Starting phenix.real_space_refine on Sat Sep 28 07:10:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/09_2024/8hjw_34840.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/09_2024/8hjw_34840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/09_2024/8hjw_34840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/09_2024/8hjw_34840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/09_2024/8hjw_34840.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/09_2024/8hjw_34840.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 11570 2.51 5 N 3408 2.21 5 O 3468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1215, 9258 Classifications: {'peptide': 1215} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 59, 'TRANS': 1151} Chain: "B" Number of atoms: 9258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1215, 9258 Classifications: {'peptide': 1215} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 59, 'TRANS': 1151} Time building chain proxies: 11.37, per 1000 atoms: 0.61 Number of scatterers: 18516 At special positions: 0 Unit cell: (95.45, 114.54, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 3468 8.00 N 3408 7.00 C 11570 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 - 3.00 Amino acid : True - 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: 4.56 Conformation dependent library (CDL) restraints added in 2.7 seconds 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 11 sheets defined 54.6% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 42 through 57 Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.501A pdb=" N ILE A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.557A pdb=" N ALA A 163 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 193 Proline residue: A 174 - end of helix removed outlier: 4.177A pdb=" N ALA A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 removed outlier: 3.539A pdb=" N ARG A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 252 through 265 removed outlier: 3.738A pdb=" N VAL A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.802A pdb=" N CYS A 329 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 358 Processing helix chain 'A' and resid 373 through 388 removed outlier: 3.682A pdb=" N ILE A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 467 through 498 Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 583 through 594 Processing helix chain 'A' and resid 605 through 623 Processing helix chain 'A' and resid 627 through 630 Processing helix chain 'A' and resid 642 through 658 Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 692 through 710 removed outlier: 3.712A pdb=" N TYR A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 734 through 756 removed outlier: 4.654A pdb=" N ARG A 753 " --> pdb=" O GLU A 749 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 811 removed outlier: 3.507A pdb=" N ARG A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 821 Processing helix chain 'A' and resid 826 through 832 Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 863 through 877 Processing helix chain 'A' and resid 898 through 916 removed outlier: 3.607A pdb=" N ILE A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 937 Processing helix chain 'A' and resid 968 through 975 removed outlier: 3.727A pdb=" N LEU A 975 " --> pdb=" O ARG A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1003 removed outlier: 3.532A pdb=" N TYR A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1024 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1041 through 1054 Processing helix chain 'A' and resid 1085 through 1097 Processing helix chain 'A' and resid 1097 through 1110 Processing helix chain 'A' and resid 1127 through 1155 removed outlier: 3.917A pdb=" N ALA A1143 " --> pdb=" O THR A1139 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A1144 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1174 Processing helix chain 'A' and resid 1177 through 1197 Processing helix chain 'A' and resid 1205 through 1212 Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 42 through 58 Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 73 through 89 Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.605A pdb=" N ALA B 163 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 190 Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 252 through 265 removed outlier: 3.820A pdb=" N VAL B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 316 through 329 removed outlier: 3.740A pdb=" N CYS B 329 " --> pdb=" O MET B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.779A pdb=" N ILE B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 424 removed outlier: 3.714A pdb=" N ILE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 441 removed outlier: 3.595A pdb=" N GLN B 441 " --> pdb=" O TYR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 497 removed outlier: 3.981A pdb=" N ARG B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 534 Processing helix chain 'B' and resid 583 through 595 Processing helix chain 'B' and resid 605 through 623 removed outlier: 3.536A pdb=" N LEU B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 630 Processing helix chain 'B' and resid 642 through 658 Processing helix chain 'B' and resid 675 through 679 Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 692 through 710 removed outlier: 3.684A pdb=" N TYR B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Proline residue: B 704 - end of helix Processing helix chain 'B' and resid 719 through 723 Processing helix chain 'B' and resid 734 through 756 removed outlier: 5.030A pdb=" N ARG B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE B 754 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 811 removed outlier: 3.822A pdb=" N THR B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 821 removed outlier: 3.580A pdb=" N LEU B 821 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 832 Processing helix chain 'B' and resid 837 through 851 Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 863 through 877 Processing helix chain 'B' and resid 898 through 916 Processing helix chain 'B' and resid 924 through 937 removed outlier: 3.765A pdb=" N ALA B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 975 removed outlier: 3.672A pdb=" N LEU B 975 " --> pdb=" O ARG B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 1003 removed outlier: 3.569A pdb=" N TYR B1002 " --> pdb=" O TYR B 998 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1024 Processing helix chain 'B' and resid 1024 through 1030 Processing helix chain 'B' and resid 1041 through 1054 Processing helix chain 'B' and resid 1085 through 1097 Processing helix chain 'B' and resid 1097 through 1109 Processing helix chain 'B' and resid 1127 through 1155 removed outlier: 3.944A pdb=" N ALA B1143 " --> pdb=" O THR B1139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B1144 " --> pdb=" O THR B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1170 through 1174 Processing helix chain 'B' and resid 1177 through 1197 Processing helix chain 'B' and resid 1205 through 1212 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.493A pdb=" N VAL A 36 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU A 67 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 38 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 14 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU A 94 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 156 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN A 96 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 153 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE A 199 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN A 155 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ILE A 276 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 198 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 291 removed outlier: 6.678A pdb=" N THR A 290 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR A 308 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLY A 336 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 310 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A 333 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N LEU A 367 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 335 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 635 removed outlier: 3.564A pdb=" N ILE A 577 " --> pdb=" O MET A 600 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 574 " --> pdb=" O TYR A 662 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 664 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 576 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 663 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 717 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASN A 665 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY A 712 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ASN A 762 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 714 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE A 764 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N PHE A 946 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA A 763 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 723 through 724 Processing sheet with id=AA6, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.530A pdb=" N VAL A 980 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR A 979 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL A1060 " --> pdb=" O THR A 979 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR A 981 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A1115 " --> pdb=" O ASN A1162 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL A1164 " --> pdb=" O LEU A1115 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU A1117 " --> pdb=" O VAL A1164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.515A pdb=" N SER B 39 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU B 94 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 156 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN B 96 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N ILE B 276 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR B 198 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 239 through 240 Processing sheet with id=AA9, first strand: chain 'B' and resid 289 through 291 removed outlier: 6.522A pdb=" N THR B 290 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LEU B 543 " --> pdb=" O ALA B 507 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN B 509 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 454 " --> pdb=" O ASN B 508 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE B 510 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 456 " --> pdb=" O ILE B 510 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR B 307 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL B 395 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU B 309 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR B 308 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY B 336 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 310 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU B 367 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE B 335 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 632 through 634 removed outlier: 6.579A pdb=" N VAL B 574 " --> pdb=" O TYR B 662 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE B 664 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 576 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B 663 " --> pdb=" O LEU B 715 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL B 717 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN B 665 " --> pdb=" O VAL B 717 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N PHE B 946 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 763 " --> pdb=" O PHE B 946 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1033 through 1037 removed outlier: 6.311A pdb=" N VAL B1007 " --> pdb=" O MET B1034 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE B1036 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N MET B1009 " --> pdb=" O ILE B1036 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 980 " --> pdb=" O GLN B1006 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR B 979 " --> pdb=" O PRO B1058 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL B1060 " --> pdb=" O THR B 979 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B 981 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU B1115 " --> pdb=" O ASN B1162 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1164 " --> pdb=" O LEU B1115 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU B1117 " --> pdb=" O VAL B1164 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ILE B1217 " --> pdb=" O ILE B1161 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B1163 " --> pdb=" O ILE B1217 " (cutoff:3.500A) 983 hydrogen bonds defined for protein. 2844 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: 7.16 Time building geometry restraints manager: 5.37 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: 6257 1.34 - 1.46: 2343 1.46 - 1.58: 10128 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 18850 Sorted by residual: bond pdb=" N ILE B 549 " pdb=" CA ILE B 549 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.16e+00 bond pdb=" N THR A1196 " pdb=" CA THR A1196 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.31e-02 5.83e+03 7.95e+00 bond pdb=" N ILE A 549 " pdb=" CA ILE A 549 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.62e+00 bond pdb=" N SER A 458 " pdb=" CA SER A 458 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.23e-02 6.61e+03 6.98e+00 bond pdb=" N VAL A1192 " pdb=" CA VAL A1192 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.19e-02 7.06e+03 6.51e+00 ... (remaining 18845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 24877 1.90 - 3.79: 627 3.79 - 5.69: 74 5.69 - 7.58: 16 7.58 - 9.48: 4 Bond angle restraints: 25598 Sorted by residual: angle pdb=" N GLU A 564 " pdb=" CA GLU A 564 " pdb=" C GLU A 564 " ideal model delta sigma weight residual 114.75 108.40 6.35 1.26e+00 6.30e-01 2.54e+01 angle pdb=" C ARG B 556 " pdb=" CA ARG B 556 " pdb=" CB ARG B 556 " ideal model delta sigma weight residual 116.54 111.42 5.12 1.15e+00 7.56e-01 1.98e+01 angle pdb=" C ARG A 556 " pdb=" CA ARG A 556 " pdb=" CB ARG A 556 " ideal model delta sigma weight residual 116.54 111.46 5.08 1.15e+00 7.56e-01 1.95e+01 angle pdb=" N GLY B 460 " pdb=" CA GLY B 460 " pdb=" C GLY B 460 " ideal model delta sigma weight residual 114.16 108.92 5.24 1.21e+00 6.83e-01 1.87e+01 angle pdb=" N GLY A 460 " pdb=" CA GLY A 460 " pdb=" C GLY A 460 " ideal model delta sigma weight residual 113.99 108.71 5.28 1.28e+00 6.10e-01 1.70e+01 ... (remaining 25593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 10507 18.07 - 36.14: 769 36.14 - 54.21: 123 54.21 - 72.28: 28 72.28 - 90.35: 23 Dihedral angle restraints: 11450 sinusoidal: 4512 harmonic: 6938 Sorted by residual: dihedral pdb=" CA ALA A 563 " pdb=" C ALA A 563 " pdb=" N GLU A 564 " pdb=" CA GLU A 564 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG A 780 " pdb=" C ARG A 780 " pdb=" N PRO A 781 " pdb=" CA PRO A 781 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TYR A 720 " pdb=" C TYR A 720 " pdb=" N PHE A 721 " pdb=" CA PHE A 721 " ideal model delta harmonic sigma weight residual 180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 11447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1915 0.034 - 0.068: 707 0.068 - 0.103: 208 0.103 - 0.137: 88 0.137 - 0.171: 12 Chirality restraints: 2930 Sorted by residual: chirality pdb=" CB THR A 552 " pdb=" CA THR A 552 " pdb=" OG1 THR A 552 " pdb=" CG2 THR A 552 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CB THR B 553 " pdb=" CA THR B 553 " pdb=" OG1 THR B 553 " pdb=" CG2 THR B 553 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CB THR B 552 " pdb=" CA THR B 552 " pdb=" OG1 THR B 552 " pdb=" CG2 THR B 552 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 2927 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 457 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LEU B 457 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU B 457 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 458 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1080 " -0.014 2.00e-02 2.50e+03 1.63e-02 6.64e+00 pdb=" CG TRP B1080 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B1080 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B1080 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B1080 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B1080 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1080 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1080 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1080 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B1080 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 731 " -0.020 2.00e-02 2.50e+03 1.58e-02 4.98e+00 pdb=" CG TYR B 731 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 731 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 731 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 731 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 731 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 731 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 731 " -0.003 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 345 2.69 - 3.24: 18558 3.24 - 3.79: 29933 3.79 - 4.35: 38508 4.35 - 4.90: 63212 Nonbonded interactions: 150556 Sorted by model distance: nonbonded pdb=" O SER B 559 " pdb=" CG2 VAL B 560 " model vdw 2.134 3.460 nonbonded pdb=" O SER A 559 " pdb=" CG2 VAL A 560 " model vdw 2.140 3.460 nonbonded pdb=" O THR B 552 " pdb=" OG1 THR B 553 " model vdw 2.166 3.040 nonbonded pdb=" O THR A 552 " pdb=" OG1 THR A 553 " model vdw 2.177 3.040 nonbonded pdb=" OG SER B1085 " pdb=" OE1 GLU B1088 " model vdw 2.197 3.040 ... (remaining 150551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 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: 1.400 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.650 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.003 0.057 18850 Z= 0.203 Angle : 0.701 9.479 25598 Z= 0.401 Chirality : 0.042 0.171 2930 Planarity : 0.005 0.059 3402 Dihedral : 13.474 90.353 6986 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.18 % Favored : 97.53 % Rotamer: Outliers : 0.47 % Allowed : 0.47 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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: 0.71 (0.17), residues: 2426 helix: 1.51 (0.15), residues: 1162 sheet: -0.22 (0.29), residues: 348 loop : -0.52 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B1080 HIS 0.005 0.001 HIS A 990 PHE 0.020 0.001 PHE A 897 TYR 0.039 0.002 TYR B 731 ARG 0.017 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 396 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8271 (mt) REVERT: A 13 LEU cc_start: 0.8900 (tp) cc_final: 0.8581 (mp) REVERT: A 279 THR cc_start: 0.8165 (p) cc_final: 0.7717 (p) REVERT: A 565 SER cc_start: 0.8071 (m) cc_final: 0.7830 (p) REVERT: A 609 LEU cc_start: 0.9210 (mm) cc_final: 0.8560 (tp) REVERT: A 620 LEU cc_start: 0.8973 (mt) cc_final: 0.8773 (mt) REVERT: A 628 VAL cc_start: 0.8626 (m) cc_final: 0.8033 (m) REVERT: A 833 ASN cc_start: 0.7718 (t0) cc_final: 0.7300 (t0) REVERT: A 843 LEU cc_start: 0.8508 (tp) cc_final: 0.8117 (tp) REVERT: B 77 VAL cc_start: 0.8952 (t) cc_final: 0.8645 (m) REVERT: B 279 THR cc_start: 0.7763 (p) cc_final: 0.7337 (p) REVERT: B 600 MET cc_start: 0.8194 (tpp) cc_final: 0.7193 (ttt) REVERT: B 609 LEU cc_start: 0.8996 (mt) cc_final: 0.8566 (tp) REVERT: B 777 THR cc_start: 0.6301 (p) cc_final: 0.5959 (p) REVERT: B 833 ASN cc_start: 0.8467 (t0) cc_final: 0.8238 (t0) REVERT: B 914 MET cc_start: 0.7546 (mmm) cc_final: 0.7297 (mmm) REVERT: B 930 MET cc_start: 0.8181 (tpt) cc_final: 0.7864 (tpp) REVERT: B 1009 MET cc_start: 0.8090 (mmm) cc_final: 0.7010 (mmp) outliers start: 9 outliers final: 1 residues processed: 404 average time/residue: 0.3344 time to fit residues: 200.3830 Evaluate side-chains 197 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 141 optimal weight: 0.0270 chunk 219 optimal weight: 10.0000 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 500 HIS A 530 GLN A 535 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 HIS ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 ASN B 816 HIS B1048 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18850 Z= 0.284 Angle : 0.642 8.185 25598 Z= 0.335 Chirality : 0.043 0.191 2930 Planarity : 0.005 0.060 3402 Dihedral : 4.420 24.851 2690 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 0.37 % Allowed : 4.58 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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 (0.17), residues: 2426 helix: 1.37 (0.15), residues: 1210 sheet: -0.18 (0.29), residues: 336 loop : -0.55 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 383 HIS 0.007 0.001 HIS A1142 PHE 0.028 0.002 PHE B 29 TYR 0.015 0.002 TYR A 165 ARG 0.016 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 245 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.9055 (tp) cc_final: 0.8757 (mp) REVERT: A 53 MET cc_start: 0.7814 (tpt) cc_final: 0.7114 (tpp) REVERT: A 59 VAL cc_start: 0.6323 (t) cc_final: 0.5883 (t) REVERT: A 609 LEU cc_start: 0.9161 (mm) cc_final: 0.8493 (tp) REVERT: A 764 ILE cc_start: 0.8761 (pt) cc_final: 0.8392 (mm) REVERT: A 914 MET cc_start: 0.7337 (mmp) cc_final: 0.7042 (mmm) REVERT: A 930 MET cc_start: 0.8008 (tpp) cc_final: 0.7754 (tpp) REVERT: A 935 TYR cc_start: 0.8087 (t80) cc_final: 0.7867 (t80) REVERT: B 147 MET cc_start: 0.7199 (mmt) cc_final: 0.6567 (mmm) REVERT: B 609 LEU cc_start: 0.9043 (mt) cc_final: 0.8711 (tp) REVERT: B 632 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8826 (t) REVERT: B 930 MET cc_start: 0.8272 (tpt) cc_final: 0.7988 (tpp) REVERT: B 1009 MET cc_start: 0.7531 (mmm) cc_final: 0.7133 (mmm) outliers start: 7 outliers final: 1 residues processed: 251 average time/residue: 0.2851 time to fit residues: 114.6718 Evaluate side-chains 159 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 0.0000 chunk 68 optimal weight: 7.9990 chunk 182 optimal weight: 0.0060 chunk 149 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 237 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 387 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 459 ASN B 537 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B1048 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18850 Z= 0.200 Angle : 0.579 8.541 25598 Z= 0.299 Chirality : 0.041 0.191 2930 Planarity : 0.005 0.066 3402 Dihedral : 4.272 35.234 2690 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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 (0.17), residues: 2426 helix: 1.55 (0.15), residues: 1190 sheet: -0.12 (0.29), residues: 342 loop : -0.41 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 383 HIS 0.003 0.001 HIS A 485 PHE 0.030 0.002 PHE A 29 TYR 0.038 0.002 TYR A 731 ARG 0.025 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7779 (tpt) cc_final: 0.7024 (tpp) REVERT: A 59 VAL cc_start: 0.6320 (t) cc_final: 0.5816 (t) REVERT: A 565 SER cc_start: 0.8057 (m) cc_final: 0.7672 (p) REVERT: A 609 LEU cc_start: 0.9177 (mm) cc_final: 0.8569 (tp) REVERT: A 764 ILE cc_start: 0.8840 (pt) cc_final: 0.8399 (mm) REVERT: A 914 MET cc_start: 0.7273 (mmp) cc_final: 0.7014 (mmm) REVERT: A 930 MET cc_start: 0.8062 (tpp) cc_final: 0.7802 (tpp) REVERT: A 935 TYR cc_start: 0.8208 (t80) cc_final: 0.7895 (t80) REVERT: B 147 MET cc_start: 0.7158 (mmt) cc_final: 0.6502 (mmm) REVERT: B 165 TYR cc_start: 0.5734 (t80) cc_final: 0.5451 (t80) REVERT: B 218 GLN cc_start: 0.7997 (pt0) cc_final: 0.7794 (pt0) REVERT: B 609 LEU cc_start: 0.8990 (mt) cc_final: 0.8741 (tp) REVERT: B 833 ASN cc_start: 0.8688 (t0) cc_final: 0.8448 (t0) REVERT: B 914 MET cc_start: 0.6847 (mmp) cc_final: 0.6568 (mmm) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.2819 time to fit residues: 103.3381 Evaluate side-chains 155 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 147 optimal weight: 0.3980 chunk 220 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A1048 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18850 Z= 0.260 Angle : 0.606 9.173 25598 Z= 0.311 Chirality : 0.042 0.184 2930 Planarity : 0.005 0.056 3402 Dihedral : 4.315 38.557 2690 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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 (0.17), residues: 2426 helix: 1.53 (0.15), residues: 1202 sheet: -0.35 (0.29), residues: 344 loop : -0.36 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 383 HIS 0.004 0.001 HIS B1025 PHE 0.027 0.002 PHE B 29 TYR 0.039 0.002 TYR A 731 ARG 0.010 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.9279 (tt) cc_final: 0.8837 (mp) REVERT: A 53 MET cc_start: 0.7864 (tpt) cc_final: 0.6955 (tpp) REVERT: A 59 VAL cc_start: 0.6510 (t) cc_final: 0.5798 (t) REVERT: A 565 SER cc_start: 0.8286 (m) cc_final: 0.7881 (p) REVERT: A 609 LEU cc_start: 0.9171 (mm) cc_final: 0.8513 (tp) REVERT: A 914 MET cc_start: 0.7365 (mmp) cc_final: 0.7128 (mmm) REVERT: A 930 MET cc_start: 0.8160 (tpp) cc_final: 0.7788 (tpp) REVERT: A 935 TYR cc_start: 0.8573 (t80) cc_final: 0.8279 (t80) REVERT: B 165 TYR cc_start: 0.5960 (t80) cc_final: 0.5546 (t80) REVERT: B 276 ILE cc_start: 0.9359 (mt) cc_final: 0.9157 (mt) REVERT: B 325 MET cc_start: 0.8205 (tpt) cc_final: 0.7901 (mmm) REVERT: B 609 LEU cc_start: 0.9030 (mt) cc_final: 0.8549 (tp) REVERT: B 833 ASN cc_start: 0.8733 (t0) cc_final: 0.8509 (t0) REVERT: B 1020 MET cc_start: 0.8403 (mmp) cc_final: 0.8138 (mmp) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.2852 time to fit residues: 93.2298 Evaluate side-chains 148 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 3 optimal weight: 9.9990 chunk 174 optimal weight: 0.0070 chunk 96 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN A 794 ASN A 876 ASN A1048 GLN B 472 GLN B 665 ASN B 666 ASN B 695 ASN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18850 Z= 0.214 Angle : 0.576 8.921 25598 Z= 0.296 Chirality : 0.041 0.190 2930 Planarity : 0.004 0.043 3402 Dihedral : 4.243 41.605 2690 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.23 % Favored : 97.61 % Rotamer: Outliers : 0.11 % Allowed : 2.37 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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: 0.83 (0.17), residues: 2426 helix: 1.52 (0.15), residues: 1206 sheet: -0.28 (0.29), residues: 336 loop : -0.37 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 562 HIS 0.003 0.001 HIS B 485 PHE 0.028 0.002 PHE B 689 TYR 0.029 0.002 TYR A 731 ARG 0.007 0.000 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7900 (tpt) cc_final: 0.6972 (tpp) REVERT: A 59 VAL cc_start: 0.6515 (t) cc_final: 0.5856 (t) REVERT: A 565 SER cc_start: 0.8305 (m) cc_final: 0.7834 (p) REVERT: A 747 MET cc_start: 0.8596 (ttp) cc_final: 0.8366 (ttp) REVERT: A 914 MET cc_start: 0.7450 (mmp) cc_final: 0.7123 (mmm) REVERT: A 930 MET cc_start: 0.8166 (tpp) cc_final: 0.7795 (tpp) REVERT: A 935 TYR cc_start: 0.8594 (t80) cc_final: 0.8276 (t80) REVERT: A 1165 ASP cc_start: 0.7026 (t0) cc_final: 0.6728 (t0) REVERT: B 276 ILE cc_start: 0.9373 (mt) cc_final: 0.9130 (mt) REVERT: B 302 ASP cc_start: 0.8141 (t0) cc_final: 0.7897 (m-30) REVERT: B 325 MET cc_start: 0.8243 (tpt) cc_final: 0.7909 (mmm) REVERT: B 815 MET cc_start: 0.5749 (ptp) cc_final: 0.4602 (ptp) REVERT: B 833 ASN cc_start: 0.8747 (t0) cc_final: 0.8517 (t0) REVERT: B 1020 MET cc_start: 0.8380 (mmp) cc_final: 0.8163 (mmp) outliers start: 2 outliers final: 0 residues processed: 199 average time/residue: 0.3095 time to fit residues: 95.4813 Evaluate side-chains 145 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 0.0470 chunk 57 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.9084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 ASN A 876 ASN A1048 GLN B 485 HIS ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN B 686 HIS B 816 HIS B1048 GLN B1142 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18850 Z= 0.211 Angle : 0.570 8.409 25598 Z= 0.292 Chirality : 0.041 0.174 2930 Planarity : 0.004 0.060 3402 Dihedral : 4.222 43.322 2690 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 0.11 % Allowed : 2.32 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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 (0.17), residues: 2426 helix: 1.57 (0.15), residues: 1204 sheet: -0.32 (0.29), residues: 334 loop : -0.34 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 684 HIS 0.009 0.001 HIS B 686 PHE 0.024 0.001 PHE B 29 TYR 0.052 0.002 TYR A 731 ARG 0.015 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.9281 (tt) cc_final: 0.8906 (mp) REVERT: A 53 MET cc_start: 0.7903 (tpt) cc_final: 0.7135 (tpp) REVERT: A 59 VAL cc_start: 0.6572 (t) cc_final: 0.6069 (t) REVERT: A 325 MET cc_start: 0.8372 (tpt) cc_final: 0.7941 (mmm) REVERT: A 565 SER cc_start: 0.8251 (m) cc_final: 0.7859 (p) REVERT: A 914 MET cc_start: 0.7472 (mmp) cc_final: 0.7108 (mmm) REVERT: A 930 MET cc_start: 0.8152 (tpp) cc_final: 0.7769 (tpp) REVERT: A 935 TYR cc_start: 0.8578 (t80) cc_final: 0.8280 (t80) REVERT: A 1169 ARG cc_start: 0.6946 (mpt-90) cc_final: 0.6741 (mtt90) REVERT: B 147 MET cc_start: 0.7220 (mmt) cc_final: 0.6977 (mmt) REVERT: B 276 ILE cc_start: 0.9380 (mt) cc_final: 0.9114 (mt) REVERT: B 302 ASP cc_start: 0.7918 (t0) cc_final: 0.7587 (m-30) REVERT: B 815 MET cc_start: 0.5967 (ptp) cc_final: 0.4938 (ptp) REVERT: B 833 ASN cc_start: 0.8726 (t0) cc_final: 0.8511 (t0) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.2761 time to fit residues: 84.6140 Evaluate side-chains 146 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A1048 GLN ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN B1048 GLN B1142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18850 Z= 0.203 Angle : 0.578 9.089 25598 Z= 0.295 Chirality : 0.041 0.209 2930 Planarity : 0.004 0.041 3402 Dihedral : 4.224 43.933 2690 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.23 % Favored : 97.65 % Rotamer: Outliers : 0.11 % Allowed : 1.63 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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 (0.17), residues: 2426 helix: 1.56 (0.15), residues: 1204 sheet: -0.30 (0.29), residues: 330 loop : -0.35 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 684 HIS 0.005 0.001 HIS B 485 PHE 0.024 0.002 PHE A 847 TYR 0.024 0.002 TYR A 737 ARG 0.006 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.9249 (tt) cc_final: 0.8871 (mp) REVERT: A 53 MET cc_start: 0.7858 (tpt) cc_final: 0.7175 (tpp) REVERT: A 565 SER cc_start: 0.8338 (m) cc_final: 0.7949 (p) REVERT: A 914 MET cc_start: 0.7462 (mmp) cc_final: 0.7077 (mmm) REVERT: A 930 MET cc_start: 0.8151 (tpp) cc_final: 0.7803 (tpp) REVERT: A 935 TYR cc_start: 0.8683 (t80) cc_final: 0.8457 (t80) REVERT: A 1048 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8288 (pp30) REVERT: A 1169 ARG cc_start: 0.7081 (mpt-90) cc_final: 0.6872 (mtt90) REVERT: B 147 MET cc_start: 0.7260 (mmt) cc_final: 0.7006 (mmt) REVERT: B 276 ILE cc_start: 0.9367 (mt) cc_final: 0.9136 (mt) REVERT: B 302 ASP cc_start: 0.7873 (t0) cc_final: 0.7561 (m-30) REVERT: B 458 SER cc_start: 0.8777 (m) cc_final: 0.8503 (t) REVERT: B 815 MET cc_start: 0.6270 (ptp) cc_final: 0.5225 (ptp) REVERT: B 833 ASN cc_start: 0.8751 (t0) cc_final: 0.8539 (t0) REVERT: B 914 MET cc_start: 0.6848 (mmp) cc_final: 0.6643 (mmm) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.3190 time to fit residues: 96.5393 Evaluate side-chains 138 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 30.0000 chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 686 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 ASN A 876 ASN ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN B1048 GLN B1142 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18850 Z= 0.223 Angle : 0.590 10.949 25598 Z= 0.300 Chirality : 0.041 0.191 2930 Planarity : 0.005 0.072 3402 Dihedral : 4.263 44.975 2690 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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: 0.79 (0.17), residues: 2426 helix: 1.52 (0.15), residues: 1206 sheet: -0.42 (0.29), residues: 328 loop : -0.39 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 562 HIS 0.009 0.001 HIS A 686 PHE 0.020 0.001 PHE A 29 TYR 0.053 0.002 TYR A 731 ARG 0.007 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.9274 (tt) cc_final: 0.8886 (mp) REVERT: A 53 MET cc_start: 0.7850 (tpt) cc_final: 0.7586 (tpp) REVERT: A 565 SER cc_start: 0.8334 (m) cc_final: 0.7995 (p) REVERT: A 914 MET cc_start: 0.7450 (mmp) cc_final: 0.7071 (mmm) REVERT: A 930 MET cc_start: 0.8175 (tpp) cc_final: 0.7803 (tpp) REVERT: B 147 MET cc_start: 0.7271 (mmt) cc_final: 0.7033 (mmt) REVERT: B 276 ILE cc_start: 0.9393 (mt) cc_final: 0.9129 (mt) REVERT: B 302 ASP cc_start: 0.7760 (t0) cc_final: 0.7510 (m-30) REVERT: B 815 MET cc_start: 0.6406 (ptp) cc_final: 0.5383 (ptp) REVERT: B 833 ASN cc_start: 0.8783 (t0) cc_final: 0.8569 (t0) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.2871 time to fit residues: 84.2982 Evaluate side-chains 136 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 66 optimal weight: 0.0770 chunk 196 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN B 96 ASN B 280 HIS ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN B1142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18850 Z= 0.351 Angle : 0.678 9.204 25598 Z= 0.351 Chirality : 0.043 0.199 2930 Planarity : 0.005 0.061 3402 Dihedral : 4.766 47.836 2690 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.79 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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: 0.42 (0.17), residues: 2426 helix: 1.24 (0.15), residues: 1200 sheet: -0.54 (0.29), residues: 306 loop : -0.62 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 562 HIS 0.005 0.001 HIS A 392 PHE 0.019 0.002 PHE A 847 TYR 0.021 0.002 TYR B 981 ARG 0.020 0.001 ARG B 953 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7848 (tpt) cc_final: 0.7579 (tpp) REVERT: A 565 SER cc_start: 0.8456 (m) cc_final: 0.8205 (p) REVERT: A 731 TYR cc_start: 0.4696 (t80) cc_final: 0.4328 (t80) REVERT: A 914 MET cc_start: 0.7397 (mmp) cc_final: 0.7012 (mmm) REVERT: B 147 MET cc_start: 0.7391 (mmt) cc_final: 0.7142 (mmt) REVERT: B 276 ILE cc_start: 0.9380 (mt) cc_final: 0.9141 (mp) REVERT: B 539 ASN cc_start: 0.8301 (p0) cc_final: 0.8061 (t0) REVERT: B 815 MET cc_start: 0.6601 (ptp) cc_final: 0.5590 (ptp) REVERT: B 833 ASN cc_start: 0.8839 (t0) cc_final: 0.8627 (t0) REVERT: B 864 ARG cc_start: 0.8139 (mmp-170) cc_final: 0.7787 (mmm160) REVERT: B 914 MET cc_start: 0.7153 (mmp) cc_final: 0.6688 (mmm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2944 time to fit residues: 78.0465 Evaluate side-chains 120 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN A 798 ASN A 876 ASN ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18850 Z= 0.351 Angle : 0.690 9.842 25598 Z= 0.358 Chirality : 0.044 0.184 2930 Planarity : 0.005 0.068 3402 Dihedral : 4.944 49.392 2690 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 0.05 % Allowed : 0.63 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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: 0.11 (0.17), residues: 2426 helix: 1.05 (0.15), residues: 1202 sheet: -0.82 (0.29), residues: 306 loop : -0.83 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 562 HIS 0.005 0.001 HIS B1142 PHE 0.019 0.002 PHE A 29 TYR 0.028 0.002 TYR B 981 ARG 0.010 0.001 ARG A 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7799 (tpt) cc_final: 0.7496 (tpp) REVERT: A 69 MET cc_start: 0.5946 (tpp) cc_final: 0.5649 (tpp) REVERT: A 565 SER cc_start: 0.8351 (m) cc_final: 0.8102 (p) REVERT: A 731 TYR cc_start: 0.4837 (t80) cc_final: 0.4316 (t80) REVERT: A 914 MET cc_start: 0.7340 (mmp) cc_final: 0.6963 (mmm) REVERT: A 930 MET cc_start: 0.8206 (tpp) cc_final: 0.7930 (tpp) REVERT: B 147 MET cc_start: 0.7504 (mmt) cc_final: 0.7239 (mmp) REVERT: B 216 MET cc_start: 0.2656 (mmm) cc_final: 0.2240 (mmm) REVERT: B 539 ASN cc_start: 0.8416 (p0) cc_final: 0.8112 (t0) REVERT: B 699 MET cc_start: 0.8864 (tpt) cc_final: 0.8549 (tpt) REVERT: B 815 MET cc_start: 0.6885 (ptp) cc_final: 0.6057 (ptp) REVERT: B 864 ARG cc_start: 0.7894 (mmp-170) cc_final: 0.7571 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2707 time to fit residues: 68.4801 Evaluate side-chains 115 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 177 optimal weight: 0.0050 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.113383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.088683 restraints weight = 62112.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.088366 restraints weight = 50942.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.089672 restraints weight = 49015.588| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18850 Z= 0.175 Angle : 0.608 8.390 25598 Z= 0.308 Chirality : 0.042 0.171 2930 Planarity : 0.004 0.059 3402 Dihedral : 4.491 46.476 2690 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.17 % 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: 0.57 (0.17), residues: 2426 helix: 1.40 (0.15), residues: 1208 sheet: -0.58 (0.30), residues: 312 loop : -0.59 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 383 HIS 0.004 0.001 HIS B 230 PHE 0.022 0.001 PHE A 29 TYR 0.028 0.002 TYR A 165 ARG 0.007 0.000 ARG B 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.87 seconds wall clock time: 60 minutes 37.18 seconds (3637.18 seconds total)