.990 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 0.247 11865 Z= 0.314 Angle : 1.138 70.140 16091 Z= 0.434 Chirality : 0.041 0.270 1844 Planarity : 0.003 0.043 2003 Dihedral : 12.929 152.181 4491 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.19 % Allowed : 4.53 % Favored : 94.27 % 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: -4.15 (0.18), residues: 1415 helix: -3.56 (0.13), residues: 564 sheet: -2.10 (0.31), residues: 219 loop : -2.01 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 36 HIS 0.003 0.000 HIS A 634 PHE 0.009 0.001 PHE A1205 TYR 0.012 0.001 TYR C 141 ARG 0.003 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 225 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 277 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6941 (tptp) REVERT: A 322 ILE cc_start: 0.7118 (mp) cc_final: 0.6525 (tt) REVERT: A 535 LYS cc_start: 0.8066 (tttt) cc_final: 0.7574 (ttmm) REVERT: A 678 THR cc_start: 0.6641 (p) cc_final: 0.6327 (p) REVERT: A 761 MET cc_start: 0.7321 (ptm) cc_final: 0.6881 (ptt) REVERT: A 790 LEU cc_start: 0.6816 (pp) cc_final: 0.6448 (mt) REVERT: A 898 ASP cc_start: 0.7811 (p0) cc_final: 0.7565 (p0) REVERT: A 1042 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6806 (tm-30) outliers start: 15 outliers final: 3 residues processed: 236 average time/residue: 1.2005 time to fit residues: 306.5436 Evaluate side-chains 118 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN C 107 ASN C 116 ASN C 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11865 Z= 0.170 Angle : 0.798 29.263 16091 Z= 0.347 Chirality : 0.043 0.202 1844 Planarity : 0.004 0.042 2003 Dihedral : 12.835 152.388 1781 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 2.78 % Allowed : 12.57 % Favored : 84.65 % 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: -2.40 (0.20), residues: 1415 helix: -1.39 (0.20), residues: 572 sheet: -1.60 (0.32), residues: 224 loop : -1.63 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1056 HIS 0.015 0.001 HIS A 202 PHE 0.024 0.001 PHE C 89 TYR 0.020 0.001 TYR A1192 ARG 0.010 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.404 Fit side-chains REVERT: A 269 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.6094 (t0) REVERT: A 277 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6928 (tptp) REVERT: A 322 ILE cc_start: 0.6993 (mp) cc_final: 0.6702 (tt) REVERT: A 400 MET cc_start: 0.7323 (tpt) cc_final: 0.6640 (tpt) REVERT: A 418 ILE cc_start: 0.5772 (OUTLIER) cc_final: 0.5154 (mp) REVERT: A 535 LYS cc_start: 0.8050 (tttt) cc_final: 0.7629 (ttmm) REVERT: A 761 MET cc_start: 0.7243 (ptm) cc_final: 0.6879 (ptt) REVERT: A 864 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6573 (tp30) REVERT: A 871 ARG cc_start: 0.6838 (mtm110) cc_final: 0.6479 (ttm110) REVERT: A 977 MET cc_start: 0.7646 (tpt) cc_final: 0.7223 (mmt) REVERT: A 1042 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: C 115 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7212 (tm-30) outliers start: 35 outliers final: 11 residues processed: 153 average time/residue: 1.0652 time to fit residues: 179.6164 Evaluate side-chains 111 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 308 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 862 ASN C 116 ASN C 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 11865 Z= 0.253 Angle : 0.821 30.440 16091 Z= 0.355 Chirality : 0.045 0.194 1844 Planarity : 0.004 0.053 2003 Dihedral : 11.342 147.971 1777 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 4.14 % Allowed : 12.97 % Favored : 82.90 % 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: -1.80 (0.21), residues: 1415 helix: -0.72 (0.21), residues: 568 sheet: -1.30 (0.33), residues: 223 loop : -1.49 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 36 HIS 0.013 0.001 HIS A 202 PHE 0.017 0.002 PHE C 269 TYR 0.021 0.002 TYR A 382 ARG 0.006 0.001 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 105 time to evaluate : 1.284 Fit side-chains REVERT: A 220 GLN cc_start: 0.7848 (tt0) cc_final: 0.7504 (tt0) REVERT: A 265 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7043 (mm-30) REVERT: A 269 ASP cc_start: 0.6514 (OUTLIER) cc_final: 0.6228 (t0) REVERT: A 277 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6748 (tptp) REVERT: A 400 MET cc_start: 0.7566 (tpt) cc_final: 0.6768 (tpt) REVERT: A 418 ILE cc_start: 0.5866 (OUTLIER) cc_final: 0.5338 (mp) REVERT: A 420 THR cc_start: 0.7074 (p) cc_final: 0.6635 (t) REVERT: A 535 LYS cc_start: 0.8049 (tttt) cc_final: 0.7603 (ttmm) REVERT: A 687 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: A 761 MET cc_start: 0.7313 (ptm) cc_final: 0.7006 (ptt) REVERT: A 864 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6602 (tp30) REVERT: A 871 ARG cc_start: 0.6803 (mtm110) cc_final: 0.6532 (ttm110) REVERT: A 977 MET cc_start: 0.7716 (tpt) cc_final: 0.7058 (mmt) REVERT: A 1042 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: C 115 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7333 (tm-30) outliers start: 52 outliers final: 20 residues processed: 150 average time/residue: 1.0651 time to fit residues: 176.0877 Evaluate side-chains 117 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN A1026 GLN C 116 ASN C 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11865 Z= 0.211 Angle : 0.811 30.243 16091 Z= 0.346 Chirality : 0.044 0.163 1844 Planarity : 0.004 0.038 2003 Dihedral : 10.115 145.610 1777 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.74 % Allowed : 14.08 % Favored : 82.18 % 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: -1.50 (0.22), residues: 1415 helix: -0.44 (0.22), residues: 573 sheet: -1.08 (0.34), residues: 224 loop : -1.38 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 299 HIS 0.011 0.001 HIS A 202 PHE 0.015 0.001 PHE A1205 TYR 0.018 0.002 TYR A1023 ARG 0.004 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 103 time to evaluate : 1.279 Fit side-chains REVERT: A 220 GLN cc_start: 0.7872 (tt0) cc_final: 0.7479 (tt0) REVERT: A 265 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7022 (mm-30) REVERT: A 269 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6271 (t0) REVERT: A 277 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6845 (tptp) REVERT: A 400 MET cc_start: 0.7514 (tpt) cc_final: 0.6804 (tpt) REVERT: A 418 ILE cc_start: 0.5813 (OUTLIER) cc_final: 0.5296 (mp) REVERT: A 420 THR cc_start: 0.7002 (p) cc_final: 0.6625 (t) REVERT: A 535 LYS cc_start: 0.8003 (tttt) cc_final: 0.7517 (ttmm) REVERT: A 761 MET cc_start: 0.7310 (ptm) cc_final: 0.6987 (ptt) REVERT: A 845 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7238 (mt) REVERT: A 864 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6549 (tp30) REVERT: A 871 ARG cc_start: 0.6729 (mtm110) cc_final: 0.6529 (ttm110) REVERT: A 1041 MET cc_start: 0.7978 (mtm) cc_final: 0.7691 (mtm) REVERT: A 1190 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6610 (mtp85) outliers start: 47 outliers final: 18 residues processed: 142 average time/residue: 1.1153 time to fit residues: 173.5718 Evaluate side-chains 116 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN C 116 ASN C 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 11865 Z= 0.241 Angle : 0.817 30.372 16091 Z= 0.351 Chirality : 0.045 0.168 1844 Planarity : 0.004 0.039 2003 Dihedral : 9.065 143.790 1774 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 4.06 % Allowed : 15.04 % Favored : 80.91 % 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: -1.33 (0.22), residues: 1415 helix: -0.34 (0.22), residues: 567 sheet: -1.01 (0.34), residues: 222 loop : -1.22 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 299 HIS 0.010 0.001 HIS A 202 PHE 0.017 0.002 PHE A1205 TYR 0.015 0.002 TYR A1139 ARG 0.003 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 104 time to evaluate : 1.382 Fit side-chains REVERT: A 220 GLN cc_start: 0.7909 (tt0) cc_final: 0.7466 (tt0) REVERT: A 265 GLU cc_start: 0.7233 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 277 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6904 (tptp) REVERT: A 400 MET cc_start: 0.7470 (tpt) cc_final: 0.6999 (tpt) REVERT: A 418 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5279 (mp) REVERT: A 420 THR cc_start: 0.7143 (p) cc_final: 0.6747 (t) REVERT: A 535 LYS cc_start: 0.8005 (tttt) cc_final: 0.7515 (ttmm) REVERT: A 761 MET cc_start: 0.7344 (ptm) cc_final: 0.6960 (ptt) REVERT: A 766 GLU cc_start: 0.7611 (mp0) cc_final: 0.7389 (pp20) REVERT: A 845 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7238 (mt) REVERT: A 864 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6622 (tp30) REVERT: A 889 ASP cc_start: 0.5963 (m-30) cc_final: 0.5571 (m-30) REVERT: A 890 MET cc_start: 0.6315 (pmm) cc_final: 0.5773 (mmt) REVERT: A 978 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: A 1041 MET cc_start: 0.7929 (mtm) cc_final: 0.7677 (mtm) REVERT: A 1190 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6717 (mtp85) outliers start: 51 outliers final: 25 residues processed: 146 average time/residue: 1.2550 time to fit residues: 200.5824 Evaluate side-chains 125 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 20.0000 chunk 122 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11865 Z= 0.149 Angle : 0.774 29.379 16091 Z= 0.327 Chirality : 0.042 0.175 1844 Planarity : 0.004 0.050 2003 Dihedral : 8.605 144.364 1774 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 3.10 % Allowed : 16.47 % Favored : 80.43 % 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: -1.01 (0.22), residues: 1415 helix: -0.00 (0.23), residues: 573 sheet: -0.77 (0.35), residues: 212 loop : -1.17 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 299 HIS 0.009 0.001 HIS A 202 PHE 0.012 0.001 PHE A1205 TYR 0.016 0.001 TYR A1023 ARG 0.009 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.5877 (m-10) cc_final: 0.5053 (m-10) REVERT: A 220 GLN cc_start: 0.7931 (tt0) cc_final: 0.7504 (tt0) REVERT: A 277 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6866 (tptp) REVERT: A 400 MET cc_start: 0.7322 (tpt) cc_final: 0.6918 (tpt) REVERT: A 535 LYS cc_start: 0.7992 (tttt) cc_final: 0.7502 (ttmm) REVERT: A 766 GLU cc_start: 0.7620 (mp0) cc_final: 0.7395 (pp20) REVERT: A 845 ILE cc_start: 0.7593 (pp) cc_final: 0.7296 (mt) REVERT: A 864 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: A 889 ASP cc_start: 0.5625 (m-30) cc_final: 0.5329 (m-30) REVERT: A 890 MET cc_start: 0.6642 (pmm) cc_final: 0.5766 (ttt) REVERT: A 1041 MET cc_start: 0.7870 (mtm) cc_final: 0.7621 (mtm) REVERT: A 1042 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6713 (tt0) REVERT: C 132 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: C 308 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6887 (mt) outliers start: 39 outliers final: 17 residues processed: 133 average time/residue: 1.0386 time to fit residues: 152.1941 Evaluate side-chains 114 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 11865 Z= 0.375 Angle : 0.882 30.974 16091 Z= 0.388 Chirality : 0.048 0.227 1844 Planarity : 0.004 0.046 2003 Dihedral : 8.969 141.979 1774 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.44 % Favored : 94.49 % Rotamer: Outliers : 3.74 % Allowed : 16.31 % Favored : 79.95 % 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 (0.22), residues: 1415 helix: -0.37 (0.22), residues: 563 sheet: -0.85 (0.35), residues: 212 loop : -1.39 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 299 HIS 0.009 0.001 HIS A 202 PHE 0.022 0.002 PHE C 269 TYR 0.018 0.002 TYR A1023 ARG 0.008 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 100 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 277 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6999 (tptp) REVERT: A 386 MET cc_start: 0.6146 (ttp) cc_final: 0.5930 (ttm) REVERT: A 400 MET cc_start: 0.7388 (tpt) cc_final: 0.6903 (tpt) REVERT: A 418 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5263 (mp) REVERT: A 535 LYS cc_start: 0.8031 (tttt) cc_final: 0.7539 (ttmm) REVERT: A 761 MET cc_start: 0.7391 (ptm) cc_final: 0.7004 (ptt) REVERT: A 845 ILE cc_start: 0.7595 (pp) cc_final: 0.7268 (mt) REVERT: A 864 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: A 889 ASP cc_start: 0.5813 (m-30) cc_final: 0.5469 (m-30) REVERT: A 890 MET cc_start: 0.6699 (pmm) cc_final: 0.5788 (ttt) REVERT: A 978 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: A 1041 MET cc_start: 0.7936 (mtm) cc_final: 0.7655 (mtm) REVERT: A 1190 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6191 (mtp85) REVERT: A 1193 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: C 168 LYS cc_start: 0.8120 (mptp) cc_final: 0.7733 (mppt) outliers start: 47 outliers final: 25 residues processed: 141 average time/residue: 1.0301 time to fit residues: 160.5355 Evaluate side-chains 122 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 106 optimal weight: 0.0370 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11865 Z= 0.185 Angle : 0.803 29.793 16091 Z= 0.341 Chirality : 0.043 0.170 1844 Planarity : 0.004 0.040 2003 Dihedral : 8.548 143.210 1774 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 3.10 % Allowed : 16.95 % Favored : 79.95 % 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: -1.06 (0.22), residues: 1415 helix: -0.04 (0.23), residues: 567 sheet: -0.77 (0.35), residues: 212 loop : -1.19 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 299 HIS 0.008 0.001 HIS A 202 PHE 0.015 0.001 PHE A1205 TYR 0.023 0.001 TYR A 198 ARG 0.007 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 93 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 277 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6980 (tptp) REVERT: A 382 TYR cc_start: 0.8032 (t80) cc_final: 0.7735 (t80) REVERT: A 400 MET cc_start: 0.7356 (tpt) cc_final: 0.6906 (tpt) REVERT: A 418 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5288 (mp) REVERT: A 420 THR cc_start: 0.7070 (p) cc_final: 0.6665 (t) REVERT: A 535 LYS cc_start: 0.8014 (tttt) cc_final: 0.7519 (ttmm) REVERT: A 761 MET cc_start: 0.7313 (ptm) cc_final: 0.6953 (ptt) REVERT: A 845 ILE cc_start: 0.7538 (pp) cc_final: 0.7330 (mt) REVERT: A 864 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6651 (tp30) REVERT: A 889 ASP cc_start: 0.5888 (m-30) cc_final: 0.5542 (m-30) REVERT: A 890 MET cc_start: 0.6649 (pmm) cc_final: 0.5775 (ttt) REVERT: A 1041 MET cc_start: 0.7817 (mtm) cc_final: 0.7510 (mtm) REVERT: A 1190 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6551 (mtp85) REVERT: C 132 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: C 168 LYS cc_start: 0.8105 (mptp) cc_final: 0.7719 (mppt) REVERT: C 184 ASP cc_start: 0.7384 (m-30) cc_final: 0.7182 (t0) outliers start: 39 outliers final: 21 residues processed: 127 average time/residue: 1.0250 time to fit residues: 144.3324 Evaluate side-chains 117 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.003 0.058 11865 Z= 0.174 Angle : 0.795 29.678 16091 Z= 0.336 Chirality : 0.043 0.177 1844 Planarity : 0.004 0.044 2003 Dihedral : 8.295 143.427 1774 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 2.55 % Allowed : 17.42 % Favored : 80.03 % 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: -0.89 (0.23), residues: 1415 helix: 0.15 (0.23), residues: 565 sheet: -0.70 (0.35), residues: 212 loop : -1.15 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 299 HIS 0.008 0.001 HIS A 202 PHE 0.014 0.001 PHE A1205 TYR 0.018 0.001 TYR A1023 ARG 0.006 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 277 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7007 (tptp) REVERT: A 535 LYS cc_start: 0.8005 (tttt) cc_final: 0.7508 (ttmm) REVERT: A 761 MET cc_start: 0.7341 (ptm) cc_final: 0.6954 (ptt) REVERT: A 889 ASP cc_start: 0.5903 (m-30) cc_final: 0.5550 (m-30) REVERT: A 890 MET cc_start: 0.6665 (pmm) cc_final: 0.5756 (ttt) REVERT: A 1041 MET cc_start: 0.7813 (mtm) cc_final: 0.7488 (mtm) REVERT: A 1190 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6582 (mtp85) REVERT: C 132 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: C 168 LYS cc_start: 0.8106 (mptp) cc_final: 0.7722 (mppt) REVERT: C 184 ASP cc_start: 0.7400 (m-30) cc_final: 0.7175 (t0) outliers start: 32 outliers final: 20 residues processed: 120 average time/residue: 1.0231 time to fit residues: 135.3795 Evaluate side-chains 112 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 119 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11865 Z= 0.173 Angle : 0.792 29.607 16091 Z= 0.334 Chirality : 0.043 0.173 1844 Planarity : 0.004 0.043 2003 Dihedral : 8.165 143.639 1774 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 2.15 % Allowed : 17.58 % Favored : 80.27 % 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: -0.81 (0.23), residues: 1415 helix: 0.20 (0.23), residues: 566 sheet: -0.62 (0.35), residues: 211 loop : -1.11 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 299 HIS 0.008 0.001 HIS A 202 PHE 0.014 0.001 PHE A1205 TYR 0.027 0.001 TYR A 198 ARG 0.006 0.000 ARG C 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 277 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7044 (tptp) REVERT: A 535 LYS cc_start: 0.8004 (tttt) cc_final: 0.7505 (ttmm) REVERT: A 761 MET cc_start: 0.7260 (ptm) cc_final: 0.6853 (ptt) REVERT: A 889 ASP cc_start: 0.5828 (m-30) cc_final: 0.5461 (m-30) REVERT: A 890 MET cc_start: 0.6705 (pmm) cc_final: 0.5786 (ttt) REVERT: A 1041 MET cc_start: 0.7861 (mtm) cc_final: 0.7559 (mtm) REVERT: A 1190 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6574 (mtp85) REVERT: C 132 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: C 168 LYS cc_start: 0.8097 (mptp) cc_final: 0.7706 (mppt) REVERT: C 308 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6939 (mt) outliers start: 27 outliers final: 21 residues processed: 114 average time/residue: 1.0837 time to fit residues: 136.0872 Evaluate side-chains 117 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 115 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 98 optimal weight: 0.0270 chunk 6 optimal weight: 0.1980 chunk 80 optimal weight: 0.1980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.113207 restraints weight = 14967.097| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.57 r_work: 0.3444 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11865 Z= 0.128 Angle : 0.769 29.722 16091 Z= 0.323 Chirality : 0.041 0.182 1844 Planarity : 0.003 0.045 2003 Dihedral : 7.816 145.030 1774 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 1.59 % Allowed : 18.22 % Favored : 80.19 % 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: -0.50 (0.23), residues: 1415 helix: 0.53 (0.23), residues: 563 sheet: -0.39 (0.36), residues: 206 loop : -1.04 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 412 HIS 0.007 0.001 HIS A 202 PHE 0.012 0.001 PHE A1205 TYR 0.018 0.001 TYR A1023 ARG 0.007 0.000 ARG C 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4051.80 seconds wall clock time: 72 minutes 41.82 seconds (4361.82 seconds total)