Starting phenix.real_space_refine on Sat Feb 17 22:11:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn4_14800/02_2024/7zn4_14800.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn4_14800/02_2024/7zn4_14800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn4_14800/02_2024/7zn4_14800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn4_14800/02_2024/7zn4_14800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn4_14800/02_2024/7zn4_14800.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn4_14800/02_2024/7zn4_14800.pdb" } resolution = 4.32 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= 0.001 sd= 0.004 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 50 5.16 5 C 12717 2.51 5 N 3348 2.21 5 O 3874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 632": "OD1" <-> "OD2" Residue "e PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 303": "OD1" <-> "OD2" Residue "e TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19989 Number of models: 1 Model: "" Number of chains: 6 Chain: "d" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1688 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "b" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1761 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "f" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5143 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 34, 'TRANS': 634} Chain breaks: 2 Chain: "e" Number of atoms: 5163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5163 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 34, 'TRANS': 636} Chain breaks: 2 Chain: "g" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4546 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 26, 'TRANS': 562} Chain breaks: 2 Chain: "c" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1688 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Time building chain proxies: 10.46, per 1000 atoms: 0.52 Number of scatterers: 19989 At special positions: 0 Unit cell: (214.809, 148.61, 124.292, 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 50 16.00 O 3874 8.00 N 3348 7.00 C 12717 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: 7.96 Conformation dependent library (CDL) restraints added in 3.6 seconds 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4738 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 44 sheets defined 7.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'd' and resid 907 through 914 removed outlier: 3.590A pdb=" N ASN d 911 " --> pdb=" O LEU d 907 " (cutoff:3.500A) Processing helix chain 'b' and resid 907 through 913 Processing helix chain 'b' and resid 914 through 921 removed outlier: 3.677A pdb=" N LEU b 918 " --> pdb=" O ASP b 914 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 90 Processing helix chain 'f' and resid 258 through 264 Processing helix chain 'f' and resid 302 through 305 Processing helix chain 'f' and resid 325 through 330 removed outlier: 3.640A pdb=" N ASN f 329 " --> pdb=" O ASN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 579 through 592 Processing helix chain 'f' and resid 661 through 667 Processing helix chain 'f' and resid 669 through 673 Processing helix chain 'e' and resid 83 through 90 Processing helix chain 'e' and resid 258 through 264 Processing helix chain 'e' and resid 325 through 330 Processing helix chain 'e' and resid 579 through 591 Processing helix chain 'e' and resid 662 through 668 Processing helix chain 'g' and resid 83 through 90 Processing helix chain 'g' and resid 258 through 265 Processing helix chain 'g' and resid 302 through 305 Processing helix chain 'g' and resid 325 through 330 removed outlier: 4.353A pdb=" N ASN g 329 " --> pdb=" O ASN g 325 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU g 330 " --> pdb=" O SER g 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 325 through 330' Processing helix chain 'g' and resid 579 through 591 removed outlier: 3.723A pdb=" N ALA g 583 " --> pdb=" O ASN g 579 " (cutoff:3.500A) Processing helix chain 'g' and resid 661 through 667 Processing helix chain 'g' and resid 669 through 673 removed outlier: 3.580A pdb=" N GLY g 672 " --> pdb=" O ASN g 669 " (cutoff:3.500A) Processing helix chain 'c' and resid 907 through 914 Processing helix chain 'c' and resid 915 through 921 Processing sheet with id=AA1, first strand: chain 'd' and resid 742 through 745 removed outlier: 3.655A pdb=" N LYS d 743 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER d 762 " --> pdb=" O LYS d 743 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR d 745 " --> pdb=" O GLU d 760 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU d 760 " --> pdb=" O THR d 745 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP d 763 " --> pdb=" O MET d 798 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 785 through 788 removed outlier: 3.685A pdb=" N ALA d 777 " --> pdb=" O GLU d 813 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU d 813 " --> pdb=" O ALA d 777 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA d 810 " --> pdb=" O VAL d 831 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL d 831 " --> pdb=" O ALA d 810 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL d 827 " --> pdb=" O LEU d 814 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 845 through 847 Processing sheet with id=AA4, first strand: chain 'd' and resid 892 through 898 removed outlier: 3.533A pdb=" N ARG d 894 " --> pdb=" O ILE d 885 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG d 932 " --> pdb=" O GLU d 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 731 through 734 removed outlier: 3.672A pdb=" N GLU c 899 " --> pdb=" O ASP b 731 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE c 885 " --> pdb=" O LEU c 893 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER c 895 " --> pdb=" O LEU c 883 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU c 883 " --> pdb=" O SER c 895 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG c 897 " --> pdb=" O TYR c 881 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR c 881 " --> pdb=" O ARG c 897 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU c 899 " --> pdb=" O ILE c 879 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE c 879 " --> pdb=" O GLU c 899 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 743 through 745 Processing sheet with id=AA7, first strand: chain 'b' and resid 785 through 788 removed outlier: 4.279A pdb=" N TYR b 773 " --> pdb=" O VAL b 817 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL b 817 " --> pdb=" O TYR b 773 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU b 813 " --> pdb=" O ALA b 777 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 846 through 847 Processing sheet with id=AA9, first strand: chain 'b' and resid 893 through 899 removed outlier: 3.509A pdb=" N ILE b 885 " --> pdb=" O LEU b 893 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER b 895 " --> pdb=" O LEU b 883 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU b 883 " --> pdb=" O SER b 895 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG b 897 " --> pdb=" O TYR b 881 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR b 881 " --> pdb=" O ARG b 897 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU b 899 " --> pdb=" O ILE b 879 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE b 879 " --> pdb=" O GLU b 899 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 16 through 18 Processing sheet with id=AB2, first strand: chain 'f' and resid 46 through 52 removed outlier: 3.872A pdb=" N GLY f 36 " --> pdb=" O TYR f 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 71 through 72 removed outlier: 3.990A pdb=" N PHE f 101 " --> pdb=" O TYR f 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 108 through 116 removed outlier: 6.506A pdb=" N ASP f 131 " --> pdb=" O THR f 110 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA f 112 " --> pdb=" O TYR f 129 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR f 129 " --> pdb=" O ALA f 112 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N CYS f 114 " --> pdb=" O ILE f 127 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE f 127 " --> pdb=" O CYS f 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 153 through 157 removed outlier: 5.638A pdb=" N LYS f 155 " --> pdb=" O LEU f 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU f 143 " --> pdb=" O LYS f 155 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR f 138 " --> pdb=" O GLN f 182 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN f 182 " --> pdb=" O TYR f 138 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR f 140 " --> pdb=" O SER f 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 173 through 175 Processing sheet with id=AB7, first strand: chain 'f' and resid 217 through 222 removed outlier: 4.044A pdb=" N ASN f 217 " --> pdb=" O ASP f 239 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN f 237 " --> pdb=" O VAL f 219 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'f' and resid 250 through 257 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 271 through 274 current: chain 'f' and resid 307 through 309 Processing sheet with id=AB9, first strand: chain 'f' and resid 331 through 335 removed outlier: 6.411A pdb=" N ILE f 340 " --> pdb=" O LEU f 355 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU f 355 " --> pdb=" O ILE f 340 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY f 342 " --> pdb=" O THR f 353 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'f' and resid 376 through 379 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 384 through 387 current: chain 'f' and resid 428 through 433 removed outlier: 3.535A pdb=" N GLY f 431 " --> pdb=" O LYS f 440 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 457 through 459 current: chain 'f' and resid 627 through 629 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 627 through 629 current: chain 'f' and resid 676 through 679 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 684 through 687 current: chain 'e' and resid 339 through 346 removed outlier: 6.998A pdb=" N ILE e 340 " --> pdb=" O LEU e 355 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU e 355 " --> pdb=" O ILE e 340 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY e 342 " --> pdb=" O THR e 353 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE e 376 " --> pdb=" O ILE e 365 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 384 through 393 current: chain 'e' and resid 427 through 433 removed outlier: 3.739A pdb=" N GLY e 427 " --> pdb=" O GLY e 444 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS e 438 " --> pdb=" O ASP e 433 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 457 through 459 current: chain 'e' and resid 627 through 629 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 627 through 629 current: chain 'e' and resid 677 through 678 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 677 through 678 current: chain 'g' and resid 339 through 345 removed outlier: 3.587A pdb=" N PHE g 354 " --> pdb=" O GLY g 342 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE g 344 " --> pdb=" O GLN g 352 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN g 352 " --> pdb=" O ILE g 344 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE g 363 " --> pdb=" O PHE g 378 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE g 376 " --> pdb=" O ILE g 365 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 384 through 387 current: chain 'g' and resid 427 through 431 removed outlier: 3.546A pdb=" N GLY g 427 " --> pdb=" O GLY g 444 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 456 through 459 current: chain 'g' and resid 627 through 629 Processing sheet with id=AC2, first strand: chain 'f' and resid 484 through 488 removed outlier: 3.876A pdb=" N TYR f 487 " --> pdb=" O ILE f 521 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE f 521 " --> pdb=" O TYR f 487 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 528 through 529 removed outlier: 3.556A pdb=" N GLN f 534 " --> pdb=" O ASP f 529 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'f' and resid 567 through 572 Processing sheet with id=AC5, first strand: chain 'e' and resid 12 through 17 Processing sheet with id=AC6, first strand: chain 'e' and resid 47 through 53 removed outlier: 4.025A pdb=" N ARG e 37 " --> pdb=" O PHE e 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 71 through 73 Processing sheet with id=AC8, first strand: chain 'e' and resid 109 through 113 removed outlier: 6.718A pdb=" N ASP e 131 " --> pdb=" O THR e 110 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA e 112 " --> pdb=" O TYR e 129 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR e 129 " --> pdb=" O ALA e 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 138 through 145 removed outlier: 7.056A pdb=" N CYS e 139 " --> pdb=" O VAL e 158 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL e 158 " --> pdb=" O CYS e 139 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE e 141 " --> pdb=" O TYR e 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 154 through 159 current: chain 'e' and resid 191 through 192 Processing sheet with id=AD1, first strand: chain 'e' and resid 216 through 222 removed outlier: 4.236A pdb=" N ILE e 218 " --> pdb=" O GLN e 237 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN e 237 " --> pdb=" O ILE e 218 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE e 220 " --> pdb=" O ARG e 235 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG e 235 " --> pdb=" O PHE e 220 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 248 through 257 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 270 through 274 current: chain 'e' and resid 308 through 309 Processing sheet with id=AD3, first strand: chain 'e' and resid 481 through 482 removed outlier: 3.513A pdb=" N GLN e 534 " --> pdb=" O ASP e 529 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'e' and resid 485 through 486 removed outlier: 4.006A pdb=" N PHE e 485 " --> pdb=" O CYS e 523 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS e 523 " --> pdb=" O PHE e 485 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 567 through 572 removed outlier: 3.599A pdb=" N ASP e 599 " --> pdb=" O TRP e 617 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR e 611 " --> pdb=" O LYS e 605 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'g' and resid 12 through 14 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 12 through 14 current: chain 'g' and resid 21 through 26 Processing sheet with id=AD7, first strand: chain 'g' and resid 46 through 53 removed outlier: 3.634A pdb=" N GLY g 36 " --> pdb=" O TYR g 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 108 through 116 removed outlier: 5.363A pdb=" N ILE g 109 " --> pdb=" O THR g 133 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR g 133 " --> pdb=" O ILE g 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 138 through 139 removed outlier: 3.642A pdb=" N TYR g 138 " --> pdb=" O GLN g 182 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR g 190 " --> pdb=" O LEU g 185 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'g' and resid 141 through 145 removed outlier: 7.005A pdb=" N ILE g 141 " --> pdb=" O TYR g 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 154 through 157 current: chain 'g' and resid 197 through 198 Processing sheet with id=AE2, first strand: chain 'g' and resid 217 through 223 removed outlier: 3.687A pdb=" N ASN g 217 " --> pdb=" O ASP g 239 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA g 223 " --> pdb=" O ASP g 233 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'g' and resid 252 through 257 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 270 through 273 current: chain 'g' and resid 307 through 309 Processing sheet with id=AE4, first strand: chain 'g' and resid 567 through 572 removed outlier: 4.170A pdb=" N LYS g 605 " --> pdb=" O THR g 611 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR g 611 " --> pdb=" O LYS g 605 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'g' and resid 675 through 678 removed outlier: 3.613A pdb=" N ILE g 678 " --> pdb=" O TYR g 684 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 740 through 745 removed outlier: 3.846A pdb=" N PHE c 742 " --> pdb=" O SER c 762 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER c 762 " --> pdb=" O PHE c 742 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR c 744 " --> pdb=" O GLU c 760 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU c 760 " --> pdb=" O TYR c 744 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 785 through 788 Processing sheet with id=AE8, first strand: chain 'c' and resid 845 through 847 451 hydrogen bonds defined for protein. 1173 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: 8.57 Time building geometry restraints manager: 8.43 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: 6517 1.34 - 1.46: 4266 1.46 - 1.57: 9571 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 20446 Sorted by residual: bond pdb=" N MET f 1 " pdb=" CA MET f 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N MET e 1 " pdb=" CA MET e 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET g 1 " pdb=" CA MET g 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" C PRO e 511 " pdb=" N PRO e 512 " ideal model delta sigma weight residual 1.326 1.341 -0.015 1.44e-02 4.82e+03 1.10e+00 bond pdb=" C THR b 747 " pdb=" N PRO b 748 " ideal model delta sigma weight residual 1.331 1.340 -0.008 7.90e-03 1.60e+04 1.06e+00 ... (remaining 20441 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.92: 645 106.92 - 113.72: 11388 113.72 - 120.52: 7264 120.52 - 127.33: 8318 127.33 - 134.13: 256 Bond angle restraints: 27871 Sorted by residual: angle pdb=" N TYR e 487 " pdb=" CA TYR e 487 " pdb=" C TYR e 487 " ideal model delta sigma weight residual 111.71 117.00 -5.29 1.34e+00 5.57e-01 1.56e+01 angle pdb=" N TYR e 487 " pdb=" CA TYR e 487 " pdb=" CB TYR e 487 " ideal model delta sigma weight residual 111.66 105.79 5.87 1.56e+00 4.11e-01 1.41e+01 angle pdb=" N LYS g 677 " pdb=" CA LYS g 677 " pdb=" C LYS g 677 " ideal model delta sigma weight residual 110.65 107.07 3.58 1.26e+00 6.30e-01 8.07e+00 angle pdb=" CA TYR e 487 " pdb=" C TYR e 487 " pdb=" N ILE e 488 " ideal model delta sigma weight residual 117.40 120.34 -2.94 1.41e+00 5.03e-01 4.35e+00 angle pdb=" C GLU d 899 " pdb=" N ASP d 900 " pdb=" CA ASP d 900 " ideal model delta sigma weight residual 121.54 125.47 -3.93 1.91e+00 2.74e-01 4.23e+00 ... (remaining 27866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11144 17.91 - 35.82: 795 35.82 - 53.72: 106 53.72 - 71.63: 15 71.63 - 89.54: 10 Dihedral angle restraints: 12070 sinusoidal: 4640 harmonic: 7430 Sorted by residual: dihedral pdb=" CA ILE e 486 " pdb=" C ILE e 486 " pdb=" N TYR e 487 " pdb=" CA TYR e 487 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA LYS e 675 " pdb=" C LYS e 675 " pdb=" N MET e 676 " pdb=" CA MET e 676 " ideal model delta harmonic sigma weight residual 180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR e 502 " pdb=" C TYR e 502 " pdb=" N PRO e 503 " pdb=" CA PRO e 503 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 12067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1954 0.031 - 0.062: 704 0.062 - 0.093: 164 0.093 - 0.124: 271 0.124 - 0.155: 40 Chirality restraints: 3133 Sorted by residual: chirality pdb=" CA ILE e 489 " pdb=" N ILE e 489 " pdb=" C ILE e 489 " pdb=" CB ILE e 489 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ILE e 486 " pdb=" N ILE e 486 " pdb=" C ILE e 486 " pdb=" CB ILE e 486 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA VAL f 484 " pdb=" N VAL f 484 " pdb=" C VAL f 484 " pdb=" CB VAL f 484 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 3130 not shown) Planarity restraints: 3604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP e 507 " -0.016 2.00e-02 2.50e+03 1.96e-02 9.65e+00 pdb=" CG TRP e 507 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP e 507 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP e 507 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP e 507 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP e 507 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP e 507 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP e 507 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP e 507 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP e 507 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR f 502 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO f 503 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO f 503 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO f 503 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS c 912 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C LYS c 912 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS c 912 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA c 913 " 0.012 2.00e-02 2.50e+03 ... (remaining 3601 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 397 2.63 - 3.20: 19441 3.20 - 3.77: 31796 3.77 - 4.33: 44449 4.33 - 4.90: 72045 Nonbonded interactions: 168128 Sorted by model distance: nonbonded pdb=" O VAL c 855 " pdb=" OG1 THR c 856 " model vdw 2.063 2.440 nonbonded pdb=" O ILE f 474 " pdb=" OG SER g 193 " model vdw 2.068 2.440 nonbonded pdb=" NH2 ARG d 932 " pdb=" O TRP d 946 " model vdw 2.095 2.520 nonbonded pdb=" OG1 THR c 745 " pdb=" OE2 GLU c 760 " model vdw 2.103 2.440 nonbonded pdb=" NH1 ARG e 242 " pdb=" O GLY e 245 " model vdw 2.109 2.520 ... (remaining 168123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'b' and resid 736 through 949) selection = chain 'c' selection = chain 'd' } ncs_group { reference = (chain 'e' and (resid 1 through 223 or resid 232 through 469 or resid 562 throug \ h 688)) selection = (chain 'f' and (resid 1 through 469 or resid 562 through 688)) selection = (chain 'g' and (resid 1 through 223 or resid 232 through 688)) } 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=0.00 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.300 Set scattering table: 0.160 Process input model: 55.170 Find NCS groups from input model: 1.450 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: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.032 20446 Z= 0.167 Angle : 0.491 5.865 27871 Z= 0.264 Chirality : 0.046 0.155 3133 Planarity : 0.003 0.054 3604 Dihedral : 12.383 89.540 7332 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2557 helix: 0.20 (0.43), residues: 175 sheet: 0.33 (0.19), residues: 791 loop : -0.86 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP e 507 HIS 0.002 0.001 HIS d 778 PHE 0.010 0.001 PHE f 52 TYR 0.017 0.001 TYR f 487 ARG 0.004 0.000 ARG d 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 815 ARG cc_start: 0.7305 (tpm170) cc_final: 0.6823 (tpp-160) REVERT: d 833 LEU cc_start: 0.7936 (tt) cc_final: 0.7648 (mp) REVERT: b 892 MET cc_start: 0.6414 (tpt) cc_final: 0.6070 (tpt) REVERT: f 10 MET cc_start: 0.8162 (ttm) cc_final: 0.7942 (ttt) REVERT: f 403 MET cc_start: 0.8640 (mtm) cc_final: 0.8407 (ptp) REVERT: f 432 MET cc_start: 0.8410 (mmm) cc_final: 0.8013 (tpp) REVERT: f 676 MET cc_start: 0.8463 (ttp) cc_final: 0.7931 (ttp) REVERT: e 430 MET cc_start: 0.7822 (ttm) cc_final: 0.7320 (tmm) REVERT: g 633 MET cc_start: 0.7802 (ttt) cc_final: 0.7309 (ttm) REVERT: g 676 MET cc_start: 0.5887 (mpp) cc_final: 0.5245 (ttm) REVERT: c 798 MET cc_start: 0.5197 (pmm) cc_final: 0.4902 (pmm) REVERT: c 915 PHE cc_start: 0.7717 (m-10) cc_final: 0.6821 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3094 time to fit residues: 82.2036 Evaluate side-chains 92 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0040 chunk 103 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 417 GLN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 237 GLN e 479 GLN ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20446 Z= 0.162 Angle : 0.520 11.084 27871 Z= 0.276 Chirality : 0.048 0.180 3133 Planarity : 0.004 0.044 3604 Dihedral : 4.329 31.621 2786 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.32 (0.17), residues: 2557 helix: 0.82 (0.46), residues: 166 sheet: 0.41 (0.19), residues: 789 loop : -0.64 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 946 HIS 0.004 0.001 HIS d 781 PHE 0.015 0.001 PHE e 327 TYR 0.032 0.001 TYR f 138 ARG 0.005 0.000 ARG c 823 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 815 ARG cc_start: 0.7478 (tpm170) cc_final: 0.6971 (tpp-160) REVERT: d 833 LEU cc_start: 0.7781 (tt) cc_final: 0.7516 (mp) REVERT: d 890 ASP cc_start: 0.7332 (t0) cc_final: 0.6732 (p0) REVERT: b 892 MET cc_start: 0.6397 (tpt) cc_final: 0.6090 (tpt) REVERT: f 633 MET cc_start: 0.8520 (tpp) cc_final: 0.8302 (tpp) REVERT: f 676 MET cc_start: 0.8266 (ttp) cc_final: 0.7776 (ttp) REVERT: e 430 MET cc_start: 0.8120 (ttm) cc_final: 0.7356 (tmm) REVERT: g 10 MET cc_start: 0.7156 (ptp) cc_final: 0.6874 (pmm) REVERT: g 430 MET cc_start: 0.8298 (ttp) cc_final: 0.8088 (ptm) REVERT: g 660 TYR cc_start: 0.8120 (m-80) cc_final: 0.7898 (m-80) REVERT: g 676 MET cc_start: 0.4983 (mpp) cc_final: 0.4187 (ttm) REVERT: c 798 MET cc_start: 0.5626 (pmm) cc_final: 0.5324 (pmm) REVERT: c 915 PHE cc_start: 0.7476 (m-10) cc_final: 0.7024 (m-10) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.3209 time to fit residues: 63.9284 Evaluate side-chains 93 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 79 optimal weight: 0.0270 chunk 186 optimal weight: 0.8980 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 278 GLN ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 618 ASN ** c 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20446 Z= 0.182 Angle : 0.500 12.394 27871 Z= 0.263 Chirality : 0.047 0.227 3133 Planarity : 0.003 0.047 3604 Dihedral : 4.295 30.332 2786 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2557 helix: 0.78 (0.47), residues: 160 sheet: 0.30 (0.18), residues: 806 loop : -0.62 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP e 507 HIS 0.004 0.001 HIS d 778 PHE 0.011 0.001 PHE e 327 TYR 0.034 0.001 TYR f 138 ARG 0.006 0.000 ARG d 897 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 798 MET cc_start: 0.2040 (ptt) cc_final: 0.1732 (ptt) REVERT: d 815 ARG cc_start: 0.7411 (tpm170) cc_final: 0.7041 (tpp-160) REVERT: d 833 LEU cc_start: 0.7796 (tt) cc_final: 0.7538 (mp) REVERT: b 892 MET cc_start: 0.6584 (tpt) cc_final: 0.6175 (tpt) REVERT: f 676 MET cc_start: 0.8275 (ttp) cc_final: 0.7928 (ttp) REVERT: e 430 MET cc_start: 0.8135 (ttm) cc_final: 0.7359 (tmm) REVERT: e 676 MET cc_start: 0.8477 (ppp) cc_final: 0.8265 (ppp) REVERT: g 676 MET cc_start: 0.5408 (mpp) cc_final: 0.4645 (ttt) REVERT: c 915 PHE cc_start: 0.7450 (m-10) cc_final: 0.6619 (m-10) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.3048 time to fit residues: 55.0376 Evaluate side-chains 88 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 155 optimal weight: 0.1980 chunk 232 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 25 GLN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 579 ASN g 618 ASN ** c 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 919 ASN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20446 Z= 0.304 Angle : 0.582 14.586 27871 Z= 0.306 Chirality : 0.048 0.265 3133 Planarity : 0.004 0.054 3604 Dihedral : 4.702 30.100 2786 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.62 (0.16), residues: 2557 helix: 0.54 (0.44), residues: 159 sheet: 0.17 (0.18), residues: 832 loop : -0.84 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP e 507 HIS 0.005 0.002 HIS f 686 PHE 0.017 0.002 PHE c 845 TYR 0.035 0.002 TYR f 138 ARG 0.017 0.001 ARG g 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 2.385 Fit side-chains revert: symmetry clash REVERT: d 798 MET cc_start: 0.2789 (ptt) cc_final: 0.2542 (ptt) REVERT: d 833 LEU cc_start: 0.7891 (tt) cc_final: 0.7588 (mt) REVERT: b 892 MET cc_start: 0.6518 (tpt) cc_final: 0.6237 (tpt) REVERT: f 676 MET cc_start: 0.8404 (ttp) cc_final: 0.8188 (ttp) REVERT: e 430 MET cc_start: 0.8216 (ttm) cc_final: 0.7321 (tmm) REVERT: e 432 MET cc_start: 0.8235 (mmp) cc_final: 0.7802 (mmm) REVERT: e 676 MET cc_start: 0.8491 (ppp) cc_final: 0.8202 (ppp) REVERT: g 10 MET cc_start: 0.7654 (ptp) cc_final: 0.7171 (pmm) REVERT: g 403 MET cc_start: 0.8724 (ttp) cc_final: 0.8049 (ptm) REVERT: g 676 MET cc_start: 0.5880 (mpp) cc_final: 0.4809 (ttt) REVERT: c 915 PHE cc_start: 0.7862 (m-10) cc_final: 0.6902 (m-10) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.2887 time to fit residues: 48.8970 Evaluate side-chains 75 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 182 GLN g 278 GLN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 618 ASN ** c 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 789 GLN c 919 ASN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20446 Z= 0.297 Angle : 0.567 13.247 27871 Z= 0.300 Chirality : 0.048 0.318 3133 Planarity : 0.004 0.068 3604 Dihedral : 4.769 30.870 2786 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.69 (0.16), residues: 2557 helix: 0.68 (0.45), residues: 153 sheet: 0.14 (0.18), residues: 814 loop : -0.90 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 541 HIS 0.005 0.001 HIS d 778 PHE 0.020 0.002 PHE e 485 TYR 0.032 0.002 TYR f 138 ARG 0.005 0.001 ARG d 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 833 LEU cc_start: 0.7837 (tt) cc_final: 0.7552 (mt) REVERT: d 890 ASP cc_start: 0.7220 (t0) cc_final: 0.6772 (p0) REVERT: b 788 GLN cc_start: 0.6497 (tm-30) cc_final: 0.6179 (tm-30) REVERT: f 676 MET cc_start: 0.8334 (ttp) cc_final: 0.8129 (ttp) REVERT: e 430 MET cc_start: 0.8306 (ttm) cc_final: 0.7518 (tmm) REVERT: e 676 MET cc_start: 0.8485 (ppp) cc_final: 0.8136 (ppp) REVERT: g 633 MET cc_start: 0.7411 (ttt) cc_final: 0.7207 (ttm) REVERT: g 676 MET cc_start: 0.6223 (mpp) cc_final: 0.4943 (mtp) REVERT: c 915 PHE cc_start: 0.7791 (m-10) cc_final: 0.6870 (m-10) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.3107 time to fit residues: 46.7872 Evaluate side-chains 69 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 919 ASN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20446 Z= 0.158 Angle : 0.516 13.405 27871 Z= 0.271 Chirality : 0.048 0.295 3133 Planarity : 0.004 0.066 3604 Dihedral : 4.511 31.409 2786 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.51 (0.16), residues: 2557 helix: 0.88 (0.47), residues: 153 sheet: 0.23 (0.18), residues: 835 loop : -0.78 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 946 HIS 0.006 0.001 HIS d 778 PHE 0.017 0.001 PHE f 586 TYR 0.029 0.001 TYR f 138 ARG 0.004 0.000 ARG g 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 2.236 Fit side-chains revert: symmetry clash REVERT: d 815 ARG cc_start: 0.7191 (tpm170) cc_final: 0.6891 (tpp-160) REVERT: d 890 ASP cc_start: 0.7537 (t0) cc_final: 0.6962 (p0) REVERT: b 788 GLN cc_start: 0.6607 (tm-30) cc_final: 0.6303 (tm-30) REVERT: f 676 MET cc_start: 0.8300 (ttp) cc_final: 0.8072 (ttp) REVERT: e 430 MET cc_start: 0.8289 (ttm) cc_final: 0.7495 (tmm) REVERT: e 432 MET cc_start: 0.8338 (mmm) cc_final: 0.8057 (mtt) REVERT: e 676 MET cc_start: 0.8528 (ppp) cc_final: 0.8142 (ppp) REVERT: g 10 MET cc_start: 0.7798 (ptp) cc_final: 0.7263 (pmm) REVERT: g 674 TYR cc_start: 0.6479 (t80) cc_final: 0.6232 (t80) REVERT: g 676 MET cc_start: 0.6212 (mpp) cc_final: 0.5359 (ttt) REVERT: c 788 GLN cc_start: 0.4627 (mm-40) cc_final: 0.4263 (pp30) REVERT: c 915 PHE cc_start: 0.7456 (m-10) cc_final: 0.6459 (m-10) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.3116 time to fit residues: 49.9443 Evaluate side-chains 73 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 686 HIS c 919 ASN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20446 Z= 0.258 Angle : 0.547 13.876 27871 Z= 0.286 Chirality : 0.048 0.265 3133 Planarity : 0.004 0.057 3604 Dihedral : 4.644 31.925 2786 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.64 (0.16), residues: 2557 helix: 0.73 (0.46), residues: 153 sheet: 0.13 (0.18), residues: 832 loop : -0.85 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 946 HIS 0.005 0.001 HIS d 778 PHE 0.017 0.002 PHE f 586 TYR 0.025 0.002 TYR f 138 ARG 0.014 0.000 ARG c 891 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 2.383 Fit side-chains revert: symmetry clash REVERT: b 788 GLN cc_start: 0.6519 (tm-30) cc_final: 0.6170 (tm-30) REVERT: e 430 MET cc_start: 0.8236 (ttm) cc_final: 0.7498 (tmm) REVERT: e 432 MET cc_start: 0.8236 (mmm) cc_final: 0.7905 (mtt) REVERT: e 486 ILE cc_start: 0.6891 (mt) cc_final: 0.6587 (mp) REVERT: e 627 MET cc_start: 0.9282 (ttp) cc_final: 0.8765 (ttp) REVERT: e 676 MET cc_start: 0.8095 (ppp) cc_final: 0.7810 (ppp) REVERT: g 456 ILE cc_start: 0.8620 (tt) cc_final: 0.8298 (mt) REVERT: g 633 MET cc_start: 0.7590 (ttm) cc_final: 0.7267 (ttm) REVERT: g 676 MET cc_start: 0.6377 (mpp) cc_final: 0.5113 (mtp) REVERT: c 892 MET cc_start: 0.8710 (tpp) cc_final: 0.8502 (tpt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2819 time to fit residues: 42.8861 Evaluate side-chains 72 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 291 HIS ** f 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** e 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 788 GLN c 889 GLN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20446 Z= 0.280 Angle : 0.568 13.816 27871 Z= 0.298 Chirality : 0.048 0.250 3133 Planarity : 0.004 0.080 3604 Dihedral : 4.810 31.819 2786 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2557 helix: 0.41 (0.43), residues: 165 sheet: 0.07 (0.18), residues: 815 loop : -0.96 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 429 HIS 0.005 0.001 HIS d 778 PHE 0.015 0.002 PHE c 845 TYR 0.024 0.002 TYR f 138 ARG 0.004 0.001 ARG f 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 788 GLN cc_start: 0.6300 (tm-30) cc_final: 0.5878 (tm-30) REVERT: e 430 MET cc_start: 0.8250 (ttm) cc_final: 0.7421 (tmm) REVERT: e 432 MET cc_start: 0.8124 (mmm) cc_final: 0.7737 (mmm) REVERT: e 627 MET cc_start: 0.9226 (ttp) cc_final: 0.8897 (ttt) REVERT: g 103 MET cc_start: 0.7661 (tpp) cc_final: 0.6710 (mmm) REVERT: g 456 ILE cc_start: 0.8612 (tt) cc_final: 0.8284 (mt) REVERT: g 676 MET cc_start: 0.6440 (mpp) cc_final: 0.5623 (mtp) REVERT: c 788 GLN cc_start: 0.5237 (mm110) cc_final: 0.4332 (pp30) REVERT: c 892 MET cc_start: 0.8572 (tpp) cc_final: 0.8368 (tpt) REVERT: c 915 PHE cc_start: 0.7605 (m-10) cc_final: 0.7353 (m-10) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.2894 time to fit residues: 44.0926 Evaluate side-chains 72 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 6.9990 chunk 235 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 179 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 182 GLN ** f 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 469 ASN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** e 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 411 ASN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20446 Z= 0.264 Angle : 0.562 14.113 27871 Z= 0.295 Chirality : 0.048 0.303 3133 Planarity : 0.004 0.057 3604 Dihedral : 4.800 29.237 2786 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2557 helix: 0.57 (0.44), residues: 159 sheet: -0.04 (0.18), residues: 822 loop : -0.96 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 946 HIS 0.006 0.001 HIS d 778 PHE 0.014 0.002 PHE c 845 TYR 0.023 0.002 TYR f 138 ARG 0.004 0.001 ARG e 688 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 2.334 Fit side-chains revert: symmetry clash REVERT: b 788 GLN cc_start: 0.6284 (tm-30) cc_final: 0.5854 (tm-30) REVERT: e 430 MET cc_start: 0.8232 (ttm) cc_final: 0.7416 (tmm) REVERT: e 432 MET cc_start: 0.8107 (mmm) cc_final: 0.7708 (mmm) REVERT: g 456 ILE cc_start: 0.8663 (tt) cc_final: 0.8343 (mt) REVERT: g 633 MET cc_start: 0.6606 (ttt) cc_final: 0.6215 (ttt) REVERT: g 676 MET cc_start: 0.6464 (mpp) cc_final: 0.5579 (mtp) REVERT: c 915 PHE cc_start: 0.7585 (m-10) cc_final: 0.6973 (m-80) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.2832 time to fit residues: 43.1108 Evaluate side-chains 69 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 114 optimal weight: 0.0020 chunk 168 optimal weight: 4.9990 chunk 254 optimal weight: 0.2980 chunk 233 optimal weight: 0.9990 chunk 202 optimal weight: 0.0670 chunk 21 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.4326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN e 482 GLN g 411 ASN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 788 GLN ** c 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20446 Z= 0.141 Angle : 0.523 13.550 27871 Z= 0.273 Chirality : 0.048 0.267 3133 Planarity : 0.004 0.053 3604 Dihedral : 4.505 28.801 2786 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2557 helix: 0.81 (0.47), residues: 153 sheet: 0.11 (0.18), residues: 831 loop : -0.82 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 300 HIS 0.008 0.001 HIS d 778 PHE 0.013 0.001 PHE g 327 TYR 0.026 0.001 TYR f 138 ARG 0.003 0.000 ARG g 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 2.140 Fit side-chains REVERT: d 890 ASP cc_start: 0.7808 (t0) cc_final: 0.7140 (p0) REVERT: b 788 GLN cc_start: 0.6446 (tm-30) cc_final: 0.6116 (tm-30) REVERT: e 430 MET cc_start: 0.8146 (ttm) cc_final: 0.7420 (tmm) REVERT: e 432 MET cc_start: 0.8219 (mmm) cc_final: 0.7807 (mtt) REVERT: e 627 MET cc_start: 0.9249 (ttp) cc_final: 0.8902 (ttt) REVERT: e 633 MET cc_start: 0.8399 (ttp) cc_final: 0.8099 (ttm) REVERT: g 10 MET cc_start: 0.7929 (ptp) cc_final: 0.7392 (pmm) REVERT: g 674 TYR cc_start: 0.6416 (t80) cc_final: 0.6189 (t80) REVERT: g 676 MET cc_start: 0.6158 (mpp) cc_final: 0.5480 (mtp) REVERT: c 788 GLN cc_start: 0.5176 (mm110) cc_final: 0.4400 (pp30) REVERT: c 915 PHE cc_start: 0.7281 (m-10) cc_final: 0.6952 (m-10) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.2796 time to fit residues: 45.4195 Evaluate side-chains 69 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 208 ASN ** f 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 479 GLN ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN e 616 GLN g 411 ASN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 919 ASN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.045161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.036155 restraints weight = 125538.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.036810 restraints weight = 71522.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.037103 restraints weight = 45131.956| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20446 Z= 0.354 Angle : 0.612 14.401 27871 Z= 0.321 Chirality : 0.049 0.263 3133 Planarity : 0.004 0.058 3604 Dihedral : 4.890 30.205 2786 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.05 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.96 (0.16), residues: 2557 helix: 0.31 (0.43), residues: 165 sheet: -0.13 (0.18), residues: 823 loop : -1.04 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP e 507 HIS 0.005 0.001 HIS f 686 PHE 0.024 0.002 PHE e 485 TYR 0.063 0.002 TYR e 487 ARG 0.005 0.001 ARG f 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.31 seconds wall clock time: 56 minutes 23.69 seconds (3383.69 seconds total)