Starting phenix.real_space_refine (version: dev) on Sat May 14 05:47:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_32507_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_32507.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_32507_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_32507_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_32507_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_32507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_32507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_32507_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/05_2022/7whp_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 Convert atoms to be neutral 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 47, 'TRANS': 1004, 'PCIS': 5} Chain: "B" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 48, 'TRANS': 1004, 'PCIS': 4} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Inner-chain residues flagged as termini: ['pdbres="SAM A1102 "'] Classifications: {'undetermined': 1, 'peptide': 2} Modifications used: {'COO': 2} 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} Inner-chain residues flagged as termini: ['pdbres="SAM B1102 "'] Classifications: {'undetermined': 1, 'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM B1102 " pdbres="ATP B1103 " Chain breaks: 1 Time building chain proxies: 9.58, per 1000 atoms: 0.56 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: 7.12 Conformation dependent library (CDL) restraints added in 2.6 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: 2.83 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: 5.75 Time building geometry restraints manager: 7.65 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=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.293 1.536 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1' ATP B1103 " pdb=" C2' ATP B1103 " ideal model delta sigma weight residual 1.293 1.535 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1' ATP B1103 " pdb=" O4' ATP B1103 " ideal model delta sigma weight residual 1.621 1.418 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.621 1.418 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" O3B ATP B1103 " pdb=" PB ATP B1103 " ideal model delta sigma weight residual 1.733 1.587 0.146 2.00e-02 2.50e+03 5.34e+01 ... (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=" C1' ATP A1103 " pdb=" N9 ATP A1103 " pdb=" C8 ATP A1103 " ideal model delta sigma weight residual 104.09 126.73 -22.64 3.00e+00 1.11e-01 5.70e+01 angle pdb=" C1' ATP B1103 " pdb=" N9 ATP B1103 " pdb=" C8 ATP B1103 " ideal model delta sigma weight residual 104.09 126.66 -22.57 3.00e+00 1.11e-01 5.66e+01 angle pdb=" C1' ATP A1103 " pdb=" N9 ATP A1103 " pdb=" C4 ATP A1103 " ideal model delta sigma weight residual 147.78 127.51 20.27 3.00e+00 1.11e-01 4.57e+01 angle pdb=" C1' ATP B1103 " pdb=" N9 ATP B1103 " pdb=" C4 ATP B1103 " ideal model delta sigma weight residual 147.78 127.67 20.11 3.00e+00 1.11e-01 4.49e+01 ... (remaining 23741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 9359 17.24 - 34.49: 964 34.49 - 51.73: 184 51.73 - 68.98: 22 68.98 - 86.22: 23 Dihedral angle restraints: 10552 sinusoidal: 4256 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 10549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1913 0.041 - 0.081: 570 0.081 - 0.122: 219 0.122 - 0.163: 27 0.163 - 0.203: 1 Chirality restraints: 2730 Sorted by residual: 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=" CA ARG A 112 " pdb=" N ARG A 112 " pdb=" C ARG A 112 " pdb=" CB ARG A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA GLU A 566 " pdb=" N GLU A 566 " pdb=" C GLU A 566 " pdb=" CB GLU A 566 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 2727 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP B1103 " 0.238 2.00e-02 2.50e+03 5.12e-01 5.89e+03 pdb=" C2' ATP B1103 " -0.254 2.00e-02 2.50e+03 pdb=" C3' ATP B1103 " -0.591 2.00e-02 2.50e+03 pdb=" C4' ATP B1103 " 0.419 2.00e-02 2.50e+03 pdb=" C5' ATP B1103 " -0.023 2.00e-02 2.50e+03 pdb=" N9 ATP B1103 " -0.754 2.00e-02 2.50e+03 pdb=" O2' ATP B1103 " 0.763 2.00e-02 2.50e+03 pdb=" O3' ATP B1103 " -0.418 2.00e-02 2.50e+03 pdb=" O4' ATP B1103 " 0.620 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A1103 " 0.249 2.00e-02 2.50e+03 4.86e-01 5.31e+03 pdb=" C2' ATP A1103 " -0.251 2.00e-02 2.50e+03 pdb=" C3' ATP A1103 " -0.595 2.00e-02 2.50e+03 pdb=" C4' ATP A1103 " 0.401 2.00e-02 2.50e+03 pdb=" C5' ATP A1103 " 0.009 2.00e-02 2.50e+03 pdb=" N9 ATP A1103 " -0.684 2.00e-02 2.50e+03 pdb=" O2' ATP A1103 " 0.780 2.00e-02 2.50e+03 pdb=" O3' ATP A1103 " -0.404 2.00e-02 2.50e+03 pdb=" O4' ATP A1103 " 0.496 2.00e-02 2.50e+03 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 ... (remaining 3021 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: 1.330 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: 0.020 Extract box with map and model: 7.850 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.150 Process input model: 44.680 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.000 ------------------------------------------------------------------------------- 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 : 0.006 0.243 17420 Z= 0.370 Angle : 0.714 22.640 23746 Z= 0.326 Chirality : 0.044 0.203 2730 Planarity : 0.014 0.512 3024 Dihedral : 14.566 86.221 6476 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.58 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 : 1.920 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3004 time to fit residues: 150.6126 Evaluate side-chains 289 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.993 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8031 ------------------------------------------------------------------------------- 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: 20.0000 chunk 54 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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: 0.7794 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 0.065 17420 Z= 0.401 Angle : 0.793 20.812 23746 Z= 0.374 Chirality : 0.049 0.214 2730 Planarity : 0.006 0.094 3024 Dihedral : 8.341 88.633 2456 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.55 % 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: -0.93 (0.18), residues: 2110 helix: -0.14 (0.18), residues: 802 sheet: -0.48 (0.31), residues: 294 loop : -0.96 (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: 38 poor density : 311 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 329 average time/residue: 0.3004 time to fit residues: 147.4338 Evaluate side-chains 309 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 282 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1540 time to fit residues: 10.6320 ------------------------------------------------------------------------------- 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: 5.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 17420 Z= 0.219 Angle : 0.692 17.731 23746 Z= 0.318 Chirality : 0.044 0.200 2730 Planarity : 0.005 0.093 3024 Dihedral : 8.052 89.028 2456 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer Outliers : 1.33 % 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: -0.67 (0.18), residues: 2110 helix: 0.19 (0.18), residues: 800 sheet: -0.55 (0.31), residues: 296 loop : -0.84 (0.19), residues: 1014 *********************** 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 341 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 316 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 329 average time/residue: 0.2991 time to fit residues: 146.8319 Evaluate side-chains 306 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 292 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1550 time to fit residues: 6.7702 ------------------------------------------------------------------------------- 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: 10.0000 chunk 21 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 202 optimal weight: 30.0000 chunk 100 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 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 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: 0.7806 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 17420 Z= 0.381 Angle : 0.781 17.929 23746 Z= 0.368 Chirality : 0.048 0.205 2730 Planarity : 0.006 0.097 3024 Dihedral : 8.536 89.153 2456 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer Outliers : 2.81 % 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: -0.97 (0.17), residues: 2110 helix: -0.09 (0.18), residues: 806 sheet: -0.78 (0.32), residues: 270 loop : -0.96 (0.18), residues: 1034 *********************** 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 354 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 301 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 333 average time/residue: 0.2939 time to fit residues: 147.9747 Evaluate side-chains 317 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 287 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1524 time to fit residues: 11.3984 ------------------------------------------------------------------------------- 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: 7.9990 chunk 115 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 17420 Z= 0.337 Angle : 0.756 17.870 23746 Z= 0.357 Chirality : 0.047 0.203 2730 Planarity : 0.006 0.096 3024 Dihedral : 8.564 88.347 2456 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.07 % 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: -1.00 (0.17), residues: 2110 helix: -0.12 (0.18), residues: 810 sheet: -0.82 (0.32), residues: 270 loop : -0.98 (0.18), residues: 1030 *********************** 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 342 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 314 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 333 average time/residue: 0.3048 time to fit residues: 153.7316 Evaluate side-chains 306 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 294 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1660 time to fit residues: 6.5869 ------------------------------------------------------------------------------- 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: 5.9990 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 737 HIS B 761 GLN B 806 HIS B1030 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.133 17420 Z= 0.290 Angle : 0.740 17.889 23746 Z= 0.351 Chirality : 0.046 0.200 2730 Planarity : 0.005 0.099 3024 Dihedral : 8.418 89.494 2456 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.07 % Rotamer Outliers : 2.60 % 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: 0.07 (0.18), residues: 788 sheet: -0.66 (0.31), residues: 290 loop : -0.92 (0.18), residues: 1032 *********************** 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: 49 poor density : 307 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 26 residues processed: 339 average time/residue: 0.2904 time to fit residues: 149.7685 Evaluate side-chains 317 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 291 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1688 time to fit residues: 10.8507 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.206 17420 Z= 0.389 Angle : 0.825 18.887 23746 Z= 0.404 Chirality : 0.048 0.206 2730 Planarity : 0.006 0.105 3024 Dihedral : 8.552 89.985 2456 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer Outliers : 2.28 % 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: -1.13 (0.17), residues: 2110 helix: -0.23 (0.18), residues: 812 sheet: -0.76 (0.31), residues: 290 loop : -1.10 (0.18), residues: 1008 *********************** 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 342 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 299 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 324 average time/residue: 0.2963 time to fit residues: 144.7167 Evaluate side-chains 309 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 290 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1703 time to fit residues: 8.6494 ------------------------------------------------------------------------------- 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: 10.0000 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 910 ASN B 299 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.615 17420 Z= 0.549 Angle : 0.842 35.716 23746 Z= 0.428 Chirality : 0.045 0.279 2730 Planarity : 0.005 0.080 3024 Dihedral : 8.239 88.908 2456 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.78 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.10 % 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: -0.87 (0.18), residues: 2110 helix: 0.06 (0.19), residues: 804 sheet: -0.70 (0.31), residues: 290 loop : -0.98 (0.18), residues: 1016 *********************** 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 338 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 319 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 329 average time/residue: 0.2929 time to fit residues: 145.6007 Evaluate side-chains 305 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 293 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1610 time to fit residues: 6.4548 ------------------------------------------------------------------------------- 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: 4.9990 chunk 176 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 82 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 0.0030 chunk 187 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 HIS B 281 ASN B 286 ASN B 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.487 17420 Z= 0.411 Angle : 0.769 28.673 23746 Z= 0.381 Chirality : 0.044 0.200 2730 Planarity : 0.006 0.128 3024 Dihedral : 7.985 89.156 2456 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.05 % 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: -0.60 (0.18), residues: 2110 helix: 0.26 (0.19), residues: 804 sheet: -0.57 (0.31), residues: 290 loop : -0.81 (0.19), residues: 1016 *********************** 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 332 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 320 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 328 average time/residue: 0.3041 time to fit residues: 151.4308 Evaluate side-chains 310 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 302 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1691 time to fit residues: 5.3021 ------------------------------------------------------------------------------- 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: 9.9990 chunk 121 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 192 optimal weight: 0.4980 chunk 166 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 ASN B 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.437 17420 Z= 0.541 Angle : 0.918 48.138 23746 Z= 0.457 Chirality : 0.046 0.202 2730 Planarity : 0.007 0.168 3024 Dihedral : 8.171 89.367 2456 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.07 % Rotamer Outliers : 0.58 % 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: -0.80 (0.18), residues: 2110 helix: 0.08 (0.18), residues: 816 sheet: -0.62 (0.31), residues: 290 loop : -0.93 (0.18), residues: 1004 ********************** 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 313 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 302 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 308 average time/residue: 0.3012 time to fit residues: 139.2925 Evaluate side-chains 300 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 294 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1714 time to fit residues: 4.7668 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 171 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.138207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.128138 restraints weight = 26986.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.129775 restraints weight = 17313.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.131026 restraints weight = 12590.076| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.419 17420 Z= 0.450 Angle : 0.829 26.165 23746 Z= 0.426 Chirality : 0.045 0.199 2730 Planarity : 0.006 0.158 3024 Dihedral : 8.085 89.611 2456 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.64 % Rotamer Outliers : 0.58 % 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: -0.70 (0.18), residues: 2110 helix: 0.15 (0.19), residues: 814 sheet: -0.62 (0.31), residues: 290 loop : -0.85 (0.19), residues: 1006 =============================================================================== Job complete usr+sys time: 3448.25 seconds wall clock time: 63 minutes 32.64 seconds (3812.64 seconds total)