Starting phenix.real_space_refine (version: dev) on Wed Feb 22 09:21:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/02_2023/7whp_32507_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/02_2023/7whp_32507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/02_2023/7whp_32507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/02_2023/7whp_32507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/02_2023/7whp_32507_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/02_2023/7whp_32507_updated.pdb" } resolution = 3.7 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= 0.010 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 PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 898": "OE1" <-> "OE2" Residue "B GLU 1023": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17038 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 5, 'PTRANS': 47, 'TRANS': 1004} Chain: "B" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 1004} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM A1102 " pdbres="ATP A1103 " Chain breaks: 1 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM B1102 " pdbres="ATP B1103 " Chain breaks: 1 Time building chain proxies: 9.73, per 1000 atoms: 0.57 Number of scatterers: 17038 At special positions: 0 Unit cell: (160.362, 107.262, 204.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 6 15.00 O 3220 8.00 N 2948 7.00 C 10770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 2.4 seconds 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 22 sheets defined 35.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 20 through 26 removed outlier: 4.371A pdb=" N ARG A 23 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 26 " --> pdb=" O ARG A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.895A pdb=" N SER A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.705A pdb=" N ASN A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 141 Processing helix chain 'A' and resid 146 through 157 removed outlier: 4.063A pdb=" N PHE A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.578A pdb=" N ARG A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 224 through 246 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 330 through 342 removed outlier: 3.946A pdb=" N LEU A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.809A pdb=" N LEU A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 467 through 479 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 530 through 542 Processing helix chain 'A' and resid 567 through 575 Processing helix chain 'A' and resid 625 through 642 Processing helix chain 'A' and resid 655 through 666 removed outlier: 3.602A pdb=" N SER A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 716 No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 752 through 764 Proline residue: A 756 - end of helix removed outlier: 3.700A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 810 removed outlier: 4.186A pdb=" N ARG A 810 " --> pdb=" O HIS A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 851 Processing helix chain 'A' and resid 867 through 870 removed outlier: 4.332A pdb=" N SER A 870 " --> pdb=" O ALA A 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 867 through 870' Processing helix chain 'A' and resid 889 through 893 Processing helix chain 'A' and resid 936 through 950 Processing helix chain 'A' and resid 965 through 971 removed outlier: 3.508A pdb=" N ILE A 968 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 969 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 971 " --> pdb=" O ILE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1010 Processing helix chain 'A' and resid 1021 through 1030 Processing helix chain 'A' and resid 1037 through 1048 removed outlier: 4.372A pdb=" N ALA A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 19 through 25 removed outlier: 4.483A pdb=" N ARG B 23 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 85 through 98 removed outlier: 3.623A pdb=" N SER B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.757A pdb=" N ARG B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 138 through 141 removed outlier: 3.543A pdb=" N LEU B 141 " --> pdb=" O PRO B 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.555A pdb=" N ASN B 151 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER B 152 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 155 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 removed outlier: 3.746A pdb=" N HIS B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 224 through 247 removed outlier: 3.700A pdb=" N ASP B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 278 removed outlier: 4.002A pdb=" N LEU B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 293 through 306 removed outlier: 3.593A pdb=" N THR B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.797A pdb=" N LEU B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 431 through 446 removed outlier: 3.525A pdb=" N ASP B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 459 Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.655A pdb=" N LYS B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.614A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 575 Processing helix chain 'B' and resid 625 through 641 Processing helix chain 'B' and resid 655 through 665 removed outlier: 3.631A pdb=" N ILE B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 717 removed outlier: 3.810A pdb=" N ARG B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR B 715 " --> pdb=" O MET B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Proline residue: B 756 - end of helix removed outlier: 3.626A pdb=" N LEU B 759 " --> pdb=" O PRO B 756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 762 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS B 763 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 764 " --> pdb=" O GLN B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 811 removed outlier: 3.502A pdb=" N GLN B 809 " --> pdb=" O TYR B 805 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG B 810 " --> pdb=" O HIS B 806 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR B 811 " --> pdb=" O GLU B 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 805 through 811' Processing helix chain 'B' and resid 833 through 851 removed outlier: 3.578A pdb=" N LEU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 870 removed outlier: 4.355A pdb=" N SER B 870 " --> pdb=" O ALA B 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 867 through 870' Processing helix chain 'B' and resid 889 through 894 removed outlier: 3.549A pdb=" N LYS B 894 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 950 Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.993A pdb=" N ASP B 972 " --> pdb=" O THR B 969 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 973 " --> pdb=" O ARG B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1010 Processing helix chain 'B' and resid 1021 through 1030 Processing helix chain 'B' and resid 1037 through 1048 removed outlier: 4.082A pdb=" N ALA B1041 " --> pdb=" O SER B1037 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP B1044 " --> pdb=" O GLY B1040 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B1045 " --> pdb=" O ALA B1041 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B1048 " --> pdb=" O ASP B1044 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.878A pdb=" N VAL A 251 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.614A pdb=" N THR A 41 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 50 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 43 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 48 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 161 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 326 through 329 Processing sheet with id= E, first strand: chain 'A' and resid 401 through 404 removed outlier: 6.195A pdb=" N THR A 823 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER A 404 " --> pdb=" O THR A 823 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU A 825 " --> pdb=" O SER A 404 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 419 through 423 removed outlier: 3.918A pdb=" N THR A 690 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 556 through 560 removed outlier: 5.922A pdb=" N ARG A 583 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 559 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 585 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 729 through 731 removed outlier: 3.583A pdb=" N CYS A 747 " --> pdb=" O HIS A 731 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 858 through 860 removed outlier: 8.094A pdb=" N VAL A 859 " --> pdb=" O ASN A 916 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 918 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN A 955 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR A 919 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 957 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE A 921 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 959 " --> pdb=" O PHE A 921 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 962 " --> pdb=" O PRO A1051 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 879 through 881 removed outlier: 6.474A pdb=" N GLU A 898 " --> pdb=" O VAL A 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 980 through 983 Processing sheet with id= L, first strand: chain 'A' and resid 205 through 207 removed outlier: 7.034A pdb=" N THR A 207 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 5 through 8 removed outlier: 4.027A pdb=" N VAL B 251 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 7 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 38 through 43 Processing sheet with id= O, first strand: chain 'B' and resid 161 through 165 Processing sheet with id= P, first strand: chain 'B' and resid 326 through 329 removed outlier: 3.579A pdb=" N PHE B 355 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 373 through 376 removed outlier: 5.509A pdb=" N GLU B 768 " --> pdb=" O ARG B 786 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG B 786 " --> pdb=" O GLU B 768 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 401 through 404 removed outlier: 6.167A pdb=" N THR B 823 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER B 404 " --> pdb=" O THR B 823 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU B 825 " --> pdb=" O SER B 404 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'B' and resid 419 through 423 removed outlier: 6.808A pdb=" N ILE B 613 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LYS B 649 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N CYS B 615 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 614 " --> pdb=" O ILE B 558 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1052 through 1056 removed outlier: 3.706A pdb=" N SER B 917 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLN B 857 " --> pdb=" O ILE B 918 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N LEU B 920 " --> pdb=" O GLN B 857 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 859 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS B 877 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER B 860 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 879 " --> pdb=" O SER B 860 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 980 through 982 Processing sheet with id= V, first strand: chain 'B' and resid 205 through 207 removed outlier: 7.109A pdb=" N THR B 207 " --> pdb=" O PRO B 262 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 7.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5561 1.34 - 1.46: 2638 1.46 - 1.57: 9035 1.57 - 1.69: 10 1.69 - 1.81: 176 Bond restraints: 17420 Sorted by residual: bond pdb=" C2 SAM A1102 " pdb=" N3 SAM A1102 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" C2 SAM B1101 " pdb=" N3 SAM B1101 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.10e+00 bond pdb=" C2 SAM A1101 " pdb=" N3 SAM A1101 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" C2 SAM B1102 " pdb=" N3 SAM B1102 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" C8 SAM B1102 " pdb=" N7 SAM B1102 " ideal model delta sigma weight residual 1.298 1.352 -0.054 2.00e-02 2.50e+03 7.21e+00 ... (remaining 17415 not shown) Histogram of bond angle deviations from ideal: 99.22 - 107.36: 708 107.36 - 115.50: 10736 115.50 - 123.64: 11842 123.64 - 131.77: 427 131.77 - 139.91: 33 Bond angle restraints: 23746 Sorted by residual: angle pdb=" C ILE B 519 " pdb=" N PRO B 520 " pdb=" CA PRO B 520 " ideal model delta sigma weight residual 120.52 112.93 7.59 9.90e-01 1.02e+00 5.89e+01 angle pdb=" N GLU A 564 " pdb=" CA GLU A 564 " pdb=" C GLU A 564 " ideal model delta sigma weight residual 110.97 106.77 4.20 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N GLU A 566 " pdb=" CA GLU A 566 " pdb=" C GLU A 566 " ideal model delta sigma weight residual 109.42 114.97 -5.55 1.48e+00 4.57e-01 1.41e+01 angle pdb=" N ARG A 112 " pdb=" CA ARG A 112 " pdb=" C ARG A 112 " ideal model delta sigma weight residual 109.23 103.84 5.39 1.55e+00 4.16e-01 1.21e+01 angle pdb=" CB LYS A 244 " pdb=" CG LYS A 244 " pdb=" CD LYS A 244 " ideal model delta sigma weight residual 111.30 118.15 -6.85 2.30e+00 1.89e-01 8.86e+00 ... (remaining 23741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 9311 17.24 - 34.49: 945 34.49 - 51.73: 170 51.73 - 68.98: 17 68.98 - 86.22: 19 Dihedral angle restraints: 10462 sinusoidal: 4166 harmonic: 6296 Sorted by residual: dihedral pdb=" CA LEU A 816 " pdb=" C LEU A 816 " pdb=" N GLY A 817 " pdb=" CA GLY A 817 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU A 551 " pdb=" C LEU A 551 " pdb=" N MET A 552 " pdb=" CA MET A 552 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG B 590 " pdb=" CD ARG B 590 " pdb=" NE ARG B 590 " pdb=" CZ ARG B 590 " ideal model delta sinusoidal sigma weight residual -180.00 -135.13 -44.87 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 10459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1937 0.042 - 0.083: 568 0.083 - 0.125: 207 0.125 - 0.166: 24 0.166 - 0.208: 6 Chirality restraints: 2742 Sorted by residual: chirality pdb=" C1' SAM A1102 " pdb=" C2' SAM A1102 " pdb=" N9 SAM A1102 " pdb=" O4' SAM A1102 " both_signs ideal model delta sigma weight residual False 2.30 2.51 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO B 554 " pdb=" N PRO B 554 " pdb=" C PRO B 554 " pdb=" CB PRO B 554 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' SAM B1102 " pdb=" C1' SAM B1102 " pdb=" C3' SAM B1102 " pdb=" O2' SAM B1102 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 2739 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 553 " -0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO A 554 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 554 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 554 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 553 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 554 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 554 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 554 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 74 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO A 75 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.039 5.00e-02 4.00e+02 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1728 2.75 - 3.29: 17080 3.29 - 3.82: 27371 3.82 - 4.36: 33342 4.36 - 4.90: 57237 Nonbonded interactions: 136758 Sorted by model distance: nonbonded pdb=" OG SER B 301 " pdb=" OH TYR B 316 " model vdw 2.209 2.440 nonbonded pdb=" O ARG B 324 " pdb=" OH TYR B 349 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR A 856 " pdb=" O ASN A 916 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR A 842 " pdb=" O SAM A1102 " model vdw 2.226 2.440 nonbonded pdb=" O VAL A 733 " pdb=" OH TYR A 741 " model vdw 2.228 2.440 ... (remaining 136753 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 'A' selection = chain 'B' } 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 94 5.16 5 C 10770 2.51 5 N 2948 2.21 5 O 3220 1.98 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 7.370 Check model and map are aligned: 0.250 Process input model: 43.920 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.004 0.066 17420 Z= 0.239 Angle : 0.623 11.338 23746 Z= 0.305 Chirality : 0.045 0.208 2742 Planarity : 0.005 0.094 3022 Dihedral : 14.193 86.221 6386 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.85 (0.18), residues: 2110 helix: -0.24 (0.18), residues: 826 sheet: -0.36 (0.32), residues: 286 loop : -0.78 (0.19), residues: 998 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.876 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3225 time to fit residues: 160.9487 Evaluate side-chains 292 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 339 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 17420 Z= 0.376 Angle : 0.640 7.949 23746 Z= 0.330 Chirality : 0.048 0.211 2742 Planarity : 0.006 0.086 3022 Dihedral : 5.136 40.104 2366 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.91 (0.18), residues: 2110 helix: -0.13 (0.18), residues: 802 sheet: -0.48 (0.31), residues: 294 loop : -0.94 (0.18), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 314 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 26 residues processed: 331 average time/residue: 0.3154 time to fit residues: 153.1184 Evaluate side-chains 312 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 286 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1508 time to fit residues: 9.8976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 623 GLN B 299 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 17420 Z= 0.289 Angle : 0.572 6.980 23746 Z= 0.295 Chirality : 0.046 0.201 2742 Planarity : 0.005 0.084 3022 Dihedral : 4.969 40.500 2366 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.90 (0.18), residues: 2110 helix: -0.06 (0.18), residues: 812 sheet: -0.64 (0.31), residues: 296 loop : -0.94 (0.19), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 310 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 323 average time/residue: 0.3196 time to fit residues: 152.8537 Evaluate side-chains 309 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 291 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1696 time to fit residues: 8.3696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 623 GLN B 299 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 17420 Z= 0.281 Angle : 0.563 6.893 23746 Z= 0.290 Chirality : 0.046 0.204 2742 Planarity : 0.005 0.082 3022 Dihedral : 4.960 40.606 2366 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.88 (0.18), residues: 2110 helix: -0.01 (0.18), residues: 812 sheet: -0.75 (0.32), residues: 270 loop : -0.92 (0.18), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 308 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 22 residues processed: 333 average time/residue: 0.3107 time to fit residues: 154.3959 Evaluate side-chains 313 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1607 time to fit residues: 9.3695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 151 optimal weight: 0.0770 chunk 83 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 217 HIS B 299 GLN B 737 HIS B 761 GLN B1030 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17420 Z= 0.183 Angle : 0.502 5.789 23746 Z= 0.259 Chirality : 0.044 0.198 2742 Planarity : 0.005 0.081 3022 Dihedral : 4.602 39.860 2366 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.59 (0.18), residues: 2110 helix: 0.25 (0.19), residues: 806 sheet: -0.68 (0.32), residues: 270 loop : -0.74 (0.18), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 331 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 342 average time/residue: 0.3094 time to fit residues: 157.4083 Evaluate side-chains 314 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 306 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1615 time to fit residues: 5.1392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 203 optimal weight: 0.0770 chunk 168 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 overall best weight: 3.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 17420 Z= 0.214 Angle : 0.517 6.575 23746 Z= 0.266 Chirality : 0.044 0.199 2742 Planarity : 0.005 0.079 3022 Dihedral : 4.645 39.111 2366 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.61 (0.18), residues: 2110 helix: 0.23 (0.18), residues: 812 sheet: -0.63 (0.32), residues: 270 loop : -0.78 (0.18), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 315 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 335 average time/residue: 0.3318 time to fit residues: 167.7124 Evaluate side-chains 324 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 300 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1690 time to fit residues: 10.5825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 115 optimal weight: 0.4980 chunk 148 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN B 299 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 17420 Z= 0.311 Angle : 0.588 11.556 23746 Z= 0.299 Chirality : 0.046 0.200 2742 Planarity : 0.005 0.077 3022 Dihedral : 5.017 46.365 2366 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.82 (0.18), residues: 2110 helix: 0.02 (0.18), residues: 818 sheet: -0.67 (0.33), residues: 270 loop : -0.88 (0.18), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 307 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 324 average time/residue: 0.3110 time to fit residues: 149.9048 Evaluate side-chains 308 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 295 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1819 time to fit residues: 6.9685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 184 optimal weight: 0.0970 overall best weight: 3.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 17420 Z= 0.219 Angle : 0.536 10.503 23746 Z= 0.273 Chirality : 0.044 0.199 2742 Planarity : 0.005 0.076 3022 Dihedral : 4.788 49.533 2366 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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 (0.18), residues: 2110 helix: 0.18 (0.19), residues: 810 sheet: -0.55 (0.31), residues: 290 loop : -0.83 (0.18), residues: 1010 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 303 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 314 average time/residue: 0.3166 time to fit residues: 147.8487 Evaluate side-chains 302 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 293 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1563 time to fit residues: 5.4714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 17420 Z= 0.327 Angle : 0.612 11.541 23746 Z= 0.310 Chirality : 0.047 0.201 2742 Planarity : 0.005 0.074 3022 Dihedral : 5.150 55.638 2366 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.86 (0.18), residues: 2110 helix: 0.00 (0.18), residues: 812 sheet: -0.64 (0.31), residues: 290 loop : -0.94 (0.18), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 297 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 311 average time/residue: 0.3164 time to fit residues: 145.6179 Evaluate side-chains 310 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 293 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1647 time to fit residues: 7.9860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN B 299 GLN B 761 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17420 Z= 0.202 Angle : 0.539 13.348 23746 Z= 0.273 Chirality : 0.044 0.197 2742 Planarity : 0.005 0.073 3022 Dihedral : 4.785 56.967 2366 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.97 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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 (0.18), residues: 2110 helix: 0.22 (0.19), residues: 802 sheet: -0.61 (0.31), residues: 290 loop : -0.82 (0.18), residues: 1018 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 312 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 316 average time/residue: 0.3186 time to fit residues: 150.0301 Evaluate side-chains 309 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 301 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1637 time to fit residues: 5.1423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.2980 chunk 51 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.135893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.125756 restraints weight = 27183.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.127448 restraints weight = 17439.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.128626 restraints weight = 12657.188| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 17420 Z= 0.266 Angle : 0.577 12.606 23746 Z= 0.292 Chirality : 0.046 0.200 2742 Planarity : 0.005 0.071 3022 Dihedral : 4.957 58.352 2366 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.75 (0.18), residues: 2110 helix: 0.13 (0.19), residues: 802 sheet: -0.66 (0.31), residues: 290 loop : -0.87 (0.18), residues: 1018 =============================================================================== Job complete usr+sys time: 3579.13 seconds wall clock time: 65 minutes 42.35 seconds (3942.35 seconds total)