Starting phenix.real_space_refine on Sun Mar 17 18:13:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/03_2024/8hjw_34840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/03_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_34840/03_2024/8hjw_34840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/03_2024/8hjw_34840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/03_2024/8hjw_34840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjw_34840/03_2024/8hjw_34840.pdb" } 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 Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A GLU 1202": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B GLU 944": "OE1" <-> "OE2" Residue "B GLU 1153": "OE1" <-> "OE2" Residue "B GLU 1184": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.69, per 1000 atoms: 0.52 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 - 3.50 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: 7.53 Conformation dependent library (CDL) restraints added in 3.9 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: 2.23 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: 7.01 Time building geometry restraints manager: 8.23 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: 98.31 - 105.45: 450 105.45 - 112.59: 9763 112.59 - 119.73: 6431 119.73 - 126.87: 8738 126.87 - 134.00: 216 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 2.440 nonbonded pdb=" O THR A 552 " pdb=" OG1 THR A 553 " model vdw 2.177 2.440 nonbonded pdb=" OG SER B1085 " pdb=" OE1 GLU B1088 " model vdw 2.197 2.440 ... (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 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: 2.500 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.800 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 51.180 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.630 ------------------------------------------------------------------------------- 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 : 2.212 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: 0.3303 time to fit residues: 198.2850 Evaluate side-chains 197 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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: 2.9990 chunk 183 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 500 HIS ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** 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** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 HIS ** 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 B1048 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18850 Z= 0.254 Angle : 0.617 8.395 25598 Z= 0.320 Chirality : 0.042 0.183 2930 Planarity : 0.005 0.045 3402 Dihedral : 4.371 33.109 2690 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.47 % Favored : 97.40 % Rotamer: Outliers : 0.32 % Allowed : 4.89 % Favored : 94.79 % 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: 0.78 (0.17), residues: 2426 helix: 1.45 (0.15), residues: 1202 sheet: -0.20 (0.29), residues: 346 loop : -0.40 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1080 HIS 0.008 0.001 HIS A 633 PHE 0.029 0.002 PHE B 29 TYR 0.015 0.002 TYR A 165 ARG 0.017 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 256 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 250 time to evaluate : 1.920 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: A 13 LEU cc_start: 0.9041 (tp) cc_final: 0.8762 (mp) REVERT: A 53 MET cc_start: 0.7795 (tpt) cc_final: 0.7138 (tpp) REVERT: A 59 VAL cc_start: 0.6256 (t) cc_final: 0.5817 (t) REVERT: A 609 LEU cc_start: 0.9176 (mm) cc_final: 0.8521 (tp) REVERT: A 764 ILE cc_start: 0.8662 (pt) cc_final: 0.8394 (mm) REVERT: A 833 ASN cc_start: 0.7773 (t0) cc_final: 0.7487 (t0) REVERT: A 930 MET cc_start: 0.7959 (tpp) cc_final: 0.7705 (tpp) REVERT: A 935 TYR cc_start: 0.8005 (t80) cc_final: 0.7802 (t80) REVERT: B 147 MET cc_start: 0.7110 (mmt) cc_final: 0.6481 (mmm) REVERT: B 609 LEU cc_start: 0.8976 (mt) cc_final: 0.8659 (tp) REVERT: B 914 MET cc_start: 0.7560 (mmm) cc_final: 0.7357 (mmm) REVERT: B 930 MET cc_start: 0.8247 (tpt) cc_final: 0.7966 (tpp) REVERT: B 1009 MET cc_start: 0.7551 (mmm) cc_final: 0.7145 (mmm) REVERT: B 1106 LYS cc_start: 0.8884 (tptp) cc_final: 0.8651 (tppt) outliers start: 6 outliers final: 1 residues processed: 255 average time/residue: 0.2807 time to fit residues: 113.5029 Evaluate side-chains 166 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 2.074 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 176 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 179 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 466 ASN ** A 530 GLN ** 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 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN B 537 HIS ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN B 794 ASN B1048 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18850 Z= 0.227 Angle : 0.584 8.513 25598 Z= 0.300 Chirality : 0.041 0.192 2930 Planarity : 0.005 0.065 3402 Dihedral : 4.280 36.933 2690 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.42 % 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: 0.92 (0.17), residues: 2426 helix: 1.57 (0.15), residues: 1200 sheet: -0.10 (0.29), residues: 340 loop : -0.33 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1080 HIS 0.003 0.001 HIS B 88 PHE 0.031 0.002 PHE A 29 TYR 0.039 0.002 TYR B 165 ARG 0.014 0.001 ARG B 168 *********************** 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 223 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 2.205 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: A 53 MET cc_start: 0.7759 (tpt) cc_final: 0.6973 (tpp) REVERT: A 59 VAL cc_start: 0.6365 (t) cc_final: 0.5864 (t) REVERT: A 200 PHE cc_start: 0.8541 (m-80) cc_final: 0.8307 (m-80) REVERT: A 565 SER cc_start: 0.8114 (m) cc_final: 0.7767 (p) REVERT: A 609 LEU cc_start: 0.9168 (mm) cc_final: 0.8539 (tp) REVERT: A 715 LEU cc_start: 0.9134 (tt) cc_final: 0.8836 (tt) REVERT: A 764 ILE cc_start: 0.8774 (pt) cc_final: 0.8515 (mp) REVERT: A 930 MET cc_start: 0.8125 (tpp) cc_final: 0.7813 (tpp) REVERT: A 935 TYR cc_start: 0.8356 (t80) cc_final: 0.7700 (t80) REVERT: B 147 MET cc_start: 0.7145 (mmt) cc_final: 0.6492 (mmm) REVERT: B 279 THR cc_start: 0.8125 (p) cc_final: 0.7370 (p) REVERT: B 458 SER cc_start: 0.8354 (m) cc_final: 0.8067 (t) REVERT: B 609 LEU cc_start: 0.8991 (mt) cc_final: 0.8709 (tp) REVERT: B 815 MET cc_start: 0.6739 (ptp) cc_final: 0.6515 (ptp) REVERT: B 833 ASN cc_start: 0.8647 (t0) cc_final: 0.8403 (t0) REVERT: B 1217 ILE cc_start: 0.7412 (pt) cc_final: 0.7194 (mt) outliers start: 2 outliers final: 1 residues processed: 222 average time/residue: 0.2861 time to fit residues: 100.6774 Evaluate side-chains 156 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.925 ------------------------------------------------------------------------------- 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: 6.9990 chunk 165 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 209 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 ASN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A1142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 508 ASN B 537 HIS B 570 HIS B 613 GLN ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1099 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18850 Z= 0.378 Angle : 0.713 9.053 25598 Z= 0.368 Chirality : 0.044 0.217 2930 Planarity : 0.006 0.136 3402 Dihedral : 4.971 46.387 2690 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.67 % Favored : 96.13 % Rotamer: Outliers : 0.26 % Allowed : 4.42 % Favored : 95.32 % 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: 0.37 (0.17), residues: 2426 helix: 1.13 (0.14), residues: 1214 sheet: -0.55 (0.28), residues: 332 loop : -0.55 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 562 HIS 0.007 0.001 HIS B 392 PHE 0.026 0.003 PHE B 29 TYR 0.032 0.003 TYR A 731 ARG 0.018 0.001 ARG A 734 *********************** 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 179 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 2.123 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: 0.7934 (tpt) cc_final: 0.7148 (tpp) REVERT: A 77 VAL cc_start: 0.9361 (t) cc_final: 0.9034 (t) REVERT: A 552 THR cc_start: 0.7293 (p) cc_final: 0.6965 (p) REVERT: A 565 SER cc_start: 0.8626 (m) cc_final: 0.8295 (p) REVERT: A 699 MET cc_start: 0.8817 (tpt) cc_final: 0.8572 (tpt) REVERT: A 833 ASN cc_start: 0.8064 (t0) cc_final: 0.7631 (t0) REVERT: A 914 MET cc_start: 0.7197 (mmp) cc_final: 0.6966 (mmp) REVERT: A 930 MET cc_start: 0.8233 (tpp) cc_final: 0.7823 (tpp) REVERT: A 1165 ASP cc_start: 0.8311 (m-30) cc_final: 0.7850 (m-30) REVERT: B 147 MET cc_start: 0.7248 (mmt) cc_final: 0.7014 (mmt) REVERT: B 833 ASN cc_start: 0.8749 (t0) cc_final: 0.8519 (t0) REVERT: B 930 MET cc_start: 0.8278 (tpp) cc_final: 0.8063 (tpp) outliers start: 5 outliers final: 2 residues processed: 177 average time/residue: 0.2940 time to fit residues: 81.9089 Evaluate side-chains 135 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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: 20.0000 chunk 3 optimal weight: 10.0000 chunk 174 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 209 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** 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 716 ASN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A1142 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 472 GLN ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18850 Z= 0.264 Angle : 0.603 8.584 25598 Z= 0.311 Chirality : 0.041 0.170 2930 Planarity : 0.005 0.044 3402 Dihedral : 4.652 46.429 2690 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.89 % Favored : 96.91 % Rotamer: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.26 % 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: 0.60 (0.17), residues: 2426 helix: 1.38 (0.15), residues: 1200 sheet: -0.43 (0.29), residues: 316 loop : -0.53 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 506 HIS 0.005 0.001 HIS B 230 PHE 0.026 0.002 PHE B 29 TYR 0.034 0.002 TYR A 731 ARG 0.008 0.001 ARG A 306 *********************** 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 169 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 2.289 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: 0.7834 (tpt) cc_final: 0.7082 (tpp) REVERT: A 216 MET cc_start: 0.1556 (mmm) cc_final: 0.1318 (mmm) REVERT: A 552 THR cc_start: 0.7490 (p) cc_final: 0.7030 (p) REVERT: A 565 SER cc_start: 0.8514 (m) cc_final: 0.8183 (p) REVERT: A 833 ASN cc_start: 0.8054 (t0) cc_final: 0.7606 (t0) REVERT: A 914 MET cc_start: 0.7233 (mmp) cc_final: 0.6855 (mmp) REVERT: A 930 MET cc_start: 0.8221 (tpp) cc_final: 0.7841 (tpp) REVERT: A 1165 ASP cc_start: 0.8303 (m-30) cc_final: 0.7861 (m-30) REVERT: B 147 MET cc_start: 0.7299 (mmt) cc_final: 0.7072 (mmp) REVERT: B 165 TYR cc_start: 0.6905 (t80) cc_final: 0.6652 (t80) REVERT: B 539 ASN cc_start: 0.8301 (p0) cc_final: 0.8060 (t0) REVERT: B 833 ASN cc_start: 0.8754 (t0) cc_final: 0.8513 (t0) REVERT: B 930 MET cc_start: 0.8221 (tpp) cc_final: 0.7941 (tpp) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.2731 time to fit residues: 75.1153 Evaluate side-chains 126 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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: 0.9980 chunk 210 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.0670 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 HIS ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS ** 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 ** A1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN B 686 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B1142 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5115 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= 0.180 Angle : 0.571 12.968 25598 Z= 0.288 Chirality : 0.040 0.200 2930 Planarity : 0.004 0.043 3402 Dihedral : 4.295 44.211 2690 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.64 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 0.85 (0.17), residues: 2426 helix: 1.56 (0.15), residues: 1204 sheet: -0.25 (0.29), residues: 324 loop : -0.40 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 684 HIS 0.010 0.001 HIS A 686 PHE 0.029 0.002 PHE B 689 TYR 0.023 0.002 TYR A 731 ARG 0.005 0.000 ARG A1169 *********************** 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 172 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.220 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 13 LEU cc_start: 0.9303 (tt) cc_final: 0.8898 (mp) REVERT: A 53 MET cc_start: 0.7908 (tpt) cc_final: 0.7223 (tpp) REVERT: A 216 MET cc_start: 0.1475 (mmm) cc_final: 0.1224 (mmm) REVERT: A 565 SER cc_start: 0.8394 (m) cc_final: 0.7874 (p) REVERT: A 833 ASN cc_start: 0.8107 (t0) cc_final: 0.7659 (t0) REVERT: A 914 MET cc_start: 0.7188 (mmp) cc_final: 0.6904 (mmp) REVERT: A 930 MET cc_start: 0.8101 (tpp) cc_final: 0.7739 (tpp) REVERT: A 1165 ASP cc_start: 0.8256 (m-30) cc_final: 0.7808 (m-30) REVERT: B 147 MET cc_start: 0.7302 (mmt) cc_final: 0.7066 (mmp) REVERT: B 165 TYR cc_start: 0.6880 (t80) cc_final: 0.6488 (t80) REVERT: B 279 THR cc_start: 0.8435 (p) cc_final: 0.7942 (p) REVERT: B 458 SER cc_start: 0.8621 (m) cc_final: 0.8371 (t) REVERT: B 815 MET cc_start: 0.6093 (ptp) cc_final: 0.5866 (ptp) REVERT: B 833 ASN cc_start: 0.8766 (t0) cc_final: 0.8526 (t0) REVERT: B 930 MET cc_start: 0.8168 (tpp) cc_final: 0.7506 (tpp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2699 time to fit residues: 76.5095 Evaluate side-chains 136 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 HIS ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18850 Z= 0.301 Angle : 0.618 8.489 25598 Z= 0.318 Chirality : 0.041 0.189 2930 Planarity : 0.005 0.039 3402 Dihedral : 4.584 46.285 2690 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.71 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 0.66 (0.17), residues: 2426 helix: 1.44 (0.15), residues: 1206 sheet: -0.54 (0.29), residues: 320 loop : -0.46 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 562 HIS 0.006 0.001 HIS A 537 PHE 0.029 0.002 PHE A 847 TYR 0.017 0.002 TYR A 731 ARG 0.010 0.001 ARG B 590 *********************** 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 159 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.549 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: 0.7921 (tpt) cc_final: 0.7274 (tpp) REVERT: A 216 MET cc_start: 0.1811 (mmm) cc_final: 0.1544 (mmm) REVERT: A 565 SER cc_start: 0.8538 (m) cc_final: 0.8112 (p) REVERT: A 914 MET cc_start: 0.7278 (mmp) cc_final: 0.6943 (mmp) REVERT: A 1165 ASP cc_start: 0.8326 (m-30) cc_final: 0.7892 (m-30) REVERT: B 147 MET cc_start: 0.7340 (mmt) cc_final: 0.7111 (mmp) REVERT: B 165 TYR cc_start: 0.6988 (t80) cc_final: 0.6424 (t80) REVERT: B 539 ASN cc_start: 0.8476 (p0) cc_final: 0.7858 (t0) REVERT: B 815 MET cc_start: 0.6285 (ptp) cc_final: 0.5974 (ptp) REVERT: B 833 ASN cc_start: 0.8772 (t0) cc_final: 0.8551 (t0) REVERT: B 864 ARG cc_start: 0.8459 (mmt90) cc_final: 0.8169 (mmp80) REVERT: B 914 MET cc_start: 0.7216 (mmp) cc_final: 0.6922 (mmm) REVERT: B 930 MET cc_start: 0.7895 (tpp) cc_final: 0.7586 (tpp) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2923 time to fit residues: 74.7989 Evaluate side-chains 120 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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: 6.9990 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** 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 798 ASN A 876 ASN ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5860 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= 0.220 Angle : 0.583 8.707 25598 Z= 0.297 Chirality : 0.041 0.173 2930 Planarity : 0.004 0.067 3402 Dihedral : 4.451 45.876 2690 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 0.76 (0.17), residues: 2426 helix: 1.51 (0.15), residues: 1206 sheet: -0.44 (0.29), residues: 328 loop : -0.43 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 562 HIS 0.007 0.001 HIS B 633 PHE 0.022 0.002 PHE A 29 TYR 0.019 0.002 TYR A 934 ARG 0.006 0.000 ARG A 306 *********************** 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 162 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7901 (tpt) cc_final: 0.7623 (tpp) REVERT: A 216 MET cc_start: 0.1770 (mmm) cc_final: 0.1509 (mmm) REVERT: A 565 SER cc_start: 0.8585 (m) cc_final: 0.8079 (p) REVERT: A 833 ASN cc_start: 0.8192 (t0) cc_final: 0.7783 (t0) REVERT: A 914 MET cc_start: 0.7215 (mmp) cc_final: 0.6917 (mmp) REVERT: A 930 MET cc_start: 0.8093 (tpp) cc_final: 0.7852 (tpp) REVERT: A 964 PHE cc_start: 0.6133 (p90) cc_final: 0.5681 (p90) REVERT: A 1165 ASP cc_start: 0.8468 (m-30) cc_final: 0.8020 (m-30) REVERT: B 147 MET cc_start: 0.7361 (mmt) cc_final: 0.7145 (mmp) REVERT: B 165 TYR cc_start: 0.6928 (t80) cc_final: 0.6333 (t80) REVERT: B 625 TYR cc_start: 0.7418 (m-80) cc_final: 0.7184 (m-80) REVERT: B 833 ASN cc_start: 0.8797 (t0) cc_final: 0.8576 (t0) REVERT: B 914 MET cc_start: 0.7140 (mmp) cc_final: 0.6885 (mmm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2775 time to fit residues: 73.5682 Evaluate side-chains 125 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.130 ------------------------------------------------------------------------------- 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: 0.9990 chunk 203 optimal weight: 4.9990 chunk 217 optimal weight: 0.3980 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 0.3980 chunk 170 optimal weight: 10.0000 chunk 66 optimal weight: 0.0470 chunk 196 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** 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 876 ASN A1100 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B 986 HIS ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18850 Z= 0.176 Angle : 0.584 9.066 25598 Z= 0.295 Chirality : 0.041 0.172 2930 Planarity : 0.005 0.187 3402 Dihedral : 4.344 44.531 2690 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.60 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.57 (0.15), residues: 1204 sheet: -0.42 (0.28), residues: 344 loop : -0.39 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 562 HIS 0.005 0.001 HIS A 875 PHE 0.035 0.002 PHE A 689 TYR 0.017 0.002 TYR A 731 ARG 0.006 0.000 ARG B 162 *********************** 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 164 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7857 (tpt) cc_final: 0.7592 (tpp) REVERT: A 69 MET cc_start: 0.6212 (tpp) cc_final: 0.5818 (tpp) REVERT: A 216 MET cc_start: 0.1755 (mmm) cc_final: 0.1530 (mmm) REVERT: A 391 ILE cc_start: 0.5454 (mp) cc_final: 0.5157 (mm) REVERT: A 565 SER cc_start: 0.8467 (m) cc_final: 0.7977 (p) REVERT: A 833 ASN cc_start: 0.8237 (t0) cc_final: 0.7833 (t0) REVERT: A 914 MET cc_start: 0.7143 (mmp) cc_final: 0.6819 (mmp) REVERT: A 930 MET cc_start: 0.8023 (tpp) cc_final: 0.7739 (tpp) REVERT: A 1165 ASP cc_start: 0.8472 (m-30) cc_final: 0.8044 (m-30) REVERT: B 147 MET cc_start: 0.7311 (mmt) cc_final: 0.7109 (mmp) REVERT: B 165 TYR cc_start: 0.6954 (t80) cc_final: 0.6361 (t80) REVERT: B 279 THR cc_start: 0.8690 (p) cc_final: 0.8231 (p) REVERT: B 458 SER cc_start: 0.8634 (m) cc_final: 0.8402 (t) REVERT: B 833 ASN cc_start: 0.8768 (t0) cc_final: 0.8553 (t0) REVERT: B 914 MET cc_start: 0.7067 (mmp) cc_final: 0.6820 (mmm) REVERT: B 1009 MET cc_start: 0.8141 (tpp) cc_final: 0.7831 (mmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2708 time to fit residues: 72.7956 Evaluate side-chains 132 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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: 9.9990 chunk 140 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** 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 733 ASN A 794 ASN A 876 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18850 Z= 0.259 Angle : 0.613 8.444 25598 Z= 0.313 Chirality : 0.042 0.184 2930 Planarity : 0.005 0.060 3402 Dihedral : 4.492 45.911 2690 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.63 % Favored : 96.21 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % 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: 0.75 (0.17), residues: 2426 helix: 1.54 (0.15), residues: 1208 sheet: -0.50 (0.28), residues: 340 loop : -0.47 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 562 HIS 0.005 0.001 HIS A 537 PHE 0.023 0.002 PHE B 29 TYR 0.029 0.002 TYR B 165 ARG 0.009 0.000 ARG B 236 ********************** 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 153 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7812 (tpt) cc_final: 0.7544 (tpp) REVERT: A 69 MET cc_start: 0.6288 (tpp) cc_final: 0.5965 (tpp) REVERT: A 216 MET cc_start: 0.2012 (mmm) cc_final: 0.1456 (mmm) REVERT: A 565 SER cc_start: 0.8504 (m) cc_final: 0.8121 (p) REVERT: A 675 MET cc_start: 0.7522 (tpp) cc_final: 0.7215 (tpp) REVERT: A 833 ASN cc_start: 0.8306 (t0) cc_final: 0.7931 (t0) REVERT: A 914 MET cc_start: 0.7140 (mmp) cc_final: 0.6869 (mmp) REVERT: A 930 MET cc_start: 0.8077 (tpp) cc_final: 0.7759 (tpp) REVERT: A 1165 ASP cc_start: 0.8513 (m-30) cc_final: 0.8102 (m-30) REVERT: B 147 MET cc_start: 0.7423 (mmt) cc_final: 0.7158 (mmp) REVERT: B 539 ASN cc_start: 0.8457 (p0) cc_final: 0.7890 (t0) REVERT: B 833 ASN cc_start: 0.8816 (t0) cc_final: 0.8596 (t0) REVERT: B 914 MET cc_start: 0.7094 (mmp) cc_final: 0.6801 (mmm) REVERT: B 1009 MET cc_start: 0.8264 (tpp) cc_final: 0.7994 (mmm) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.2659 time to fit residues: 66.3091 Evaluate side-chains 121 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 HIS ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN A 876 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.113694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.091374 restraints weight = 61786.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088842 restraints weight = 80276.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.088303 restraints weight = 57157.154| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18850 Z= 0.189 Angle : 0.580 8.380 25598 Z= 0.294 Chirality : 0.041 0.172 2930 Planarity : 0.004 0.056 3402 Dihedral : 4.340 45.164 2690 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.76 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.86 (0.17), residues: 2426 helix: 1.61 (0.15), residues: 1206 sheet: -0.32 (0.29), residues: 338 loop : -0.44 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 562 HIS 0.006 0.001 HIS A 607 PHE 0.022 0.002 PHE B 29 TYR 0.026 0.002 TYR B 934 ARG 0.010 0.000 ARG B 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.85 seconds wall clock time: 57 minutes 20.86 seconds (3440.86 seconds total)