Starting phenix.real_space_refine on Fri Feb 16 06:16:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/02_2024/8hya_35085_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/02_2024/8hya_35085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/02_2024/8hya_35085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/02_2024/8hya_35085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/02_2024/8hya_35085_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/02_2024/8hya_35085_updated.pdb" } resolution = 3.4 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= -0.003 sd= 0.065 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 60 5.16 5 C 9536 2.51 5 N 2364 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A ASP 783": "OD1" <-> "OD2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 823": "OD1" <-> "OD2" Residue "A ASP 827": "OD1" <-> "OD2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "B GLU 771": "OE1" <-> "OE2" Residue "B ASP 783": "OD1" <-> "OD2" Residue "B TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 823": "OD1" <-> "OD2" Residue "B ASP 827": "OD1" <-> "OD2" Residue "B PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 14586 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'R16': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'R16': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 8.06, per 1000 atoms: 0.55 Number of scatterers: 14586 At special positions: 0 Unit cell: (115.44, 107.12, 127.92, 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 60 16.00 O 2626 8.00 N 2364 7.00 C 9536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 3.0 seconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 6 sheets defined 62.2% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 33 through 53 Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 98 through 113 Proline residue: A 107 - end of helix removed outlier: 4.659A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 126 through 150 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 188 through 212 removed outlier: 3.713A pdb=" N GLY A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 253 removed outlier: 4.086A pdb=" N ALA A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 278 removed outlier: 3.556A pdb=" N ILE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 307 through 338 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 350 through 376 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 420 through 449 removed outlier: 4.009A pdb=" N PHE A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 483 removed outlier: 3.678A pdb=" N ILE A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 528 through 549 Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.837A pdb=" N ASP A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 584 removed outlier: 3.891A pdb=" N LEU A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 603 through 637 removed outlier: 5.885A pdb=" N SER A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 667 removed outlier: 4.108A pdb=" N GLU A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 698 Processing helix chain 'A' and resid 705 through 722 Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.534A pdb=" N VAL A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 811 through 816 Processing helix chain 'A' and resid 837 through 845 removed outlier: 4.185A pdb=" N SER A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 865 Processing helix chain 'A' and resid 867 through 870 No H-bonds generated for 'chain 'A' and resid 867 through 870' Processing helix chain 'A' and resid 875 through 883 removed outlier: 3.506A pdb=" N ARG A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1041 Processing helix chain 'B' and resid 33 through 53 Processing helix chain 'B' and resid 61 through 76 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 98 through 113 Proline residue: B 107 - end of helix removed outlier: 4.659A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 126 through 150 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 188 through 212 removed outlier: 3.713A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 253 removed outlier: 4.086A pdb=" N ALA B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 278 removed outlier: 3.557A pdb=" N ILE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 307 through 338 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 350 through 376 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 399 through 408 Processing helix chain 'B' and resid 420 through 449 removed outlier: 4.009A pdb=" N PHE B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 483 removed outlier: 3.679A pdb=" N ILE B 463 " --> pdb=" O PRO B 459 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 528 through 549 Processing helix chain 'B' and resid 554 through 570 removed outlier: 3.836A pdb=" N ASP B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 584 removed outlier: 3.891A pdb=" N LEU B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Proline residue: B 583 - end of helix Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 603 through 637 removed outlier: 5.886A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 667 removed outlier: 4.108A pdb=" N GLU B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 698 Processing helix chain 'B' and resid 705 through 722 Processing helix chain 'B' and resid 732 through 738 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.533A pdb=" N VAL B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 811 through 816 Processing helix chain 'B' and resid 837 through 845 removed outlier: 4.185A pdb=" N SER B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 865 Processing helix chain 'B' and resid 867 through 870 No H-bonds generated for 'chain 'B' and resid 867 through 870' Processing helix chain 'B' and resid 875 through 883 removed outlier: 3.506A pdb=" N ARG B 879 " --> pdb=" O MET B 875 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1041 Processing sheet with id= A, first strand: chain 'A' and resid 807 through 809 removed outlier: 3.567A pdb=" N SER A 807 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 831 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 787 through 789 Processing sheet with id= C, first strand: chain 'A' and resid 889 through 892 removed outlier: 6.582A pdb=" N ILE A 968 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU A 908 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE A 970 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY A 906 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 807 through 809 removed outlier: 3.567A pdb=" N SER B 807 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 831 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 787 through 789 Processing sheet with id= F, first strand: chain 'B' and resid 889 through 892 removed outlier: 6.581A pdb=" N ILE B 968 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU B 908 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE B 970 " --> pdb=" O GLY B 906 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY B 906 " --> pdb=" O PHE B 970 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2478 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: 4.60 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2314 1.32 - 1.44: 3852 1.44 - 1.56: 8616 1.56 - 1.69: 2 1.69 - 1.81: 102 Bond restraints: 14886 Sorted by residual: bond pdb=" C THR B 423 " pdb=" O THR B 423 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" C THR A 423 " pdb=" O THR A 423 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" N SER A 418 " pdb=" CA SER A 418 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N SER B 418 " pdb=" CA SER B 418 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" CA SER A 418 " pdb=" CB SER A 418 " ideal model delta sigma weight residual 1.530 1.477 0.054 1.69e-02 3.50e+03 1.01e+01 ... (remaining 14881 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.09: 289 106.09 - 113.07: 8301 113.07 - 120.05: 5239 120.05 - 127.03: 6144 127.03 - 134.02: 183 Bond angle restraints: 20156 Sorted by residual: angle pdb=" N LEU B 424 " pdb=" CA LEU B 424 " pdb=" C LEU B 424 " ideal model delta sigma weight residual 111.33 104.16 7.17 1.21e+00 6.83e-01 3.51e+01 angle pdb=" N LEU A 424 " pdb=" CA LEU A 424 " pdb=" C LEU A 424 " ideal model delta sigma weight residual 111.33 104.17 7.16 1.21e+00 6.83e-01 3.50e+01 angle pdb=" C LEU B 424 " pdb=" N PHE B 425 " pdb=" CA PHE B 425 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" C LEU A 424 " pdb=" N PHE A 425 " pdb=" CA PHE A 425 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" N GLU A 420 " pdb=" CA GLU A 420 " pdb=" C GLU A 420 " ideal model delta sigma weight residual 111.07 105.65 5.42 1.07e+00 8.73e-01 2.57e+01 ... (remaining 20151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7965 17.76 - 35.52: 765 35.52 - 53.28: 110 53.28 - 71.03: 12 71.03 - 88.79: 14 Dihedral angle restraints: 8866 sinusoidal: 3506 harmonic: 5360 Sorted by residual: dihedral pdb=" CA PHE A 152 " pdb=" C PHE A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta harmonic sigma weight residual -180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PHE B 152 " pdb=" C PHE B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta harmonic sigma weight residual 180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU B 168 " pdb=" C LEU B 168 " pdb=" N SER B 169 " pdb=" CA SER B 169 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2089 0.064 - 0.129: 263 0.129 - 0.193: 14 0.193 - 0.258: 2 0.258 - 0.322: 4 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CB THR B 421 " pdb=" CA THR B 421 " pdb=" OG1 THR B 421 " pdb=" CG2 THR B 421 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB THR A 421 " pdb=" CA THR A 421 " pdb=" OG1 THR A 421 " pdb=" CG2 THR A 421 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLU B 420 " pdb=" N GLU B 420 " pdb=" C GLU B 420 " pdb=" CB GLU B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2369 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 489 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 490 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 489 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 490 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 156 " 0.020 2.00e-02 2.50e+03 1.90e-02 9.03e+00 pdb=" CG TRP B 156 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 156 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 156 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 156 " 0.002 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2845 2.77 - 3.31: 15281 3.31 - 3.84: 24857 3.84 - 4.37: 28060 4.37 - 4.90: 48527 Nonbonded interactions: 119570 Sorted by model distance: nonbonded pdb=" OG SER A 897 " pdb=" O GLN A 958 " model vdw 2.242 2.440 nonbonded pdb=" OG SER B 897 " pdb=" O GLN B 958 " model vdw 2.243 2.440 nonbonded pdb=" NE2 GLN A 128 " pdb=" O TYR A 381 " model vdw 2.252 2.520 nonbonded pdb=" NE2 GLN B 128 " pdb=" O TYR B 381 " model vdw 2.252 2.520 nonbonded pdb=" NZ LYS A 386 " pdb=" O LEU A 451 " model vdw 2.276 2.520 ... (remaining 119565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.370 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: 7.590 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 42.790 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.004 0.080 14886 Z= 0.244 Angle : 0.712 10.486 20156 Z= 0.400 Chirality : 0.044 0.322 2372 Planarity : 0.005 0.112 2472 Dihedral : 13.946 88.793 5410 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.88 (0.20), residues: 1836 helix: 1.41 (0.15), residues: 1212 sheet: 1.66 (0.57), residues: 80 loop : -1.47 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 156 HIS 0.003 0.001 HIS B 626 PHE 0.029 0.001 PHE B 425 TYR 0.041 0.002 TYR A 617 ARG 0.008 0.001 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.803 Fit side-chains REVERT: A 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8613 (t0) REVERT: A 172 ASP cc_start: 0.8508 (t0) cc_final: 0.8222 (t70) REVERT: A 355 PHE cc_start: 0.8176 (m-10) cc_final: 0.7946 (m-80) REVERT: A 492 ASP cc_start: 0.7556 (t70) cc_final: 0.7344 (t70) REVERT: A 533 MET cc_start: 0.7611 (tmm) cc_final: 0.6994 (tmm) REVERT: A 613 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 755 HIS cc_start: 0.6008 (m-70) cc_final: 0.5565 (m-70) REVERT: A 914 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8413 (mmmt) REVERT: B 94 ASN cc_start: 0.8886 (t0) cc_final: 0.8608 (t0) REVERT: B 172 ASP cc_start: 0.8472 (t0) cc_final: 0.8222 (t0) REVERT: B 533 MET cc_start: 0.7573 (tmm) cc_final: 0.6928 (tmm) REVERT: B 613 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 755 HIS cc_start: 0.5964 (m-70) cc_final: 0.5569 (m-70) REVERT: B 865 LEU cc_start: 0.8822 (mm) cc_final: 0.8477 (mt) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2401 time to fit residues: 116.8807 Evaluate side-chains 247 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14886 Z= 0.211 Angle : 0.602 10.184 20156 Z= 0.299 Chirality : 0.041 0.241 2372 Planarity : 0.004 0.073 2472 Dihedral : 5.087 30.779 2028 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.31 % Allowed : 9.94 % Favored : 88.75 % 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: 0.98 (0.20), residues: 1836 helix: 1.47 (0.15), residues: 1210 sheet: 1.39 (0.57), residues: 80 loop : -1.34 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 544 HIS 0.004 0.001 HIS A 805 PHE 0.019 0.001 PHE B 298 TYR 0.026 0.001 TYR A 617 ARG 0.005 0.001 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 279 time to evaluate : 3.707 Fit side-chains REVERT: A 172 ASP cc_start: 0.8483 (t0) cc_final: 0.8051 (t0) REVERT: A 492 ASP cc_start: 0.7556 (t70) cc_final: 0.7263 (t70) REVERT: A 570 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: A 597 LYS cc_start: 0.2575 (mptt) cc_final: 0.2266 (tptp) REVERT: A 613 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7073 (tt0) REVERT: A 755 HIS cc_start: 0.6078 (m-70) cc_final: 0.5835 (m90) REVERT: A 761 MET cc_start: 0.7236 (tmm) cc_final: 0.6989 (tmm) REVERT: B 172 ASP cc_start: 0.8490 (t0) cc_final: 0.8058 (t0) REVERT: B 533 MET cc_start: 0.7561 (tmm) cc_final: 0.6936 (tmm) REVERT: B 570 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7948 (pt0) REVERT: B 613 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7079 (tt0) REVERT: B 761 MET cc_start: 0.7238 (tmm) cc_final: 0.6989 (tmm) outliers start: 21 outliers final: 14 residues processed: 288 average time/residue: 0.2304 time to fit residues: 104.0953 Evaluate side-chains 268 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 252 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14886 Z= 0.204 Angle : 0.571 9.769 20156 Z= 0.284 Chirality : 0.040 0.232 2372 Planarity : 0.004 0.062 2472 Dihedral : 4.961 30.095 2028 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.00 % Allowed : 12.69 % Favored : 85.31 % 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: 1.05 (0.20), residues: 1836 helix: 1.52 (0.15), residues: 1210 sheet: 1.23 (0.60), residues: 76 loop : -1.24 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 854 HIS 0.004 0.001 HIS A 805 PHE 0.017 0.001 PHE A 970 TYR 0.014 0.001 TYR B 617 ARG 0.005 0.000 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 262 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8898 (t0) cc_final: 0.8573 (t0) REVERT: A 156 TRP cc_start: 0.7591 (m100) cc_final: 0.7256 (m100) REVERT: A 172 ASP cc_start: 0.8567 (t0) cc_final: 0.8018 (t0) REVERT: A 492 ASP cc_start: 0.7497 (t70) cc_final: 0.7134 (t70) REVERT: A 533 MET cc_start: 0.7974 (tmm) cc_final: 0.7643 (tmm) REVERT: A 570 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: A 656 GLU cc_start: 0.7278 (tm-30) cc_final: 0.7002 (tm-30) REVERT: A 693 GLU cc_start: 0.7937 (tp30) cc_final: 0.7710 (tp30) REVERT: A 755 HIS cc_start: 0.6061 (m-70) cc_final: 0.5838 (m-70) REVERT: A 829 MET cc_start: 0.8560 (ppp) cc_final: 0.8155 (tmm) REVERT: A 891 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8478 (t) REVERT: A 966 ARG cc_start: 0.6902 (ttp-110) cc_final: 0.6462 (ttp-170) REVERT: B 94 ASN cc_start: 0.8891 (t0) cc_final: 0.8551 (t0) REVERT: B 156 TRP cc_start: 0.7681 (m100) cc_final: 0.7274 (m100) REVERT: B 172 ASP cc_start: 0.8547 (t0) cc_final: 0.7993 (t0) REVERT: B 426 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7780 (tp) REVERT: B 533 MET cc_start: 0.7494 (tmm) cc_final: 0.6877 (tmm) REVERT: B 570 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: B 610 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7385 (mt-10) REVERT: B 656 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 693 GLU cc_start: 0.7960 (tp30) cc_final: 0.7680 (tp30) REVERT: B 761 MET cc_start: 0.7140 (tmm) cc_final: 0.6801 (tmm) REVERT: B 891 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8535 (t) outliers start: 32 outliers final: 20 residues processed: 277 average time/residue: 0.2255 time to fit residues: 97.2399 Evaluate side-chains 268 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 243 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 0.0050 chunk 177 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14886 Z= 0.303 Angle : 0.614 8.875 20156 Z= 0.305 Chirality : 0.041 0.197 2372 Planarity : 0.004 0.057 2472 Dihedral : 5.167 37.375 2028 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.06 % Allowed : 15.06 % Favored : 81.88 % 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: 0.97 (0.20), residues: 1836 helix: 1.43 (0.15), residues: 1210 sheet: 1.30 (0.59), residues: 80 loop : -1.23 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 854 HIS 0.004 0.001 HIS A 805 PHE 0.022 0.001 PHE B 970 TYR 0.015 0.001 TYR A 617 ARG 0.006 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 264 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8908 (t0) cc_final: 0.8547 (t0) REVERT: A 120 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7905 (p90) REVERT: A 172 ASP cc_start: 0.8573 (t0) cc_final: 0.7983 (t0) REVERT: A 214 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.4798 (ppp) REVERT: A 492 ASP cc_start: 0.7549 (t70) cc_final: 0.7164 (t70) REVERT: A 570 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: A 610 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7398 (mt-10) REVERT: A 617 TYR cc_start: 0.7883 (m-10) cc_final: 0.7610 (m-10) REVERT: A 693 GLU cc_start: 0.8018 (tp30) cc_final: 0.7697 (tp30) REVERT: A 755 HIS cc_start: 0.6200 (m-70) cc_final: 0.5855 (m-70) REVERT: A 829 MET cc_start: 0.8600 (ppp) cc_final: 0.8194 (tmm) REVERT: A 1037 MET cc_start: 0.6993 (ttm) cc_final: 0.6762 (ttm) REVERT: B 94 ASN cc_start: 0.8902 (t0) cc_final: 0.8560 (t0) REVERT: B 172 ASP cc_start: 0.8557 (t0) cc_final: 0.7920 (t0) REVERT: B 214 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.4843 (ppp) REVERT: B 426 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 492 ASP cc_start: 0.7677 (t70) cc_final: 0.7249 (t70) REVERT: B 533 MET cc_start: 0.7536 (tmm) cc_final: 0.7240 (tmm) REVERT: B 570 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: B 610 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 693 GLU cc_start: 0.8039 (tp30) cc_final: 0.7736 (tp30) REVERT: B 829 MET cc_start: 0.8442 (ppp) cc_final: 0.8152 (tmm) REVERT: B 1011 MET cc_start: 0.7294 (ttm) cc_final: 0.7088 (ttm) outliers start: 49 outliers final: 30 residues processed: 291 average time/residue: 0.2304 time to fit residues: 103.8085 Evaluate side-chains 292 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 256 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 chunk 159 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14886 Z= 0.198 Angle : 0.578 9.482 20156 Z= 0.284 Chirality : 0.040 0.228 2372 Planarity : 0.004 0.052 2472 Dihedral : 4.965 31.581 2028 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.69 % Allowed : 16.81 % Favored : 80.50 % 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: 1.09 (0.20), residues: 1836 helix: 1.55 (0.15), residues: 1208 sheet: 1.29 (0.60), residues: 78 loop : -1.25 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 854 HIS 0.004 0.001 HIS B 626 PHE 0.013 0.001 PHE B 970 TYR 0.012 0.001 TYR B 617 ARG 0.006 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 267 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.6983 (mtm110) cc_final: 0.6709 (mtm110) REVERT: A 94 ASN cc_start: 0.8884 (t0) cc_final: 0.8531 (t0) REVERT: A 172 ASP cc_start: 0.8544 (t0) cc_final: 0.7946 (t0) REVERT: A 214 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.4759 (ppp) REVERT: A 492 ASP cc_start: 0.7497 (t70) cc_final: 0.7098 (t70) REVERT: A 570 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: A 617 TYR cc_start: 0.7845 (m-10) cc_final: 0.7601 (m-10) REVERT: A 693 GLU cc_start: 0.7987 (tp30) cc_final: 0.7682 (tp30) REVERT: A 755 HIS cc_start: 0.6207 (m-70) cc_final: 0.5945 (m-70) REVERT: A 829 MET cc_start: 0.8592 (ppp) cc_final: 0.8191 (tmm) REVERT: A 875 MET cc_start: 0.8644 (ttm) cc_final: 0.8401 (tpp) REVERT: A 891 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8676 (t) REVERT: A 966 ARG cc_start: 0.6722 (ttm-80) cc_final: 0.5677 (ttp80) REVERT: B 91 ARG cc_start: 0.7058 (mtm110) cc_final: 0.6802 (mtm110) REVERT: B 94 ASN cc_start: 0.8889 (t0) cc_final: 0.8530 (t0) REVERT: B 172 ASP cc_start: 0.8549 (t0) cc_final: 0.7910 (t0) REVERT: B 214 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.4960 (ppp) REVERT: B 492 ASP cc_start: 0.7627 (t70) cc_final: 0.7423 (t0) REVERT: B 533 MET cc_start: 0.7567 (tmm) cc_final: 0.7237 (tmm) REVERT: B 656 GLU cc_start: 0.7741 (tp30) cc_final: 0.7486 (tm-30) REVERT: B 693 GLU cc_start: 0.7947 (tp30) cc_final: 0.7650 (tp30) REVERT: B 829 MET cc_start: 0.8529 (ppp) cc_final: 0.8191 (tmm) REVERT: B 891 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8696 (t) outliers start: 43 outliers final: 27 residues processed: 289 average time/residue: 0.2288 time to fit residues: 101.7743 Evaluate side-chains 286 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 chunk 147 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14886 Z= 0.191 Angle : 0.575 10.116 20156 Z= 0.280 Chirality : 0.040 0.225 2372 Planarity : 0.004 0.049 2472 Dihedral : 4.864 28.725 2028 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.25 % Allowed : 17.50 % Favored : 79.25 % 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: 1.15 (0.20), residues: 1836 helix: 1.62 (0.15), residues: 1206 sheet: 1.26 (0.60), residues: 78 loop : -1.25 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 854 HIS 0.004 0.001 HIS B 626 PHE 0.011 0.001 PHE A 622 TYR 0.014 0.001 TYR B 617 ARG 0.007 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 276 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.6936 (mtm110) cc_final: 0.6592 (mtm110) REVERT: A 94 ASN cc_start: 0.8858 (t0) cc_final: 0.8428 (t0) REVERT: A 172 ASP cc_start: 0.8503 (t0) cc_final: 0.7812 (t0) REVERT: A 214 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.4746 (ppp) REVERT: A 492 ASP cc_start: 0.7476 (t70) cc_final: 0.7068 (t70) REVERT: A 617 TYR cc_start: 0.7944 (m-10) cc_final: 0.7621 (m-10) REVERT: A 693 GLU cc_start: 0.8017 (tp30) cc_final: 0.7719 (tp30) REVERT: A 755 HIS cc_start: 0.6129 (m-70) cc_final: 0.5885 (m-70) REVERT: A 829 MET cc_start: 0.8578 (ppp) cc_final: 0.8173 (tmm) REVERT: A 891 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8713 (t) REVERT: A 1042 PHE cc_start: 0.7961 (m-10) cc_final: 0.7702 (m-10) REVERT: B 91 ARG cc_start: 0.7033 (mtm110) cc_final: 0.6691 (mtm110) REVERT: B 94 ASN cc_start: 0.8875 (t0) cc_final: 0.8442 (t0) REVERT: B 172 ASP cc_start: 0.8509 (t0) cc_final: 0.7836 (t0) REVERT: B 214 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.4866 (ppp) REVERT: B 492 ASP cc_start: 0.7570 (t70) cc_final: 0.7364 (t0) REVERT: B 533 MET cc_start: 0.7519 (tmm) cc_final: 0.7173 (tmm) REVERT: B 559 ILE cc_start: 0.8157 (mt) cc_final: 0.7903 (mp) REVERT: B 693 GLU cc_start: 0.8005 (tp30) cc_final: 0.7717 (tp30) REVERT: B 805 HIS cc_start: 0.7699 (p90) cc_final: 0.7498 (p90) REVERT: B 829 MET cc_start: 0.8541 (ppp) cc_final: 0.8147 (tmm) REVERT: B 891 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8709 (t) REVERT: B 1042 PHE cc_start: 0.7932 (m-10) cc_final: 0.7684 (m-10) outliers start: 52 outliers final: 33 residues processed: 305 average time/residue: 0.2346 time to fit residues: 110.8686 Evaluate side-chains 299 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 262 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 0.0020 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14886 Z= 0.191 Angle : 0.580 10.694 20156 Z= 0.282 Chirality : 0.039 0.227 2372 Planarity : 0.004 0.048 2472 Dihedral : 4.803 27.906 2028 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.31 % Allowed : 17.50 % Favored : 79.19 % 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: 1.19 (0.20), residues: 1836 helix: 1.66 (0.15), residues: 1204 sheet: 1.24 (0.60), residues: 78 loop : -1.24 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 854 HIS 0.005 0.001 HIS B 626 PHE 0.011 0.001 PHE A 622 TYR 0.012 0.001 TYR B 617 ARG 0.007 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 280 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8853 (t0) cc_final: 0.8432 (t0) REVERT: A 172 ASP cc_start: 0.8511 (t0) cc_final: 0.7807 (t0) REVERT: A 214 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.4744 (ppp) REVERT: A 492 ASP cc_start: 0.7472 (t70) cc_final: 0.7057 (t70) REVERT: A 559 ILE cc_start: 0.8147 (mt) cc_final: 0.7888 (mp) REVERT: A 617 TYR cc_start: 0.7989 (m-10) cc_final: 0.7652 (m-10) REVERT: A 693 GLU cc_start: 0.8021 (tp30) cc_final: 0.7729 (tp30) REVERT: A 755 HIS cc_start: 0.6075 (m-70) cc_final: 0.5856 (m-70) REVERT: A 829 MET cc_start: 0.8495 (ppp) cc_final: 0.8106 (tmm) REVERT: A 891 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8668 (t) REVERT: A 966 ARG cc_start: 0.6733 (ttm-80) cc_final: 0.6297 (ptm160) REVERT: A 1042 PHE cc_start: 0.8104 (m-10) cc_final: 0.7869 (m-10) REVERT: B 94 ASN cc_start: 0.8876 (t0) cc_final: 0.8444 (t0) REVERT: B 172 ASP cc_start: 0.8488 (t0) cc_final: 0.7767 (t0) REVERT: B 214 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.4936 (ppp) REVERT: B 241 LEU cc_start: 0.8708 (mt) cc_final: 0.8492 (mt) REVERT: B 492 ASP cc_start: 0.7575 (t70) cc_final: 0.7361 (t0) REVERT: B 533 MET cc_start: 0.7532 (tmm) cc_final: 0.7173 (tmm) REVERT: B 559 ILE cc_start: 0.8148 (mt) cc_final: 0.7894 (mp) REVERT: B 693 GLU cc_start: 0.7990 (tp30) cc_final: 0.7693 (tp30) REVERT: B 829 MET cc_start: 0.8542 (ppp) cc_final: 0.8148 (tmm) REVERT: B 891 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8675 (t) REVERT: B 966 ARG cc_start: 0.6769 (ttm-80) cc_final: 0.6316 (ptm160) outliers start: 53 outliers final: 40 residues processed: 311 average time/residue: 0.2332 time to fit residues: 112.5848 Evaluate side-chains 314 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 959 TYR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 0.0370 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14886 Z= 0.194 Angle : 0.586 10.742 20156 Z= 0.285 Chirality : 0.040 0.228 2372 Planarity : 0.004 0.045 2472 Dihedral : 4.760 27.453 2028 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.38 % Allowed : 17.69 % Favored : 78.94 % 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: 1.21 (0.20), residues: 1836 helix: 1.68 (0.15), residues: 1204 sheet: 1.23 (0.59), residues: 78 loop : -1.23 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 854 HIS 0.004 0.001 HIS A 626 PHE 0.011 0.001 PHE B 622 TYR 0.012 0.001 TYR B 617 ARG 0.007 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 279 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8861 (t0) cc_final: 0.8459 (t0) REVERT: A 118 GLU cc_start: 0.7385 (pt0) cc_final: 0.7182 (pt0) REVERT: A 214 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.4754 (ppp) REVERT: A 492 ASP cc_start: 0.7482 (t70) cc_final: 0.7058 (t70) REVERT: A 559 ILE cc_start: 0.8144 (mt) cc_final: 0.7884 (mp) REVERT: A 617 TYR cc_start: 0.8039 (m-10) cc_final: 0.7797 (m-10) REVERT: A 693 GLU cc_start: 0.8038 (tp30) cc_final: 0.7752 (tp30) REVERT: A 755 HIS cc_start: 0.6051 (m-70) cc_final: 0.5837 (m-70) REVERT: A 805 HIS cc_start: 0.7761 (p90) cc_final: 0.7530 (p90) REVERT: A 829 MET cc_start: 0.8482 (ppp) cc_final: 0.8089 (tmm) REVERT: A 891 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8697 (t) REVERT: A 1042 PHE cc_start: 0.7933 (m-10) cc_final: 0.7710 (m-10) REVERT: B 94 ASN cc_start: 0.8896 (t0) cc_final: 0.8456 (t0) REVERT: B 172 ASP cc_start: 0.8491 (t0) cc_final: 0.7783 (t0) REVERT: B 214 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.4888 (ppp) REVERT: B 241 LEU cc_start: 0.8719 (mt) cc_final: 0.8498 (mt) REVERT: B 492 ASP cc_start: 0.7576 (t70) cc_final: 0.7360 (t0) REVERT: B 559 ILE cc_start: 0.8148 (mt) cc_final: 0.7890 (mp) REVERT: B 693 GLU cc_start: 0.7991 (tp30) cc_final: 0.7695 (tp30) REVERT: B 829 MET cc_start: 0.8461 (ppp) cc_final: 0.8073 (tmm) REVERT: B 891 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8670 (t) REVERT: B 966 ARG cc_start: 0.6778 (ttm-80) cc_final: 0.5518 (ttp80) outliers start: 54 outliers final: 41 residues processed: 313 average time/residue: 0.2263 time to fit residues: 109.4463 Evaluate side-chains 303 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 258 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 959 TYR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14886 Z= 0.189 Angle : 0.597 11.089 20156 Z= 0.289 Chirality : 0.041 0.272 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.743 27.049 2028 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.44 % Allowed : 18.19 % Favored : 78.38 % 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: 1.22 (0.20), residues: 1836 helix: 1.67 (0.15), residues: 1204 sheet: 1.21 (0.59), residues: 78 loop : -1.19 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 854 HIS 0.004 0.001 HIS B 626 PHE 0.011 0.001 PHE A 622 TYR 0.015 0.001 TYR B 892 ARG 0.007 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 279 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8858 (t0) cc_final: 0.8491 (t0) REVERT: A 214 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.4781 (ppp) REVERT: A 492 ASP cc_start: 0.7473 (t70) cc_final: 0.7046 (t70) REVERT: A 559 ILE cc_start: 0.8154 (mt) cc_final: 0.7897 (mp) REVERT: A 617 TYR cc_start: 0.8035 (m-10) cc_final: 0.7767 (m-10) REVERT: A 693 GLU cc_start: 0.8040 (tp30) cc_final: 0.7752 (tp30) REVERT: A 805 HIS cc_start: 0.7742 (p90) cc_final: 0.7500 (p90) REVERT: A 829 MET cc_start: 0.8365 (ppp) cc_final: 0.7998 (tmm) REVERT: A 891 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8672 (t) REVERT: A 966 ARG cc_start: 0.6708 (ttm-80) cc_final: 0.6215 (ptm160) REVERT: B 94 ASN cc_start: 0.8885 (t0) cc_final: 0.8443 (t0) REVERT: B 214 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.4924 (ppp) REVERT: B 241 LEU cc_start: 0.8733 (mt) cc_final: 0.8524 (mt) REVERT: B 492 ASP cc_start: 0.7524 (t70) cc_final: 0.7314 (t0) REVERT: B 559 ILE cc_start: 0.8139 (mt) cc_final: 0.7784 (mp) REVERT: B 562 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 656 GLU cc_start: 0.7643 (tp30) cc_final: 0.7346 (tm-30) REVERT: B 693 GLU cc_start: 0.7997 (tp30) cc_final: 0.7706 (tp30) REVERT: B 697 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8699 (ttpp) REVERT: B 829 MET cc_start: 0.8374 (ppp) cc_final: 0.8032 (tmm) REVERT: B 891 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8653 (t) REVERT: B 966 ARG cc_start: 0.6705 (ttm-80) cc_final: 0.5525 (ttp80) outliers start: 55 outliers final: 42 residues processed: 313 average time/residue: 0.2275 time to fit residues: 110.3657 Evaluate side-chains 303 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 257 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 959 TYR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 82 optimal weight: 0.0270 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14886 Z= 0.195 Angle : 0.617 10.645 20156 Z= 0.296 Chirality : 0.041 0.221 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.728 26.651 2028 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.06 % Allowed : 19.00 % Favored : 77.94 % 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: 1.17 (0.20), residues: 1836 helix: 1.62 (0.15), residues: 1210 sheet: 1.15 (0.58), residues: 78 loop : -1.22 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1013 HIS 0.007 0.001 HIS A 755 PHE 0.017 0.001 PHE B 228 TYR 0.014 0.001 TYR B 617 ARG 0.007 0.000 ARG B 601 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 270 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8867 (t0) cc_final: 0.8522 (t0) REVERT: A 156 TRP cc_start: 0.7401 (m100) cc_final: 0.7166 (m100) REVERT: A 172 ASP cc_start: 0.8401 (t70) cc_final: 0.7225 (t0) REVERT: A 214 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.4813 (ppp) REVERT: A 241 LEU cc_start: 0.8724 (mt) cc_final: 0.8520 (mt) REVERT: A 492 ASP cc_start: 0.7476 (t70) cc_final: 0.7243 (t0) REVERT: A 559 ILE cc_start: 0.8152 (mt) cc_final: 0.7797 (mp) REVERT: A 562 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 617 TYR cc_start: 0.8038 (m-10) cc_final: 0.7774 (m-10) REVERT: A 693 GLU cc_start: 0.8042 (tp30) cc_final: 0.7757 (tp30) REVERT: A 770 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8369 (mptt) REVERT: A 829 MET cc_start: 0.8382 (ppp) cc_final: 0.8028 (tmm) REVERT: A 891 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8716 (t) REVERT: B 94 ASN cc_start: 0.8878 (t0) cc_final: 0.8494 (t0) REVERT: B 214 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.4859 (ppp) REVERT: B 241 LEU cc_start: 0.8728 (mt) cc_final: 0.8525 (mt) REVERT: B 492 ASP cc_start: 0.7530 (t70) cc_final: 0.7317 (t0) REVERT: B 559 ILE cc_start: 0.8156 (mt) cc_final: 0.7812 (mp) REVERT: B 562 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7328 (tm-30) REVERT: B 597 LYS cc_start: 0.2853 (mptt) cc_final: 0.2359 (tptp) REVERT: B 656 GLU cc_start: 0.7643 (tp30) cc_final: 0.7348 (tm-30) REVERT: B 693 GLU cc_start: 0.7982 (tp30) cc_final: 0.7692 (tp30) REVERT: B 697 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8716 (ttpp) REVERT: B 770 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8377 (mptt) REVERT: B 829 MET cc_start: 0.8368 (ppp) cc_final: 0.8025 (tmm) REVERT: B 891 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8671 (t) REVERT: B 966 ARG cc_start: 0.6673 (ttm-80) cc_final: 0.5473 (ttp80) outliers start: 49 outliers final: 44 residues processed: 300 average time/residue: 0.2263 time to fit residues: 106.8376 Evaluate side-chains 312 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 264 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 959 TYR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 0.0020 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 18 optimal weight: 0.0050 chunk 26 optimal weight: 0.5980 chunk 128 optimal weight: 0.4980 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN A 800 HIS ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.147169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118455 restraints weight = 22882.049| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.09 r_work: 0.3400 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14886 Z= 0.171 Angle : 0.620 10.566 20156 Z= 0.295 Chirality : 0.040 0.226 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.645 26.366 2028 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.19 % Allowed : 19.06 % Favored : 77.75 % 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: 1.21 (0.20), residues: 1836 helix: 1.67 (0.15), residues: 1204 sheet: 1.16 (0.58), residues: 78 loop : -1.21 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1013 HIS 0.004 0.001 HIS B 626 PHE 0.018 0.001 PHE B 228 TYR 0.041 0.001 TYR B 892 ARG 0.007 0.000 ARG B 601 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3308.73 seconds wall clock time: 60 minutes 40.92 seconds (3640.92 seconds total)