Starting phenix.real_space_refine on Sun Jul 21 14:19:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/07_2024/7y3e_33592.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/07_2024/7y3e_33592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/07_2024/7y3e_33592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/07_2024/7y3e_33592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/07_2024/7y3e_33592.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/07_2024/7y3e_33592.cif" } resolution = 2.8 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= 0.142 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 9522 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 GLU 95": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 827": "OD1" <-> "OD2" Residue "A PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 827": "OD1" <-> "OD2" Residue "B PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 856": "OE1" <-> "OE2" Residue "B PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14572 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.89, per 1000 atoms: 0.61 Number of scatterers: 14572 At special positions: 0 Unit cell: (115.44, 105.04, 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 9522 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: 5.95 Conformation dependent library (CDL) restraints added in 2.6 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... Secondary structure from input PDB file: 80 helices and 8 sheets defined 69.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.625A pdb=" N LEU A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 4.061A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 97 through 116 Proline residue: A 107 - end of helix removed outlier: 4.568A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 151 removed outlier: 5.825A pdb=" N GLY A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.729A pdb=" N GLU A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 216 removed outlier: 3.672A pdb=" N ASP A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 253 removed outlier: 3.955A pdb=" N ALA A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.597A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 306 through 339 removed outlier: 4.357A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.784A pdb=" N GLN A 347 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 377 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 418 through 442 removed outlier: 3.752A pdb=" N SER A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 457 through 482 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 527 through 549 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 603 through 638 removed outlier: 5.736A pdb=" N SER A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 654 through 668 removed outlier: 3.756A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 699 Processing helix chain 'A' and resid 704 through 723 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.815A pdb=" N VAL A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 837 through 842 Processing helix chain 'A' and resid 846 through 866 removed outlier: 3.654A pdb=" N PHE A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.525A pdb=" N GLU A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 3.682A pdb=" N ILE A1017 " --> pdb=" O TRP A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1042 Processing helix chain 'B' and resid 34 through 54 removed outlier: 3.625A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 4.061A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 97 through 116 Proline residue: B 107 - end of helix removed outlier: 4.568A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 151 removed outlier: 5.825A pdb=" N GLY B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.729A pdb=" N GLU B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 216 removed outlier: 3.673A pdb=" N ASP B 201 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 253 removed outlier: 3.956A pdb=" N ALA B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 3.597A pdb=" N THR B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 306 through 339 removed outlier: 4.357A pdb=" N SER B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.784A pdb=" N GLN B 347 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 377 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 418 through 442 removed outlier: 3.752A pdb=" N SER B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 457 through 482 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 527 through 549 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 602 through 638 removed outlier: 4.189A pdb=" N TYR B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.756A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 699 Processing helix chain 'B' and resid 704 through 723 Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.814A pdb=" N VAL B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 810 through 817 Processing helix chain 'B' and resid 837 through 842 Processing helix chain 'B' and resid 846 through 866 removed outlier: 3.654A pdb=" N PHE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 871 removed outlier: 3.525A pdb=" N GLU B 871 " --> pdb=" O PRO B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 884 Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.682A pdb=" N ILE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1042 Processing sheet with id=AA1, first strand: chain 'A' and resid 761 through 762 removed outlier: 6.413A pdb=" N LEU A 831 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 767 through 769 removed outlier: 6.938A pdb=" N LEU A 824 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 888 through 892 removed outlier: 6.264A pdb=" N ARG A 966 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 914 Processing sheet with id=AA5, first strand: chain 'B' and resid 761 through 762 removed outlier: 6.413A pdb=" N LEU B 831 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 767 through 769 removed outlier: 6.938A pdb=" N LEU B 824 " --> pdb=" O LEU B 768 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 888 through 892 removed outlier: 6.264A pdb=" N ARG B 966 " --> pdb=" O LEU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 913 through 914 980 hydrogen bonds defined for protein. 2856 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: 4.96 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4413 1.34 - 1.45: 2051 1.45 - 1.57: 8308 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 14874 Sorted by residual: bond pdb=" CA SER A 116 " pdb=" C SER A 116 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.39e+00 bond pdb=" CA SER B 116 " pdb=" C SER B 116 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.35e+00 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.331 1.345 -0.014 7.90e-03 1.60e+04 2.98e+00 bond pdb=" C PHE A 152 " pdb=" N PRO A 153 " ideal model delta sigma weight residual 1.331 1.345 -0.013 7.90e-03 1.60e+04 2.87e+00 bond pdb=" CG1 ILE A 361 " pdb=" CD1 ILE A 361 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 258 105.81 - 112.87: 8288 112.87 - 119.93: 4923 119.93 - 126.99: 6494 126.99 - 134.05: 183 Bond angle restraints: 20146 Sorted by residual: angle pdb=" N GLN A 876 " pdb=" CA GLN A 876 " pdb=" C GLN A 876 " ideal model delta sigma weight residual 113.55 107.83 5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" N GLN B 876 " pdb=" CA GLN B 876 " pdb=" C GLN B 876 " ideal model delta sigma weight residual 113.55 107.83 5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" N VAL B 119 " pdb=" CA VAL B 119 " pdb=" C VAL B 119 " ideal model delta sigma weight residual 110.72 114.10 -3.38 1.01e+00 9.80e-01 1.12e+01 angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 110.72 114.09 -3.37 1.01e+00 9.80e-01 1.12e+01 angle pdb=" C ILE B1041 " pdb=" N PHE B1042 " pdb=" CA PHE B1042 " ideal model delta sigma weight residual 122.12 127.94 -5.82 1.76e+00 3.23e-01 1.09e+01 ... (remaining 20141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8021 17.87 - 35.74: 709 35.74 - 53.62: 88 53.62 - 71.49: 22 71.49 - 89.36: 18 Dihedral angle restraints: 8858 sinusoidal: 3498 harmonic: 5360 Sorted by residual: dihedral pdb=" CA ARG A 449 " pdb=" C ARG A 449 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ARG B 449 " pdb=" C ARG B 449 " pdb=" N LEU B 450 " pdb=" CA LEU B 450 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU A 109 " pdb=" C LEU A 109 " pdb=" N LEU A 110 " pdb=" CA LEU A 110 " ideal model delta harmonic sigma weight residual 180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1456 0.034 - 0.068: 654 0.068 - 0.101: 209 0.101 - 0.135: 47 0.135 - 0.169: 6 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CA SER A 925 " pdb=" N SER A 925 " pdb=" C SER A 925 " pdb=" CB SER A 925 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA SER B 925 " pdb=" N SER B 925 " pdb=" C SER B 925 " pdb=" CB SER B 925 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CG LEU A 700 " pdb=" CB LEU A 700 " pdb=" CD1 LEU A 700 " pdb=" CD2 LEU A 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2369 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1044 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C SER B1044 " -0.032 2.00e-02 2.50e+03 pdb=" O SER B1044 " 0.012 2.00e-02 2.50e+03 pdb=" N MET B1045 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1044 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.29e+00 pdb=" C SER A1044 " 0.031 2.00e-02 2.50e+03 pdb=" O SER A1044 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A1045 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 774 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 775 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 775 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 775 " -0.024 5.00e-02 4.00e+02 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1210 2.74 - 3.28: 15269 3.28 - 3.82: 25266 3.82 - 4.36: 31008 4.36 - 4.90: 53542 Nonbonded interactions: 126295 Sorted by model distance: nonbonded pdb=" O VAL B 439 " pdb=" OG1 THR B 443 " model vdw 2.197 2.440 nonbonded pdb=" O VAL A 439 " pdb=" OG1 THR A 443 " model vdw 2.197 2.440 nonbonded pdb=" OE1 GLU A 470 " pdb=" OH TYR B 691 " model vdw 2.198 2.440 nonbonded pdb=" OG SER A 140 " pdb=" OG SER A 169 " model vdw 2.203 2.440 nonbonded pdb=" OG SER B 140 " pdb=" OG SER B 169 " model vdw 2.203 2.440 ... (remaining 126290 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 42.160 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 0.054 14874 Z= 0.285 Angle : 0.709 6.858 20146 Z= 0.392 Chirality : 0.042 0.169 2372 Planarity : 0.004 0.042 2472 Dihedral : 14.073 89.359 5402 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.52 (0.20), residues: 1836 helix: 1.04 (0.15), residues: 1210 sheet: 1.67 (0.62), residues: 76 loop : -1.36 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.026 0.002 PHE A 834 TYR 0.012 0.002 TYR A 590 ARG 0.008 0.001 ARG A 966 *********************** 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 275 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.633 Fit side-chains REVERT: A 99 GLU cc_start: 0.7119 (tt0) cc_final: 0.6888 (mm-30) REVERT: A 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7905 (mp) REVERT: A 375 LEU cc_start: 0.8641 (mp) cc_final: 0.8416 (mp) REVERT: A 445 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7176 (mp-120) REVERT: A 449 ARG cc_start: 0.6648 (mtm110) cc_final: 0.6353 (ttp-110) REVERT: A 562 GLN cc_start: 0.7540 (tt0) cc_final: 0.7336 (tt0) REVERT: A 579 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7161 (ttp80) REVERT: A 652 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7613 (pttm) REVERT: A 771 GLU cc_start: 0.7561 (tt0) cc_final: 0.6874 (tt0) REVERT: B 234 LEU cc_start: 0.8243 (mp) cc_final: 0.7963 (mp) REVERT: B 375 LEU cc_start: 0.8553 (mp) cc_final: 0.8320 (mp) REVERT: B 445 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7171 (mp-120) REVERT: B 449 ARG cc_start: 0.6622 (mtm110) cc_final: 0.6334 (ttp-110) REVERT: B 562 GLN cc_start: 0.7548 (tt0) cc_final: 0.7345 (tt0) REVERT: B 579 ARG cc_start: 0.7401 (ttm170) cc_final: 0.7172 (ttp80) REVERT: B 652 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7605 (pttm) REVERT: B 771 GLU cc_start: 0.7605 (tt0) cc_final: 0.7078 (tt0) REVERT: B 822 CYS cc_start: 0.8250 (p) cc_final: 0.7925 (p) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 1.2161 time to fit residues: 368.0615 Evaluate side-chains 196 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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: 0.9990 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 219 ASN A 277 GLN A 347 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 277 GLN B 347 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14874 Z= 0.317 Angle : 0.653 6.718 20146 Z= 0.329 Chirality : 0.043 0.149 2372 Planarity : 0.005 0.044 2472 Dihedral : 5.580 52.350 2020 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.38 % Allowed : 11.50 % Favored : 85.12 % 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: 0.64 (0.20), residues: 1836 helix: 1.09 (0.15), residues: 1222 sheet: 1.86 (0.61), residues: 72 loop : -1.25 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 493 HIS 0.008 0.002 HIS B 120 PHE 0.024 0.002 PHE B 607 TYR 0.019 0.002 TYR A 769 ARG 0.004 0.001 ARG B 58 *********************** 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 271 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 217 time to evaluate : 1.638 Fit side-chains REVERT: A 449 ARG cc_start: 0.6897 (mtm110) cc_final: 0.6455 (ttp-110) REVERT: A 579 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7120 (ttp80) REVERT: A 652 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7635 (pttm) REVERT: A 697 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7531 (mtmt) REVERT: A 728 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7300 (tttt) REVERT: A 763 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8264 (mt) REVERT: A 866 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6608 (tpt-90) REVERT: A 875 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7981 (ttp) REVERT: B 449 ARG cc_start: 0.6876 (mtm110) cc_final: 0.6440 (ttp-110) REVERT: B 579 ARG cc_start: 0.7381 (ttm170) cc_final: 0.7126 (ttp80) REVERT: B 652 LYS cc_start: 0.7932 (mmtm) cc_final: 0.7691 (pttm) REVERT: B 697 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7519 (mtmt) REVERT: B 761 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.6925 (tmm) REVERT: B 763 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8332 (mt) outliers start: 54 outliers final: 22 residues processed: 241 average time/residue: 1.3282 time to fit residues: 351.7397 Evaluate side-chains 226 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 876 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 167 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 134 optimal weight: 0.0270 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 94 ASN A 347 GLN A 480 GLN A 679 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 0.036 14874 Z= 0.207 Angle : 0.551 6.159 20146 Z= 0.281 Chirality : 0.039 0.139 2372 Planarity : 0.004 0.037 2472 Dihedral : 5.190 46.192 2020 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.81 % Allowed : 14.00 % Favored : 82.19 % 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: 0.98 (0.20), residues: 1836 helix: 1.33 (0.15), residues: 1226 sheet: 1.74 (0.60), residues: 72 loop : -1.07 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 493 HIS 0.004 0.001 HIS B 120 PHE 0.016 0.001 PHE A 353 TYR 0.012 0.001 TYR A 769 ARG 0.007 0.000 ARG B 866 *********************** 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 275 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 214 time to evaluate : 1.712 Fit side-chains REVERT: A 123 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7957 (pttt) REVERT: A 342 ASP cc_start: 0.7579 (t0) cc_final: 0.7312 (t0) REVERT: A 419 LYS cc_start: 0.8328 (tttm) cc_final: 0.8119 (tttp) REVERT: A 449 ARG cc_start: 0.6887 (mtm110) cc_final: 0.6391 (ttp-110) REVERT: A 579 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7122 (ttp80) REVERT: A 652 LYS cc_start: 0.7826 (mmtm) cc_final: 0.7607 (pttm) REVERT: A 703 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6910 (mt-10) REVERT: A 771 GLU cc_start: 0.7464 (tt0) cc_final: 0.6535 (tt0) REVERT: A 866 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6671 (tpt-90) REVERT: A 876 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: B 123 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7922 (pttt) REVERT: B 199 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7574 (mtt) REVERT: B 342 ASP cc_start: 0.7591 (t0) cc_final: 0.7315 (t0) REVERT: B 449 ARG cc_start: 0.6880 (mtm110) cc_final: 0.6394 (ttp-110) REVERT: B 579 ARG cc_start: 0.7388 (ttm170) cc_final: 0.7123 (ttp80) REVERT: B 652 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7600 (pttm) REVERT: B 703 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: B 866 ARG cc_start: 0.7203 (tpt170) cc_final: 0.6955 (tpp80) REVERT: B 876 GLN cc_start: 0.7561 (pt0) cc_final: 0.7350 (pt0) outliers start: 61 outliers final: 23 residues processed: 245 average time/residue: 1.2200 time to fit residues: 330.5818 Evaluate side-chains 229 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE 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: 0.9980 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 159 optimal weight: 0.0030 chunk 47 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN A 679 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14874 Z= 0.222 Angle : 0.549 6.321 20146 Z= 0.279 Chirality : 0.039 0.139 2372 Planarity : 0.004 0.037 2472 Dihedral : 5.079 45.169 2020 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.56 % Allowed : 15.94 % 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: 1.13 (0.20), residues: 1836 helix: 1.42 (0.15), residues: 1226 sheet: 1.76 (0.61), residues: 72 loop : -0.91 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 493 HIS 0.005 0.001 HIS A 120 PHE 0.015 0.002 PHE A 636 TYR 0.011 0.001 TYR A 769 ARG 0.002 0.000 ARG B 452 *********************** 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 266 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 209 time to evaluate : 1.671 Fit side-chains REVERT: A 123 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7867 (pttt) REVERT: A 199 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7534 (mtt) REVERT: A 342 ASP cc_start: 0.7705 (t0) cc_final: 0.7340 (t0) REVERT: A 419 LYS cc_start: 0.8313 (tttm) cc_final: 0.8110 (tttp) REVERT: A 449 ARG cc_start: 0.6904 (mtm110) cc_final: 0.6397 (ttp-110) REVERT: A 652 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7606 (pttm) REVERT: A 697 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7635 (mtmt) REVERT: A 708 HIS cc_start: 0.7417 (t-170) cc_final: 0.7200 (t70) REVERT: A 771 GLU cc_start: 0.7474 (tt0) cc_final: 0.6551 (tt0) REVERT: A 866 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6530 (tpt-90) REVERT: B 123 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7866 (pttt) REVERT: B 199 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7668 (mtt) REVERT: B 342 ASP cc_start: 0.7679 (t0) cc_final: 0.7357 (t0) REVERT: B 449 ARG cc_start: 0.6898 (mtm110) cc_final: 0.6387 (ttp-110) REVERT: B 652 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7599 (pttm) REVERT: B 697 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7631 (mtmt) REVERT: B 771 GLU cc_start: 0.7514 (tt0) cc_final: 0.6575 (tt0) REVERT: B 1045 MET cc_start: 0.5832 (tpp) cc_final: 0.5627 (tpp) outliers start: 57 outliers final: 32 residues processed: 241 average time/residue: 1.2151 time to fit residues: 323.9338 Evaluate side-chains 239 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 159 optimal weight: 0.0270 chunk 44 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14874 Z= 0.176 Angle : 0.525 7.194 20146 Z= 0.265 Chirality : 0.038 0.138 2372 Planarity : 0.004 0.037 2472 Dihedral : 4.896 41.884 2020 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.50 % Allowed : 16.12 % Favored : 79.38 % 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: 1.28 (0.20), residues: 1836 helix: 1.53 (0.15), residues: 1226 sheet: 1.79 (0.62), residues: 72 loop : -0.85 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 493 HIS 0.004 0.001 HIS B 739 PHE 0.015 0.001 PHE A 636 TYR 0.010 0.001 TYR A 634 ARG 0.002 0.000 ARG B 58 *********************** 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 283 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 211 time to evaluate : 1.692 Fit side-chains REVERT: A 123 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7862 (ptmt) REVERT: A 199 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7603 (mtt) REVERT: A 342 ASP cc_start: 0.7622 (t0) cc_final: 0.7376 (t0) REVERT: A 449 ARG cc_start: 0.6940 (mtm110) cc_final: 0.6454 (ttp-110) REVERT: A 555 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8254 (m) REVERT: A 652 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7595 (pttm) REVERT: A 697 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7604 (mtmt) REVERT: A 703 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: A 708 HIS cc_start: 0.7386 (t-170) cc_final: 0.7178 (t70) REVERT: A 771 GLU cc_start: 0.7512 (tt0) cc_final: 0.6586 (tt0) REVERT: A 866 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6448 (tpt-90) REVERT: B 123 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7850 (pttt) REVERT: B 129 MET cc_start: 0.7202 (mmp) cc_final: 0.6878 (mmp) REVERT: B 199 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7693 (mtt) REVERT: B 342 ASP cc_start: 0.7614 (t0) cc_final: 0.7388 (t0) REVERT: B 449 ARG cc_start: 0.6928 (mtm110) cc_final: 0.6494 (ttp-110) REVERT: B 555 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8264 (m) REVERT: B 652 LYS cc_start: 0.7801 (mmtm) cc_final: 0.7596 (pttm) REVERT: B 697 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7619 (mtmt) REVERT: B 703 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: B 771 GLU cc_start: 0.7565 (tt0) cc_final: 0.6643 (tt0) outliers start: 72 outliers final: 36 residues processed: 252 average time/residue: 1.2095 time to fit residues: 338.2407 Evaluate side-chains 240 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14874 Z= 0.244 Angle : 0.552 6.302 20146 Z= 0.278 Chirality : 0.040 0.137 2372 Planarity : 0.004 0.036 2472 Dihedral : 4.959 43.576 2020 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.25 % Allowed : 17.00 % Favored : 78.75 % 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: 1.45 (0.15), residues: 1226 sheet: 1.86 (0.63), residues: 72 loop : -0.81 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.006 0.001 HIS B 120 PHE 0.015 0.002 PHE A 636 TYR 0.011 0.001 TYR A 769 ARG 0.002 0.000 ARG B 452 *********************** 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 271 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 203 time to evaluate : 1.642 Fit side-chains REVERT: A 123 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7885 (ptmt) REVERT: A 199 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7627 (mtt) REVERT: A 342 ASP cc_start: 0.7588 (t0) cc_final: 0.7356 (t0) REVERT: A 449 ARG cc_start: 0.6919 (mtm110) cc_final: 0.6534 (ttp-110) REVERT: A 503 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7828 (tp) REVERT: A 555 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8251 (m) REVERT: A 697 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7659 (mtmt) REVERT: A 703 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6985 (mt-10) REVERT: A 708 HIS cc_start: 0.7434 (t-170) cc_final: 0.7204 (t70) REVERT: A 771 GLU cc_start: 0.7536 (tt0) cc_final: 0.6607 (tt0) REVERT: A 866 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6513 (tpt-90) REVERT: B 123 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7881 (ptmt) REVERT: B 342 ASP cc_start: 0.7560 (t0) cc_final: 0.7314 (t0) REVERT: B 449 ARG cc_start: 0.7025 (mtm110) cc_final: 0.6488 (ttp-110) REVERT: B 555 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8288 (m) REVERT: B 652 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7616 (pttm) REVERT: B 697 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7660 (mtmt) REVERT: B 703 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: B 708 HIS cc_start: 0.7414 (t-170) cc_final: 0.7208 (t70) outliers start: 68 outliers final: 38 residues processed: 240 average time/residue: 1.1864 time to fit residues: 315.7944 Evaluate side-chains 240 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.214 Angle : 0.541 7.840 20146 Z= 0.272 Chirality : 0.039 0.138 2372 Planarity : 0.004 0.037 2472 Dihedral : 4.921 43.675 2020 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.06 % Allowed : 18.19 % 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: 1.24 (0.20), residues: 1836 helix: 1.48 (0.15), residues: 1226 sheet: 1.86 (0.63), residues: 72 loop : -0.82 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.005 0.001 HIS B 120 PHE 0.015 0.001 PHE A 636 TYR 0.010 0.001 TYR A 634 ARG 0.002 0.000 ARG A 452 *********************** 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 264 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 199 time to evaluate : 1.499 Fit side-chains REVERT: A 99 GLU cc_start: 0.7116 (tt0) cc_final: 0.6789 (tt0) REVERT: A 123 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7863 (ptmt) REVERT: A 199 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7507 (mtt) REVERT: A 342 ASP cc_start: 0.7590 (t0) cc_final: 0.7336 (t0) REVERT: A 449 ARG cc_start: 0.6948 (mtm110) cc_final: 0.6533 (ttp-110) REVERT: A 503 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8032 (tp) REVERT: A 555 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8244 (m) REVERT: A 703 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6994 (mt-10) REVERT: A 708 HIS cc_start: 0.7415 (t-170) cc_final: 0.7204 (t70) REVERT: A 771 GLU cc_start: 0.7534 (tt0) cc_final: 0.6589 (tt0) REVERT: A 866 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6478 (tpt-90) REVERT: A 875 MET cc_start: 0.7591 (tpp) cc_final: 0.7236 (tpt) REVERT: B 123 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7873 (ptmt) REVERT: B 129 MET cc_start: 0.7173 (mmp) cc_final: 0.6850 (mmp) REVERT: B 199 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7705 (mtt) REVERT: B 342 ASP cc_start: 0.7579 (t0) cc_final: 0.7310 (t0) REVERT: B 449 ARG cc_start: 0.6940 (mtm110) cc_final: 0.6538 (ttp-110) REVERT: B 555 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8249 (m) REVERT: B 697 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7667 (mtmt) REVERT: B 703 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7005 (mt-10) REVERT: B 708 HIS cc_start: 0.7420 (t-170) cc_final: 0.7202 (t70) outliers start: 65 outliers final: 41 residues processed: 237 average time/residue: 1.0290 time to fit residues: 272.9295 Evaluate side-chains 242 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 190 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14874 Z= 0.246 Angle : 0.564 7.641 20146 Z= 0.282 Chirality : 0.040 0.139 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.945 44.976 2020 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.19 % Allowed : 18.31 % Favored : 77.50 % 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: 1.19 (0.20), residues: 1836 helix: 1.44 (0.15), residues: 1228 sheet: 1.87 (0.64), residues: 72 loop : -0.84 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 493 HIS 0.006 0.001 HIS B 120 PHE 0.016 0.002 PHE B 636 TYR 0.011 0.001 TYR B 769 ARG 0.002 0.000 ARG A 452 *********************** 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 258 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 191 time to evaluate : 1.523 Fit side-chains REVERT: A 123 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7884 (ptmt) REVERT: A 129 MET cc_start: 0.7151 (mmp) cc_final: 0.6808 (mmp) REVERT: A 199 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7517 (mtt) REVERT: A 342 ASP cc_start: 0.7574 (t0) cc_final: 0.7303 (t0) REVERT: A 449 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6489 (ttp-110) REVERT: A 503 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8136 (mt) REVERT: A 555 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8251 (m) REVERT: A 610 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7695 (mp0) REVERT: A 611 ARG cc_start: 0.6888 (ttp-170) cc_final: 0.5865 (mtp180) REVERT: A 697 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7697 (mtmt) REVERT: A 703 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: A 771 GLU cc_start: 0.7543 (tt0) cc_final: 0.6596 (tt0) REVERT: A 866 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6473 (tpt-90) REVERT: A 875 MET cc_start: 0.7493 (tpp) cc_final: 0.7113 (tpt) REVERT: B 123 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7891 (ptmt) REVERT: B 129 MET cc_start: 0.7186 (mmp) cc_final: 0.6882 (mmp) REVERT: B 199 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7633 (mtt) REVERT: B 342 ASP cc_start: 0.7558 (t0) cc_final: 0.7300 (t0) REVERT: B 449 ARG cc_start: 0.6923 (mtm110) cc_final: 0.6489 (ttp-110) REVERT: B 461 LYS cc_start: 0.7864 (tptp) cc_final: 0.7349 (mttp) REVERT: B 555 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8252 (m) REVERT: B 610 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7669 (mp0) REVERT: B 611 ARG cc_start: 0.6907 (ttp-170) cc_final: 0.5949 (mtp180) REVERT: B 697 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7741 (mtmt) REVERT: B 703 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: B 866 ARG cc_start: 0.7151 (tpt170) cc_final: 0.6823 (tpp80) outliers start: 67 outliers final: 45 residues processed: 232 average time/residue: 1.1331 time to fit residues: 293.2532 Evaluate side-chains 241 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 184 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 1011 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.2980 chunk 155 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 164 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 94 ASN A 347 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 94 ASN B 347 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14874 Z= 0.197 Angle : 0.540 7.366 20146 Z= 0.271 Chirality : 0.039 0.140 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.830 43.831 2020 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.00 % Allowed : 18.69 % Favored : 77.31 % 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: 1.33 (0.21), residues: 1836 helix: 1.58 (0.15), residues: 1228 sheet: 1.90 (0.63), residues: 72 loop : -0.85 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 493 HIS 0.004 0.001 HIS B 120 PHE 0.017 0.001 PHE A 636 TYR 0.012 0.001 TYR A 346 ARG 0.002 0.000 ARG A 58 *********************** 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 264 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 200 time to evaluate : 1.574 Fit side-chains REVERT: A 99 GLU cc_start: 0.7118 (tt0) cc_final: 0.6742 (tt0) REVERT: A 115 PHE cc_start: 0.7940 (t80) cc_final: 0.7603 (t80) REVERT: A 123 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7794 (ptmt) REVERT: A 129 MET cc_start: 0.7164 (mmp) cc_final: 0.6787 (mmp) REVERT: A 199 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7519 (mtt) REVERT: A 342 ASP cc_start: 0.7563 (t0) cc_final: 0.7292 (t0) REVERT: A 397 ARG cc_start: 0.8576 (mpt180) cc_final: 0.8304 (mpt180) REVERT: A 449 ARG cc_start: 0.6924 (mtm110) cc_final: 0.6529 (ttp-110) REVERT: A 476 LEU cc_start: 0.8537 (mp) cc_final: 0.8297 (mt) REVERT: A 503 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8124 (mt) REVERT: A 555 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8243 (m) REVERT: A 610 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7637 (mp0) REVERT: A 611 ARG cc_start: 0.6767 (ttp-170) cc_final: 0.5730 (mtp180) REVERT: A 697 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7704 (mtmt) REVERT: A 703 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: A 866 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6446 (tpt-90) REVERT: B 123 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7868 (ptmt) REVERT: B 129 MET cc_start: 0.7207 (mmp) cc_final: 0.6880 (mmp) REVERT: B 199 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7551 (mtt) REVERT: B 342 ASP cc_start: 0.7537 (t0) cc_final: 0.7276 (t0) REVERT: B 397 ARG cc_start: 0.8574 (mpt180) cc_final: 0.8314 (mpt180) REVERT: B 449 ARG cc_start: 0.6943 (mtm110) cc_final: 0.6409 (ttp-110) REVERT: B 555 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8235 (m) REVERT: B 610 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7697 (mp0) REVERT: B 611 ARG cc_start: 0.6751 (ttp-170) cc_final: 0.5792 (mtp180) REVERT: B 697 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7751 (mtmt) REVERT: B 703 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7000 (mt-10) REVERT: B 866 ARG cc_start: 0.7081 (tpt170) cc_final: 0.6766 (tpp80) REVERT: B 1045 MET cc_start: 0.5596 (tpp) cc_final: 0.5364 (tpp) outliers start: 64 outliers final: 41 residues processed: 239 average time/residue: 1.1414 time to fit residues: 303.0667 Evaluate side-chains 245 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 1011 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.0980 chunk 106 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.214 Angle : 0.547 7.122 20146 Z= 0.274 Chirality : 0.039 0.150 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.839 44.205 2020 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.06 % Allowed : 18.88 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1836 helix: 1.55 (0.15), residues: 1228 sheet: 1.95 (0.63), residues: 72 loop : -0.87 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 493 HIS 0.009 0.001 HIS B 120 PHE 0.017 0.001 PHE A 636 TYR 0.012 0.001 TYR A 346 ARG 0.003 0.000 ARG B 452 ********************** 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 261 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 196 time to evaluate : 1.695 Fit side-chains REVERT: A 99 GLU cc_start: 0.7119 (tt0) cc_final: 0.6776 (tt0) REVERT: A 115 PHE cc_start: 0.7944 (t80) cc_final: 0.7627 (t80) REVERT: A 123 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7778 (ptmt) REVERT: A 129 MET cc_start: 0.7185 (mmp) cc_final: 0.6825 (mmp) REVERT: A 199 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7528 (mtt) REVERT: A 342 ASP cc_start: 0.7543 (t0) cc_final: 0.7287 (t0) REVERT: A 397 ARG cc_start: 0.8608 (mpt180) cc_final: 0.8341 (mpt180) REVERT: A 449 ARG cc_start: 0.6967 (mtm110) cc_final: 0.6465 (ttp-110) REVERT: A 555 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8249 (m) REVERT: A 611 ARG cc_start: 0.6858 (ttp-170) cc_final: 0.5828 (mtp180) REVERT: A 697 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7674 (mtmt) REVERT: A 703 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: A 866 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6421 (tpt-90) REVERT: B 123 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7892 (pttt) REVERT: B 129 MET cc_start: 0.7258 (mmp) cc_final: 0.6940 (mmp) REVERT: B 199 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7556 (mtt) REVERT: B 342 ASP cc_start: 0.7518 (t0) cc_final: 0.7251 (t0) REVERT: B 397 ARG cc_start: 0.8599 (mpt180) cc_final: 0.8350 (mpt180) REVERT: B 449 ARG cc_start: 0.6947 (mtm110) cc_final: 0.6514 (ttp-110) REVERT: B 555 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8281 (m) REVERT: B 611 ARG cc_start: 0.6849 (ttp-170) cc_final: 0.5856 (mtp180) REVERT: B 697 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7773 (mtmt) REVERT: B 703 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: B 866 ARG cc_start: 0.7009 (tpt170) cc_final: 0.6690 (tpp80) REVERT: B 1045 MET cc_start: 0.5607 (tpp) cc_final: 0.5386 (tpp) outliers start: 65 outliers final: 42 residues processed: 235 average time/residue: 1.1307 time to fit residues: 295.4962 Evaluate side-chains 248 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 195 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 1011 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 94 ASN B 347 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148160 restraints weight = 14741.603| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.53 r_work: 0.3478 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14874 Z= 0.227 Angle : 0.554 7.960 20146 Z= 0.277 Chirality : 0.040 0.153 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.878 44.629 2020 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.88 % Allowed : 19.25 % Favored : 76.88 % 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: 1.27 (0.20), residues: 1836 helix: 1.51 (0.15), residues: 1228 sheet: 1.97 (0.62), residues: 72 loop : -0.86 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 493 HIS 0.006 0.001 HIS B 120 PHE 0.019 0.002 PHE B 636 TYR 0.011 0.001 TYR A 769 ARG 0.002 0.000 ARG A 879 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5558.34 seconds wall clock time: 98 minutes 18.23 seconds (5898.23 seconds total)