Starting phenix.real_space_refine (version: dev) on Tue Feb 21 04:45:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2023/7aio_11800.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2023/7aio_11800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2023/7aio_11800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2023/7aio_11800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2023/7aio_11800.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2023/7aio_11800.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B GLU 580": "OE1" <-> "OE2" Residue "B TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B GLU 921": "OE1" <-> "OE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 921": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13915 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6918 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 34, 'TRANS': 875} Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 6891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 6891 Classifications: {'peptide': 909} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 34, 'TRANS': 874} Chain breaks: 3 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.64, per 1000 atoms: 0.55 Number of scatterers: 13915 At special positions: 0 Unit cell: (104.811, 93.093, 147.777, 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 94 16.00 O 2485 8.00 N 2308 7.00 C 9028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.02 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1101 " - " ASN A 377 " " NAG B1101 " - " ASN B 377 " " NAG C 1 " - " ASN B 328 " " NAG G 1 " - " ASN A 328 " Time building additional restraints: 6.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3354 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 61.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.659A pdb=" N THR B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 131' Processing helix chain 'B' and resid 135 through 149 removed outlier: 5.137A pdb=" N LEU B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.320A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.559A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 258 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.685A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 370 through 376 Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.521A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.742A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 460 through 491 Proline residue: B 466 - end of helix removed outlier: 3.704A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.229A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.943A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.760A pdb=" N LEU B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.679A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.663A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 675 removed outlier: 3.616A pdb=" N ILE B 653 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.216A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.938A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.538A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 3.547A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 899 through 917 removed outlier: 4.067A pdb=" N GLN B 904 " --> pdb=" O ASP B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 946 Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 3.931A pdb=" N LYS B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1065 No H-bonds generated for 'chain 'B' and resid 1063 through 1065' Processing helix chain 'B' and resid 1066 through 1078 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.710A pdb=" N THR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 135 through 149 removed outlier: 5.246A pdb=" N LEU A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.327A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.570A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 256 through 284 removed outlier: 3.606A pdb=" N MET A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.724A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 370 through 376 Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.523A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.704A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.662A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.253A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.925A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 561 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.648A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.625A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.679A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 675 removed outlier: 3.566A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.598A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.244A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.886A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.585A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.652A pdb=" N LEU A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 902 through 917 Processing helix chain 'A' and resid 932 through 949 Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.928A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.594A pdb=" N VAL B 350 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.633A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 858 through 860 removed outlier: 9.716A pdb=" N GLU B 921 " --> pdb=" O CYS B 888 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.554A pdb=" N VAL A 350 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.646A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 859 through 860 removed outlier: 6.860A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2382 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: 4.49 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3310 1.33 - 1.45: 2891 1.45 - 1.57: 7877 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14228 Sorted by residual: bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.20e+00 bond pdb=" N ILE B 250 " pdb=" CA ILE B 250 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.17e+00 bond pdb=" N GLU B1093 " pdb=" CA GLU B1093 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.22e-02 6.72e+03 6.93e+00 bond pdb=" N GLN B 897 " pdb=" CA GLN B 897 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.73e+00 bond pdb=" N ARG B 334 " pdb=" CA ARG B 334 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.33e-02 5.65e+03 6.69e+00 ... (remaining 14223 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.66: 296 105.66 - 112.80: 7873 112.80 - 119.95: 4865 119.95 - 127.09: 6139 127.09 - 134.23: 183 Bond angle restraints: 19356 Sorted by residual: angle pdb=" C2 NAG B1101 " pdb=" C1 NAG B1101 " pdb=" O5 NAG B1101 " ideal model delta sigma weight residual 109.64 106.61 3.03 5.38e-01 3.45e+00 3.18e+01 angle pdb=" C6 NAG B1101 " pdb=" C5 NAG B1101 " pdb=" O5 NAG B1101 " ideal model delta sigma weight residual 106.77 113.51 -6.74 1.25e+00 6.39e-01 2.90e+01 angle pdb=" C ILE B 639 " pdb=" N CYS B 640 " pdb=" CA CYS B 640 " ideal model delta sigma weight residual 122.38 113.67 8.71 1.81e+00 3.05e-01 2.32e+01 angle pdb=" C ASP A 255 " pdb=" CA ASP A 255 " pdb=" CB ASP A 255 " ideal model delta sigma weight residual 116.63 111.60 5.03 1.16e+00 7.43e-01 1.88e+01 angle pdb=" N ASN B 266 " pdb=" CA ASN B 266 " pdb=" C ASN B 266 " ideal model delta sigma weight residual 111.28 107.13 4.15 1.09e+00 8.42e-01 1.45e+01 ... (remaining 19351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 7732 17.22 - 34.44: 500 34.44 - 51.66: 78 51.66 - 68.88: 30 68.88 - 86.10: 3 Dihedral angle restraints: 8343 sinusoidal: 3127 harmonic: 5216 Sorted by residual: dihedral pdb=" CA CYS A 640 " pdb=" C CYS A 640 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" C ASN B 265 " pdb=" N ASN B 265 " pdb=" CA ASN B 265 " pdb=" CB ASN B 265 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 8340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.960: 2294 0.960 - 1.920: 0 1.920 - 2.880: 0 2.880 - 3.840: 0 3.840 - 4.800: 1 Chirality restraints: 2295 Sorted by residual: chirality pdb=" C1 NAG B1101 " pdb=" ND2 ASN B 377 " pdb=" C2 NAG B1101 " pdb=" O5 NAG B1101 " both_signs ideal model delta sigma weight residual False -2.40 2.40 -4.80 2.00e-01 2.50e+01 5.76e+02 chirality pdb=" C5 NAG B1101 " pdb=" C4 NAG B1101 " pdb=" C6 NAG B1101 " pdb=" O5 NAG B1101 " both_signs ideal model delta sigma weight residual False -2.50 -2.20 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA CYS A 640 " pdb=" N CYS A 640 " pdb=" C CYS A 640 " pdb=" CB CYS A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 2292 not shown) Planarity restraints: 2414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1101 " 0.202 2.00e-02 2.50e+03 1.72e-01 3.69e+02 pdb=" C7 NAG B1101 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B1101 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG B1101 " -0.282 2.00e-02 2.50e+03 pdb=" O7 NAG B1101 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 497 " -0.090 9.50e-02 1.11e+02 5.47e-02 1.79e+01 pdb=" NE ARG B 497 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 497 " -0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG B 497 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 497 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 497 " 0.098 9.50e-02 1.11e+02 5.64e-02 1.70e+01 pdb=" NE ARG A 497 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " 0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " -0.019 2.00e-02 2.50e+03 ... (remaining 2411 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1710 2.74 - 3.28: 14723 3.28 - 3.82: 23398 3.82 - 4.36: 27386 4.36 - 4.90: 47358 Nonbonded interactions: 114575 Sorted by model distance: nonbonded pdb=" ND2 ASN A1040 " pdb=" O VAL A1076 " model vdw 2.205 2.520 nonbonded pdb=" O PRO A1058 " pdb=" OH TYR A1070 " model vdw 2.226 2.440 nonbonded pdb=" OD1 ASN A 376 " pdb=" N SER A 415 " model vdw 2.285 2.520 nonbonded pdb=" NH1 ARG B 680 " pdb=" O PRO A 698 " model vdw 2.286 2.520 nonbonded pdb=" ND2 ASN B1040 " pdb=" O VAL B1076 " model vdw 2.286 2.520 ... (remaining 114570 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' and (resid 102 through 947 or resid 1029 through 1094 or resid 1101)) \ selection = (chain 'B' and (resid 102 through 896 or (resid 901 and (name N or name CA or na \ me C or name O or name CB )) or resid 902 through 907 or (resid 908 through 915 \ and (name N or name CA or name C or name O or name CB )) or resid 916 through 94 \ 6 or (resid 1028 and (name N or name CA or name C or name O or name CB )) or res \ id 1029 through 1094 or resid 1101)) } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 9028 2.51 5 N 2308 2.21 5 O 2485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.520 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: 13.980 Check model and map are aligned: 0.220 Process input model: 39.290 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 14228 Z= 0.376 Angle : 0.775 11.895 19356 Z= 0.472 Chirality : 0.112 4.800 2295 Planarity : 0.007 0.172 2410 Dihedral : 12.160 86.100 4971 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.01 % Rotamer Outliers : 0.83 % 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: -1.55 (0.18), residues: 1805 helix: -0.33 (0.15), residues: 1001 sheet: -1.74 (0.43), residues: 102 loop : -1.84 (0.22), residues: 702 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 313 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 322 average time/residue: 0.2913 time to fit residues: 132.4108 Evaluate side-chains 176 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1648 time to fit residues: 2.3587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 1.9990 chunk 137 optimal weight: 0.0010 chunk 76 optimal weight: 0.3980 chunk 46 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN B 382 GLN ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN B 752 ASN B 882 HIS A 133 GLN A 752 ASN A 882 HIS A1045 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 14228 Z= 0.201 Angle : 0.628 9.343 19356 Z= 0.323 Chirality : 0.052 1.489 2295 Planarity : 0.004 0.044 2410 Dihedral : 4.338 24.722 1984 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.84 % Rotamer Outliers : 1.60 % 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: -0.26 (0.19), residues: 1805 helix: 0.88 (0.16), residues: 1010 sheet: -1.60 (0.42), residues: 116 loop : -1.47 (0.23), residues: 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 219 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 235 average time/residue: 0.2375 time to fit residues: 85.0962 Evaluate side-chains 184 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1619 time to fit residues: 5.3140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 136 optimal weight: 0.0970 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 164 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14228 Z= 0.217 Angle : 0.591 9.148 19356 Z= 0.300 Chirality : 0.045 0.672 2295 Planarity : 0.004 0.036 2410 Dihedral : 4.187 22.743 1984 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer Outliers : 1.87 % 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: 0.15 (0.19), residues: 1805 helix: 1.17 (0.16), residues: 1016 sheet: -1.28 (0.44), residues: 116 loop : -1.29 (0.23), residues: 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 203 average time/residue: 0.2367 time to fit residues: 73.7265 Evaluate side-chains 171 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1264 time to fit residues: 4.1893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN B 613 GLN B1045 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS A 859 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.077 14228 Z= 0.515 Angle : 0.752 8.371 19356 Z= 0.386 Chirality : 0.050 0.430 2295 Planarity : 0.005 0.053 2410 Dihedral : 4.547 27.458 1984 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.73 % Rotamer Outliers : 2.91 % 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: -0.12 (0.19), residues: 1805 helix: 0.88 (0.16), residues: 1003 sheet: -1.42 (0.44), residues: 116 loop : -1.22 (0.23), residues: 686 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 191 average time/residue: 0.2559 time to fit residues: 76.3815 Evaluate side-chains 165 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1439 time to fit residues: 8.4859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN A 120 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14228 Z= 0.195 Angle : 0.591 9.333 19356 Z= 0.296 Chirality : 0.043 0.330 2295 Planarity : 0.004 0.032 2410 Dihedral : 4.313 28.743 1984 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer Outliers : 1.53 % 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: 0.38 (0.20), residues: 1805 helix: 1.31 (0.16), residues: 1012 sheet: -1.20 (0.47), residues: 117 loop : -1.09 (0.23), residues: 676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 188 average time/residue: 0.2171 time to fit residues: 64.2491 Evaluate side-chains 161 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.630 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1357 time to fit residues: 4.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.0770 chunk 91 optimal weight: 10.0000 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 14228 Z= 0.313 Angle : 0.635 10.181 19356 Z= 0.317 Chirality : 0.046 0.534 2295 Planarity : 0.004 0.034 2410 Dihedral : 4.317 27.705 1984 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer Outliers : 2.01 % 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: 0.41 (0.20), residues: 1805 helix: 1.30 (0.16), residues: 1011 sheet: -1.20 (0.47), residues: 117 loop : -1.01 (0.23), residues: 677 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 182 average time/residue: 0.2383 time to fit residues: 68.6011 Evaluate side-chains 170 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1340 time to fit residues: 6.2174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14228 Z= 0.206 Angle : 0.596 10.717 19356 Z= 0.294 Chirality : 0.044 0.416 2295 Planarity : 0.003 0.034 2410 Dihedral : 4.221 28.977 1984 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.84 % Rotamer Outliers : 1.18 % 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: 0.63 (0.20), residues: 1805 helix: 1.49 (0.16), residues: 1015 sheet: -1.00 (0.48), residues: 117 loop : -0.97 (0.23), residues: 673 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 185 average time/residue: 0.2271 time to fit residues: 66.3881 Evaluate side-chains 168 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1337 time to fit residues: 4.1067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14228 Z= 0.179 Angle : 0.591 11.694 19356 Z= 0.290 Chirality : 0.043 0.380 2295 Planarity : 0.003 0.032 2410 Dihedral : 4.102 29.281 1984 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Rotamer Outliers : 1.11 % 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: 0.86 (0.20), residues: 1805 helix: 1.72 (0.16), residues: 1012 sheet: -0.99 (0.46), residues: 127 loop : -0.90 (0.24), residues: 666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 188 average time/residue: 0.2247 time to fit residues: 67.0050 Evaluate side-chains 174 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1269 time to fit residues: 3.4575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 3.9990 chunk 152 optimal weight: 0.0170 chunk 162 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 0.0030 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 overall best weight: 0.5228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 14228 Z= 0.176 Angle : 0.618 15.227 19356 Z= 0.300 Chirality : 0.043 0.350 2295 Planarity : 0.003 0.033 2410 Dihedral : 4.064 29.124 1984 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer Outliers : 0.21 % 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: 0.96 (0.20), residues: 1805 helix: 1.77 (0.16), residues: 1012 sheet: -0.83 (0.48), residues: 116 loop : -0.83 (0.24), residues: 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 0.2189 time to fit residues: 62.5647 Evaluate side-chains 167 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 0.0060 chunk 152 optimal weight: 0.9980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14228 Z= 0.206 Angle : 0.625 13.196 19356 Z= 0.303 Chirality : 0.044 0.337 2295 Planarity : 0.003 0.034 2410 Dihedral : 4.055 29.373 1984 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Rotamer Outliers : 0.35 % 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: 0.97 (0.20), residues: 1805 helix: 1.74 (0.16), residues: 1014 sheet: -0.77 (0.47), residues: 116 loop : -0.78 (0.24), residues: 675 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 170 average time/residue: 0.2248 time to fit residues: 61.1086 Evaluate side-chains 164 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1565 time to fit residues: 2.8176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.131082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.100318 restraints weight = 25617.489| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.39 r_work: 0.3381 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14228 Z= 0.201 Angle : 0.627 13.130 19356 Z= 0.303 Chirality : 0.044 0.341 2295 Planarity : 0.003 0.034 2410 Dihedral : 4.084 29.951 1984 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.88 % Favored : 96.01 % Rotamer Outliers : 0.49 % 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: 1.02 (0.20), residues: 1805 helix: 1.74 (0.16), residues: 1015 sheet: -0.74 (0.47), residues: 116 loop : -0.69 (0.24), residues: 674 =============================================================================== Job complete usr+sys time: 3085.58 seconds wall clock time: 56 minutes 26.02 seconds (3386.02 seconds total)