Starting phenix.real_space_refine on Fri Feb 16 01:21:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2024/7aio_11800.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2024/7aio_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_2024/7aio_11800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2024/7aio_11800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2024/7aio_11800.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aio_11800/02_2024/7aio_11800.pdb" } resolution = 3.31 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= 0.002 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9 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: 9 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.08, per 1000 atoms: 0.51 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: 5.82 Conformation dependent library (CDL) restraints added in 2.8 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: 1.58 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: 5.24 Time building geometry restraints manager: 6.21 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=" 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 angle pdb=" C VAL A 866 " pdb=" N HIS A 867 " pdb=" CA HIS A 867 " ideal model delta sigma weight residual 122.53 116.43 6.10 1.61e+00 3.86e-01 1.44e+01 angle pdb=" CA ILE A 250 " pdb=" C ILE A 250 " pdb=" O ILE A 250 " ideal model delta sigma weight residual 120.95 117.02 3.93 1.04e+00 9.25e-01 1.43e+01 ... (remaining 19351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.84: 7984 20.84 - 41.68: 362 41.68 - 62.51: 78 62.51 - 83.35: 18 83.35 - 104.19: 9 Dihedral angle restraints: 8451 sinusoidal: 3235 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 8448 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=" 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 chirality pdb=" CA ASN B 265 " pdb=" N ASN B 265 " pdb=" C ASN B 265 " pdb=" CB ASN B 265 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+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 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.620 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 40.180 Find NCS groups from input model: 0.990 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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= 0.384 Angle : 0.790 11.895 19356 Z= 0.469 Chirality : 0.112 4.800 2295 Planarity : 0.007 0.172 2410 Dihedral : 13.631 104.188 5079 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.01 % Rotamer: Outliers : 0.83 % Allowed : 5.76 % Favored : 93.41 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 649 HIS 0.009 0.001 HIS B 790 PHE 0.018 0.002 PHE A 877 TYR 0.017 0.002 TYR A 937 ARG 0.071 0.002 ARG B 497 *********************** 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 : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4020 (tpt) cc_final: 0.3652 (tpt) outliers start: 12 outliers final: 1 residues processed: 322 average time/residue: 0.3009 time to fit residues: 136.8482 Evaluate side-chains 176 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 GLU 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: 0.7393 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14228 Z= 0.203 Angle : 0.650 12.111 19356 Z= 0.325 Chirality : 0.048 0.995 2295 Planarity : 0.004 0.045 2410 Dihedral : 7.813 58.551 2095 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 1.46 % Allowed : 13.31 % Favored : 85.23 % 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: 0.86 (0.16), residues: 1010 sheet: -1.55 (0.43), residues: 112 loop : -1.48 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 649 HIS 0.005 0.001 HIS B 867 PHE 0.021 0.002 PHE A 877 TYR 0.017 0.001 TYR B 105 ARG 0.006 0.001 ARG A 785 *********************** 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 236 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4449 (tpt) cc_final: 0.3978 (tpt) REVERT: B 381 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6779 (mt) REVERT: A 329 ARG cc_start: 0.7875 (mmt90) cc_final: 0.6890 (mtt90) REVERT: A 580 GLU cc_start: 0.7771 (tp30) cc_final: 0.7502 (tp30) REVERT: A 942 MET cc_start: 0.7052 (tmm) cc_final: 0.6405 (ptt) outliers start: 21 outliers final: 10 residues processed: 230 average time/residue: 0.2314 time to fit residues: 81.7902 Evaluate side-chains 185 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 662 ILE 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: 6.9990 chunk 136 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 164 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN A 629 HIS A 859 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14228 Z= 0.245 Angle : 0.607 9.161 19356 Z= 0.304 Chirality : 0.044 0.497 2295 Planarity : 0.004 0.034 2410 Dihedral : 5.860 57.280 2092 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 2.64 % Allowed : 13.45 % Favored : 83.91 % 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: 0.13 (0.19), residues: 1805 helix: 1.16 (0.16), residues: 1017 sheet: -1.27 (0.44), residues: 116 loop : -1.31 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 649 HIS 0.004 0.001 HIS B 802 PHE 0.021 0.001 PHE A 357 TYR 0.015 0.001 TYR B 105 ARG 0.008 0.001 ARG B 939 *********************** 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 222 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4725 (tpt) cc_final: 0.4185 (tpt) REVERT: B 431 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7473 (t) REVERT: A 329 ARG cc_start: 0.7972 (mmt90) cc_final: 0.7666 (mmt90) outliers start: 38 outliers final: 17 residues processed: 207 average time/residue: 0.2335 time to fit residues: 74.6150 Evaluate side-chains 183 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.6980 chunk 123 optimal weight: 0.0010 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 165 optimal weight: 0.0570 chunk 174 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 overall best weight: 1.7508 ------------------------------------------------------------------------------- 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** B1045 ASN A 382 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14228 Z= 0.252 Angle : 0.602 8.945 19356 Z= 0.300 Chirality : 0.044 0.418 2295 Planarity : 0.004 0.031 2410 Dihedral : 5.413 55.099 2092 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.12 % Rotamer: Outliers : 2.43 % Allowed : 15.33 % Favored : 82.25 % 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: 0.36 (0.20), residues: 1805 helix: 1.34 (0.16), residues: 1013 sheet: -1.15 (0.45), residues: 117 loop : -1.19 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 649 HIS 0.004 0.001 HIS B 802 PHE 0.017 0.001 PHE B 689 TYR 0.016 0.001 TYR B 105 ARG 0.004 0.000 ARG B 820 *********************** 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 208 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4826 (tpt) cc_final: 0.4270 (tpt) REVERT: B 138 MET cc_start: 0.7783 (tpp) cc_final: 0.7553 (tpp) REVERT: B 431 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7449 (t) outliers start: 35 outliers final: 23 residues processed: 197 average time/residue: 0.2357 time to fit residues: 72.3764 Evaluate side-chains 183 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14228 Z= 0.302 Angle : 0.623 9.767 19356 Z= 0.311 Chirality : 0.045 0.364 2295 Planarity : 0.004 0.031 2410 Dihedral : 5.269 54.177 2092 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 3.26 % Allowed : 15.95 % Favored : 80.79 % 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: 0.43 (0.20), residues: 1805 helix: 1.38 (0.16), residues: 1011 sheet: -1.11 (0.47), residues: 107 loop : -1.11 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 355 HIS 0.003 0.001 HIS B 802 PHE 0.021 0.002 PHE A 728 TYR 0.013 0.001 TYR B 105 ARG 0.003 0.000 ARG A 814 *********************** 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 214 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 167 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4704 (tpt) cc_final: 0.4115 (tpt) REVERT: B 148 ILE cc_start: 0.8186 (mm) cc_final: 0.7940 (mm) REVERT: B 431 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7498 (t) REVERT: A 105 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6050 (p90) REVERT: A 871 MET cc_start: 0.7481 (mmp) cc_final: 0.7165 (mmp) outliers start: 47 outliers final: 29 residues processed: 202 average time/residue: 0.2281 time to fit residues: 72.4832 Evaluate side-chains 185 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1069 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3179 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= 0.181 Angle : 0.586 10.625 19356 Z= 0.287 Chirality : 0.043 0.345 2295 Planarity : 0.003 0.032 2410 Dihedral : 5.071 54.232 2092 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 17.41 % Favored : 79.96 % 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: 0.70 (0.20), residues: 1805 helix: 1.60 (0.16), residues: 1010 sheet: -0.96 (0.48), residues: 107 loop : -1.02 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 649 HIS 0.003 0.000 HIS B 802 PHE 0.016 0.001 PHE A 442 TYR 0.014 0.001 TYR B 105 ARG 0.005 0.000 ARG A 329 *********************** 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 218 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4720 (tpt) cc_final: 0.4353 (tpt) REVERT: B 148 ILE cc_start: 0.8168 (mm) cc_final: 0.7889 (mm) REVERT: B 431 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7488 (t) REVERT: A 105 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.5937 (p90) REVERT: A 336 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7737 (mp) REVERT: A 871 MET cc_start: 0.7494 (mmp) cc_final: 0.7036 (mmp) outliers start: 38 outliers final: 26 residues processed: 207 average time/residue: 0.2125 time to fit residues: 69.9742 Evaluate side-chains 196 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14228 Z= 0.395 Angle : 0.690 10.974 19356 Z= 0.340 Chirality : 0.048 0.564 2295 Planarity : 0.004 0.040 2410 Dihedral : 5.236 53.866 2092 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 2.77 % Allowed : 18.59 % Favored : 78.64 % 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: 0.49 (0.20), residues: 1805 helix: 1.35 (0.16), residues: 1012 sheet: -1.09 (0.47), residues: 107 loop : -0.95 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 355 HIS 0.005 0.001 HIS B 867 PHE 0.023 0.002 PHE A 728 TYR 0.016 0.002 TYR B 105 ARG 0.006 0.000 ARG A 329 *********************** 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 204 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4797 (tpt) cc_final: 0.4444 (tpt) REVERT: B 148 ILE cc_start: 0.8240 (mm) cc_final: 0.7999 (mm) REVERT: A 105 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6132 (p90) REVERT: A 336 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 871 MET cc_start: 0.7753 (mmp) cc_final: 0.7264 (mmp) outliers start: 40 outliers final: 26 residues processed: 194 average time/residue: 0.2225 time to fit residues: 67.7697 Evaluate side-chains 181 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 B 629 HIS B1069 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14228 Z= 0.186 Angle : 0.608 12.267 19356 Z= 0.294 Chirality : 0.044 0.449 2295 Planarity : 0.003 0.034 2410 Dihedral : 5.020 54.050 2092 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.12 % Rotamer: Outliers : 2.50 % Allowed : 18.45 % Favored : 79.06 % 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: 0.79 (0.20), residues: 1805 helix: 1.64 (0.16), residues: 1010 sheet: -1.01 (0.46), residues: 111 loop : -0.89 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 649 HIS 0.004 0.000 HIS B 867 PHE 0.017 0.001 PHE A 728 TYR 0.017 0.001 TYR B 105 ARG 0.004 0.000 ARG A 329 *********************** 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 211 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4836 (tpt) cc_final: 0.4478 (tpt) REVERT: B 117 GLU cc_start: 0.8067 (tp30) cc_final: 0.7834 (tm-30) REVERT: B 148 ILE cc_start: 0.8201 (mm) cc_final: 0.7941 (mm) REVERT: A 105 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6046 (p90) REVERT: A 117 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7108 (mp0) REVERT: A 280 LEU cc_start: 0.8518 (tp) cc_final: 0.8145 (tt) REVERT: A 871 MET cc_start: 0.7609 (mmp) cc_final: 0.7056 (mmp) outliers start: 36 outliers final: 26 residues processed: 204 average time/residue: 0.2175 time to fit residues: 70.3198 Evaluate side-chains 195 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 5.9990 chunk 152 optimal weight: 0.0060 chunk 162 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 171 optimal weight: 0.8980 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14228 Z= 0.226 Angle : 0.636 12.415 19356 Z= 0.309 Chirality : 0.045 0.418 2295 Planarity : 0.003 0.034 2410 Dihedral : 5.029 53.764 2092 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Rotamer: Outliers : 2.15 % Allowed : 19.14 % Favored : 78.71 % 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: 0.78 (0.20), residues: 1805 helix: 1.61 (0.16), residues: 1011 sheet: -1.08 (0.44), residues: 118 loop : -0.84 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 649 HIS 0.004 0.001 HIS B 867 PHE 0.024 0.001 PHE A 728 TYR 0.017 0.001 TYR B 105 ARG 0.004 0.000 ARG A 329 *********************** 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 200 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8088 (tp30) cc_final: 0.7882 (tm-30) REVERT: B 148 ILE cc_start: 0.8175 (mm) cc_final: 0.7926 (mm) REVERT: A 105 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6053 (p90) REVERT: A 117 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7118 (mp0) REVERT: A 871 MET cc_start: 0.7606 (mmp) cc_final: 0.7146 (mmp) outliers start: 31 outliers final: 25 residues processed: 193 average time/residue: 0.2126 time to fit residues: 65.6328 Evaluate side-chains 191 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 152 optimal weight: 0.0060 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14228 Z= 0.179 Angle : 0.623 13.257 19356 Z= 0.300 Chirality : 0.043 0.404 2295 Planarity : 0.003 0.032 2410 Dihedral : 4.914 54.156 2092 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 1.66 % Allowed : 20.11 % Favored : 78.22 % 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: 0.93 (0.20), residues: 1805 helix: 1.75 (0.16), residues: 1011 sheet: -1.03 (0.43), residues: 136 loop : -0.77 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 649 HIS 0.004 0.001 HIS B 802 PHE 0.023 0.001 PHE A 728 TYR 0.018 0.001 TYR B 105 ARG 0.004 0.000 ARG A 329 ********************** 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 205 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4973 (tpt) cc_final: 0.4548 (tpt) REVERT: A 117 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7097 (mp0) REVERT: A 597 MET cc_start: 0.7731 (tpp) cc_final: 0.7454 (tpp) REVERT: A 871 MET cc_start: 0.7573 (mmp) cc_final: 0.7033 (mmp) outliers start: 24 outliers final: 22 residues processed: 200 average time/residue: 0.2163 time to fit residues: 69.3339 Evaluate side-chains 192 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** A 815 GLN ** 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 = 0.3976 r_free = 0.3976 target = 0.131630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100888 restraints weight = 25357.933| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.36 r_work: 0.3397 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14228 Z= 0.188 Angle : 0.618 13.444 19356 Z= 0.298 Chirality : 0.044 0.390 2295 Planarity : 0.003 0.031 2410 Dihedral : 4.856 53.726 2092 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.12 % Rotamer: Outliers : 1.80 % Allowed : 20.32 % Favored : 77.88 % 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: 0.99 (0.20), residues: 1805 helix: 1.77 (0.16), residues: 1010 sheet: -0.98 (0.43), residues: 136 loop : -0.71 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 649 HIS 0.004 0.000 HIS B 802 PHE 0.022 0.001 PHE A 847 TYR 0.018 0.001 TYR B 105 ARG 0.004 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.11 seconds wall clock time: 60 minutes 12.36 seconds (3612.36 seconds total)