Starting phenix.real_space_refine (version: dev) on Mon Feb 20 07:37:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/02_2023/7oh5_12894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/02_2023/7oh5_12894.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/02_2023/7oh5_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_12894/02_2023/7oh5_12894_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/02_2023/7oh5_12894_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/02_2023/7oh5_12894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/02_2023/7oh5_12894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/02_2023/7oh5_12894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh5_12894/02_2023/7oh5_12894_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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 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 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: 2 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 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: 6.95, per 1000 atoms: 0.60 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: 4.74 Conformation dependent library (CDL) restraints added in 2.4 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: 1.63 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: 3.92 Time building geometry restraints manager: 5.05 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: 6950 30.44 - 60.87: 87 60.87 - 91.31: 10 91.31 - 121.74: 1 121.74 - 152.18: 2 Dihedral angle restraints: 7050 sinusoidal: 2887 harmonic: 4163 Sorted by residual: dihedral pdb=" C1 NAG C 501 " pdb=" C5 NAG C 501 " pdb=" O5 NAG C 501 " pdb=" C4 NAG C 501 " ideal model delta sinusoidal sigma weight residual -50.00 51.98 -101.98 1 2.00e+01 2.50e-03 2.90e+01 dihedral pdb=" C2 NAG C 501 " pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " pdb=" C5 NAG C 501 " ideal model delta sinusoidal sigma weight residual -50.00 41.15 -91.15 1 2.00e+01 2.50e-03 2.45e+01 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 ... (remaining 7047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1314 0.037 - 0.074: 401 0.074 - 0.111: 102 0.111 - 0.148: 26 0.148 - 0.185: 1 Chirality restraints: 1844 Sorted by residual: 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 chirality pdb=" C1' ADP A1504 " pdb=" C2' ADP A1504 " pdb=" N9 ADP A1504 " pdb=" O4' ADP A1504 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A 586 " pdb=" N ILE A 586 " pdb=" C ILE A 586 " pdb=" CB ILE A 586 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-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 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. 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: 0.010 Normalize map: mean=0, sd=1: 1.030 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: 4.530 Check model and map are aligned: 0.160 Process input model: 32.990 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.005 0.247 11865 Z= 0.301 Angle : 1.122 70.140 16091 Z= 0.430 Chirality : 0.040 0.185 1844 Planarity : 0.003 0.043 2003 Dihedral : 10.739 152.181 4360 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 % 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 *********************** 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 : 1.336 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 236 average time/residue: 1.2952 time to fit residues: 331.0523 Evaluate side-chains 114 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.8763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 A1084 GLN C 107 ASN C 116 ASN C 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1995 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= 0.196 Angle : 0.797 30.481 16091 Z= 0.351 Chirality : 0.043 0.182 1844 Planarity : 0.004 0.042 2003 Dihedral : 9.198 149.278 1637 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer Outliers : 2.94 % 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: -2.48 (0.20), residues: 1415 helix: -1.48 (0.19), residues: 571 sheet: -1.60 (0.32), residues: 224 loop : -1.66 (0.23), residues: 620 *********************** 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 156 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 1.374 Fit side-chains outliers start: 37 outliers final: 14 residues processed: 150 average time/residue: 1.0784 time to fit residues: 178.5080 Evaluate side-chains 105 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.4793 time to fit residues: 3.6521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11865 Z= 0.183 Angle : 0.776 29.914 16091 Z= 0.334 Chirality : 0.043 0.184 1844 Planarity : 0.004 0.042 2003 Dihedral : 8.639 146.315 1637 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.48 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1415 helix: -0.59 (0.22), residues: 567 sheet: -1.26 (0.34), residues: 223 loop : -1.41 (0.24), residues: 625 *********************** 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 145 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 102 time to evaluate : 1.283 Fit side-chains outliers start: 43 outliers final: 19 residues processed: 138 average time/residue: 1.0663 time to fit residues: 163.6178 Evaluate side-chains 111 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.4235 time to fit residues: 4.1190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 122 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11865 Z= 0.160 Angle : 0.768 29.916 16091 Z= 0.328 Chirality : 0.042 0.186 1844 Planarity : 0.003 0.041 2003 Dihedral : 8.202 143.872 1637 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer Outliers : 2.94 % 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: -1.27 (0.22), residues: 1415 helix: -0.19 (0.22), residues: 575 sheet: -0.97 (0.34), residues: 222 loop : -1.31 (0.24), residues: 618 *********************** 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 143 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.467 Fit side-chains outliers start: 37 outliers final: 17 residues processed: 137 average time/residue: 1.1215 time to fit residues: 170.0400 Evaluate side-chains 107 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.1226 time to fit residues: 2.2182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 101 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 122 optimal weight: 0.0970 chunk 34 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11865 Z= 0.174 Angle : 0.772 29.880 16091 Z= 0.329 Chirality : 0.043 0.185 1844 Planarity : 0.004 0.050 2003 Dihedral : 8.022 142.268 1637 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer Outliers : 3.58 % 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: -1.04 (0.22), residues: 1415 helix: 0.02 (0.23), residues: 568 sheet: -0.81 (0.35), residues: 214 loop : -1.21 (0.25), residues: 633 *********************** 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 142 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 97 time to evaluate : 1.357 Fit side-chains outliers start: 45 outliers final: 20 residues processed: 135 average time/residue: 1.1120 time to fit residues: 165.9332 Evaluate side-chains 113 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.6172 time to fit residues: 3.3620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 0.0050 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.6112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 11865 Z= 0.150 Angle : 0.760 29.645 16091 Z= 0.322 Chirality : 0.042 0.186 1844 Planarity : 0.003 0.041 2003 Dihedral : 7.845 141.594 1637 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer Outliers : 2.55 % 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: -0.84 (0.22), residues: 1415 helix: 0.24 (0.23), residues: 569 sheet: -0.70 (0.35), residues: 214 loop : -1.17 (0.24), residues: 632 *********************** 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 135 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.517 Fit side-chains outliers start: 32 outliers final: 18 residues processed: 131 average time/residue: 1.0843 time to fit residues: 157.6549 Evaluate side-chains 112 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.1051 time to fit residues: 2.0064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 76 optimal weight: 0.0670 chunk 135 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- 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** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 11865 Z= 0.222 Angle : 0.800 30.242 16091 Z= 0.344 Chirality : 0.044 0.187 1844 Planarity : 0.004 0.040 2003 Dihedral : 7.879 139.875 1637 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1415 helix: 0.12 (0.23), residues: 567 sheet: -0.66 (0.35), residues: 212 loop : -1.11 (0.25), residues: 636 *********************** 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 132 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.388 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 131 average time/residue: 1.0706 time to fit residues: 155.3275 Evaluate side-chains 111 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 1.6381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 106 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 155 GLN C 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 11865 Z= 0.193 Angle : 0.791 29.894 16091 Z= 0.339 Chirality : 0.043 0.191 1844 Planarity : 0.004 0.040 2003 Dihedral : 7.827 139.698 1637 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer Outliers : 2.63 % 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: -0.78 (0.23), residues: 1415 helix: 0.21 (0.23), residues: 567 sheet: -0.60 (0.35), residues: 212 loop : -1.08 (0.25), residues: 636 *********************** 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 124 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 1.409 Fit side-chains outliers start: 33 outliers final: 22 residues processed: 119 average time/residue: 1.0520 time to fit residues: 139.2516 Evaluate side-chains 109 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.1149 time to fit residues: 2.0818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11865 Z= 0.158 Angle : 0.773 29.514 16091 Z= 0.328 Chirality : 0.042 0.188 1844 Planarity : 0.003 0.043 2003 Dihedral : 7.682 139.925 1637 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1415 helix: 0.38 (0.23), residues: 568 sheet: -0.49 (0.35), residues: 212 loop : -1.10 (0.24), residues: 635 *********************** 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 117 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.390 Fit side-chains outliers start: 26 outliers final: 21 residues processed: 115 average time/residue: 1.1472 time to fit residues: 148.4121 Evaluate side-chains 107 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 1.6940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7567 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 11865 Z= 0.215 Angle : 0.807 30.012 16091 Z= 0.349 Chirality : 0.043 0.191 1844 Planarity : 0.004 0.044 2003 Dihedral : 7.760 139.193 1637 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.12 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1415 helix: 0.20 (0.23), residues: 574 sheet: -0.54 (0.35), residues: 211 loop : -1.06 (0.25), residues: 630 ********************** 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 121 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.303 Fit side-chains outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 1.0582 time to fit residues: 143.3370 Evaluate side-chains 112 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 1.9974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 6 optimal weight: 0.0040 chunk 80 optimal weight: 0.7980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.150287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118810 restraints weight = 14922.126| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.05 r_work: 0.3623 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11865 Z= 0.176 Angle : 0.792 29.704 16091 Z= 0.339 Chirality : 0.042 0.190 1844 Planarity : 0.003 0.041 2003 Dihedral : 7.710 139.277 1637 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer Outliers : 1.67 % 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: -0.65 (0.23), residues: 1415 helix: 0.30 (0.23), residues: 574 sheet: -0.60 (0.34), residues: 221 loop : -0.96 (0.25), residues: 620 =============================================================================== Job complete usr+sys time: 3822.42 seconds wall clock time: 69 minutes 43.11 seconds (4183.11 seconds total)