Starting phenix.real_space_refine on Sun Feb 18 17:24:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2024/7zgy_14715_neut_trim_updated.pdb" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.060 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: 7 Type Number sf(0) Gaussians Fe 3 7.16 5 Cu 9 5.60 5 P 6 5.49 5 S 18 5.16 5 C 13626 2.51 5 N 3807 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21861 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 170 Unusual residues: {' CU': 3, ' FE': 1, 'JPI': 1, 'JPX': 1, 'JQ6': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 236 Unusual residues: {' CU': 3, ' FE': 1, 'JPI': 1, 'JPX': 2, 'JQ6': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Unusual residues: {' CU': 3, ' FE': 1, 'JPI': 1, 'JQ6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 12.18, per 1000 atoms: 0.56 Number of scatterers: 21861 At special positions: 0 Unit cell: (164.418, 155.42, 128.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 9 28.99 Fe 3 26.01 S 18 16.00 P 6 15.00 O 4392 8.00 N 3807 7.00 C 13626 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.98 Conformation dependent library (CDL) restraints added in 4.5 seconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 32 sheets defined 6.0% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.35 Creating SS restraints... Processing helix chain 'A' and resid 222 through 251 removed outlier: 3.570A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 452 through 455 No H-bonds generated for 'chain 'A' and resid 452 through 455' Processing helix chain 'A' and resid 590 through 593 No H-bonds generated for 'chain 'A' and resid 590 through 593' Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 871 through 874 Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'B' and resid 222 through 251 removed outlier: 3.579A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 452 through 455 No H-bonds generated for 'chain 'B' and resid 452 through 455' Processing helix chain 'B' and resid 590 through 593 No H-bonds generated for 'chain 'B' and resid 590 through 593' Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 871 through 874 Processing helix chain 'B' and resid 921 through 923 No H-bonds generated for 'chain 'B' and resid 921 through 923' Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'C' and resid 222 through 251 removed outlier: 3.604A pdb=" N GLU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 452 through 455 No H-bonds generated for 'chain 'C' and resid 452 through 455' Processing helix chain 'C' and resid 590 through 593 No H-bonds generated for 'chain 'C' and resid 590 through 593' Processing helix chain 'C' and resid 785 through 787 No H-bonds generated for 'chain 'C' and resid 785 through 787' Processing helix chain 'C' and resid 871 through 874 Processing helix chain 'C' and resid 921 through 923 No H-bonds generated for 'chain 'C' and resid 921 through 923' Processing helix chain 'C' and resid 1030 through 1032 No H-bonds generated for 'chain 'C' and resid 1030 through 1032' Processing sheet with id= A, first strand: chain 'A' and resid 1033 through 1035 removed outlier: 3.720A pdb=" N TYR A1163 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 262 " --> pdb=" O TYR A1163 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU A 390 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 429 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 267 through 269 Processing sheet with id= C, first strand: chain 'A' and resid 334 through 337 Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 Processing sheet with id= E, first strand: chain 'A' and resid 487 through 490 removed outlier: 5.807A pdb=" N VAL A 562 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS A 761 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 678 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 759 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR A 680 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 757 " --> pdb=" O TYR A 680 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 682 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN A 755 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 792 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 850 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR A 978 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 819 through 821 Processing sheet with id= G, first strand: chain 'A' and resid 951 through 953 Processing sheet with id= H, first strand: chain 'A' and resid 1045 through 1048 Processing sheet with id= I, first strand: chain 'A' and resid 1088 through 1091 Processing sheet with id= J, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id= K, first strand: chain 'A' and resid 724 through 729 removed outlier: 5.767A pdb=" N ARG A 726 " --> pdb=" O LYS A 752 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 752 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA A 728 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASN A 750 " --> pdb=" O ALA A 728 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1033 through 1035 removed outlier: 3.730A pdb=" N TYR B1163 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 262 " --> pdb=" O TYR B1163 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU B 390 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 429 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 267 through 269 Processing sheet with id= N, first strand: chain 'B' and resid 334 through 337 Processing sheet with id= O, first strand: chain 'B' and resid 400 through 402 Processing sheet with id= P, first strand: chain 'B' and resid 487 through 490 removed outlier: 5.807A pdb=" N VAL B 562 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 678 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS B 761 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 678 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY B 759 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR B 680 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 757 " --> pdb=" O TYR B 680 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 682 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN B 755 " --> pdb=" O LYS B 682 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 792 " --> pdb=" O THR B 811 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 850 " --> pdb=" O GLY B 938 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR B 978 " --> pdb=" O THR B1001 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 819 through 821 Processing sheet with id= R, first strand: chain 'B' and resid 951 through 953 Processing sheet with id= S, first strand: chain 'B' and resid 1045 through 1048 Processing sheet with id= T, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id= U, first strand: chain 'B' and resid 1109 through 1111 Processing sheet with id= V, first strand: chain 'B' and resid 724 through 729 removed outlier: 5.747A pdb=" N ARG B 726 " --> pdb=" O LYS B 752 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS B 752 " --> pdb=" O ARG B 726 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA B 728 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN B 750 " --> pdb=" O ALA B 728 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 951 through 953 removed outlier: 3.713A pdb=" N TYR C1163 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE C 262 " --> pdb=" O TYR C1163 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 390 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 429 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 267 through 269 Processing sheet with id= Y, first strand: chain 'C' and resid 334 through 337 Processing sheet with id= Z, first strand: chain 'C' and resid 400 through 402 Processing sheet with id= AA, first strand: chain 'C' and resid 487 through 490 removed outlier: 5.763A pdb=" N VAL C 562 " --> pdb=" O ARG C 549 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 622 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS C 761 " --> pdb=" O TYR C 676 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 678 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY C 759 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR C 680 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 757 " --> pdb=" O TYR C 680 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 682 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN C 755 " --> pdb=" O LYS C 682 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 792 " --> pdb=" O THR C 811 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 850 " --> pdb=" O GLY C 938 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 819 through 821 Processing sheet with id= AC, first strand: chain 'C' and resid 1045 through 1048 Processing sheet with id= AD, first strand: chain 'C' and resid 1088 through 1091 Processing sheet with id= AE, first strand: chain 'C' and resid 1109 through 1111 Processing sheet with id= AF, first strand: chain 'C' and resid 724 through 729 removed outlier: 3.823A pdb=" N GLY C 754 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ARG C 726 " --> pdb=" O LYS C 752 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LYS C 752 " --> pdb=" O ARG C 726 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA C 728 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN C 750 " --> pdb=" O ALA C 728 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.88 Time building geometry restraints manager: 9.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3705 1.31 - 1.44: 6378 1.44 - 1.56: 12147 1.56 - 1.68: 12 1.68 - 1.81: 30 Bond restraints: 22272 Sorted by residual: bond pdb=" C5 JPI C1201 " pdb=" C6 JPI C1201 " ideal model delta sigma weight residual 1.557 1.341 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C5 JPI A1201 " pdb=" C6 JPI A1201 " ideal model delta sigma weight residual 1.557 1.343 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C5 JPI B1302 " pdb=" C6 JPI B1302 " ideal model delta sigma weight residual 1.557 1.348 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4 JPI A1201 " pdb=" O1 JPI A1201 " ideal model delta sigma weight residual 1.414 1.243 0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C4 JPI B1302 " pdb=" O1 JPI B1302 " ideal model delta sigma weight residual 1.414 1.246 0.168 2.00e-02 2.50e+03 7.09e+01 ... (remaining 22267 not shown) Histogram of bond angle deviations from ideal: 95.79 - 103.42: 161 103.42 - 111.05: 7991 111.05 - 118.68: 8908 118.68 - 126.31: 13048 126.31 - 133.94: 114 Bond angle restraints: 30222 Sorted by residual: angle pdb=" C ASN A 632 " pdb=" CA ASN A 632 " pdb=" CB ASN A 632 " ideal model delta sigma weight residual 116.54 109.61 6.93 1.15e+00 7.56e-01 3.63e+01 angle pdb=" C THR B 597 " pdb=" CA THR B 597 " pdb=" CB THR B 597 " ideal model delta sigma weight residual 116.63 110.16 6.47 1.16e+00 7.43e-01 3.11e+01 angle pdb=" C THR A 597 " pdb=" CA THR A 597 " pdb=" CB THR A 597 " ideal model delta sigma weight residual 116.63 110.24 6.39 1.16e+00 7.43e-01 3.04e+01 angle pdb=" C THR C 597 " pdb=" CA THR C 597 " pdb=" CB THR C 597 " ideal model delta sigma weight residual 116.63 110.26 6.37 1.16e+00 7.43e-01 3.02e+01 angle pdb=" C SER C 801 " pdb=" CA SER C 801 " pdb=" CB SER C 801 " ideal model delta sigma weight residual 117.23 110.17 7.06 1.36e+00 5.41e-01 2.70e+01 ... (remaining 30217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 12620 35.75 - 71.50: 255 71.50 - 107.25: 53 107.25 - 142.99: 24 142.99 - 178.74: 14 Dihedral angle restraints: 12966 sinusoidal: 5019 harmonic: 7947 Sorted by residual: dihedral pdb=" CA TYR C 696 " pdb=" C TYR C 696 " pdb=" N GLY C 697 " pdb=" CA GLY C 697 " ideal model delta harmonic sigma weight residual 180.00 149.79 30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA TYR A 696 " pdb=" C TYR A 696 " pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR B 696 " pdb=" C TYR B 696 " pdb=" N GLY B 697 " pdb=" CA GLY B 697 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 12963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.989: 3261 0.989 - 1.978: 0 1.978 - 2.967: 9 2.967 - 3.956: 0 3.956 - 4.945: 3 Chirality restraints: 3273 Sorted by residual: chirality pdb=" C2 JPI B1302 " pdb=" C1 JPI B1302 " pdb=" C3 JPI B1302 " pdb=" O2 JPI B1302 " both_signs ideal model delta sigma weight residual False 2.39 -2.56 4.94 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" C2 JPI A1201 " pdb=" C1 JPI A1201 " pdb=" C3 JPI A1201 " pdb=" O2 JPI A1201 " both_signs ideal model delta sigma weight residual False 2.39 -2.48 4.87 2.00e-01 2.50e+01 5.93e+02 chirality pdb=" C2 JPI C1201 " pdb=" C1 JPI C1201 " pdb=" C3 JPI C1201 " pdb=" O2 JPI C1201 " both_signs ideal model delta sigma weight residual False 2.39 -2.39 4.78 2.00e-01 2.50e+01 5.72e+02 ... (remaining 3270 not shown) Planarity restraints: 4041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 JPX B1301 " 0.119 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C3 JPX B1301 " -0.080 2.00e-02 2.50e+03 pdb=" C9 JPX B1301 " 0.349 2.00e-02 2.50e+03 pdb=" N1 JPX B1301 " -0.535 2.00e-02 2.50e+03 pdb=" O7 JPX B1301 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 JPX A1203 " -0.124 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C3 JPX A1203 " 0.073 2.00e-02 2.50e+03 pdb=" C9 JPX A1203 " -0.341 2.00e-02 2.50e+03 pdb=" N1 JPX A1203 " 0.526 2.00e-02 2.50e+03 pdb=" O7 JPX A1203 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 JQ6 C1202 " -0.069 2.00e-02 2.50e+03 2.93e-01 1.08e+03 pdb=" C16 JQ6 C1202 " 0.102 2.00e-02 2.50e+03 pdb=" C8 JQ6 C1202 " 0.338 2.00e-02 2.50e+03 pdb=" N2 JQ6 C1202 " -0.526 2.00e-02 2.50e+03 pdb=" O11 JQ6 C1202 " 0.154 2.00e-02 2.50e+03 ... (remaining 4038 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 71 2.26 - 2.92: 10321 2.92 - 3.58: 29626 3.58 - 4.24: 53958 4.24 - 4.90: 93649 Nonbonded interactions: 187625 Sorted by model distance: nonbonded pdb=" OD1 ASP C 513 " pdb="CU CU C1204 " model vdw 1.605 2.240 nonbonded pdb=" OD1 ASP B 513 " pdb="CU CU B1306 " model vdw 1.661 2.240 nonbonded pdb=" O GLY A 559 " pdb="CU CU A1204 " model vdw 1.780 2.240 nonbonded pdb=" OD1 ASN C 442 " pdb="FE FE C1206 " model vdw 1.786 2.260 nonbonded pdb=" OD1 ASP A 513 " pdb="CU CU A1205 " model vdw 1.793 2.240 ... (remaining 187620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 218 through 1167 or resid 1205)) selection = (chain 'B' and (resid 218 through 1167 or resid 1305)) selection = (chain 'C' and (resid 218 through 1167 or resid 1205)) } 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: 12.790 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: 0.030 Extract box with map and model: 32.820 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 63.650 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.007 0.216 22272 Z= 0.465 Angle : 0.840 13.588 30222 Z= 0.400 Chirality : 0.199 4.945 3273 Planarity : 0.015 0.300 4041 Dihedral : 17.807 178.744 8034 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.24 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2841 helix: -0.01 (0.41), residues: 186 sheet: -0.50 (0.16), residues: 1149 loop : -2.06 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.004 0.001 HIS C 612 PHE 0.039 0.001 PHE B 512 TYR 0.022 0.001 TYR B 698 ARG 0.004 0.000 ARG B 856 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.545 Fit side-chains REVERT: A 826 THR cc_start: 0.8419 (p) cc_final: 0.8113 (t) REVERT: B 1028 ASN cc_start: 0.7609 (t0) cc_final: 0.7375 (t0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 1.3001 time to fit residues: 288.0434 Evaluate side-chains 108 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 134 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 654 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN A1166 ASN B 424 ASN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1166 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22272 Z= 0.338 Angle : 0.692 12.135 30222 Z= 0.357 Chirality : 0.050 0.523 3273 Planarity : 0.005 0.058 4041 Dihedral : 17.735 178.876 3609 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.63 % Favored : 89.19 % Rotamer: Outliers : 2.48 % Allowed : 8.31 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.83 (0.16), residues: 2841 helix: -0.37 (0.40), residues: 189 sheet: -0.36 (0.16), residues: 1143 loop : -2.07 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.004 0.001 HIS A 612 PHE 0.028 0.002 PHE B 512 TYR 0.022 0.002 TYR B 698 ARG 0.006 0.001 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 117 time to evaluate : 2.433 Fit side-chains REVERT: A 826 THR cc_start: 0.8495 (p) cc_final: 0.8118 (t) REVERT: A 842 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6552 (m-30) REVERT: A 907 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7855 (p0) REVERT: A 1045 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: B 512 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: B 541 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: B 766 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7098 (mm) REVERT: B 842 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6878 (m-30) REVERT: B 949 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7043 (tmtm) REVERT: B 1028 ASN cc_start: 0.7538 (t0) cc_final: 0.7300 (t0) REVERT: C 541 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: C 908 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7900 (mp) REVERT: C 1045 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7289 (m-30) outliers start: 54 outliers final: 14 residues processed: 154 average time/residue: 1.1766 time to fit residues: 213.4476 Evaluate side-chains 128 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1045 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 256 optimal weight: 0.3980 chunk 277 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 254 optimal weight: 0.0570 chunk 87 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22272 Z= 0.162 Angle : 0.583 11.623 30222 Z= 0.306 Chirality : 0.045 0.354 3273 Planarity : 0.004 0.054 4041 Dihedral : 16.490 175.665 3609 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.26 % Favored : 90.64 % Rotamer: Outliers : 2.34 % Allowed : 10.47 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2841 helix: -0.19 (0.40), residues: 186 sheet: -0.35 (0.16), residues: 1161 loop : -2.01 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 538 HIS 0.001 0.000 HIS A 939 PHE 0.021 0.001 PHE B 512 TYR 0.015 0.001 TYR B 698 ARG 0.014 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 124 time to evaluate : 2.304 Fit side-chains REVERT: A 826 THR cc_start: 0.8421 (p) cc_final: 0.8130 (t) REVERT: A 842 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: A 949 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7179 (tmtm) REVERT: A 1045 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: B 766 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6966 (mm) REVERT: B 842 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: C 512 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.6886 (m-10) REVERT: C 541 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: C 665 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7712 (mmpt) REVERT: C 908 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7810 (mp) outliers start: 51 outliers final: 16 residues processed: 165 average time/residue: 0.9747 time to fit residues: 192.2828 Evaluate side-chains 128 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 833 LYS Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 908 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22272 Z= 0.339 Angle : 0.658 11.687 30222 Z= 0.346 Chirality : 0.049 0.393 3273 Planarity : 0.005 0.065 4041 Dihedral : 16.038 178.424 3609 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.56 % Favored : 89.26 % Rotamer: Outliers : 3.67 % Allowed : 11.20 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.74 (0.16), residues: 2841 helix: -0.41 (0.40), residues: 189 sheet: -0.34 (0.15), residues: 1191 loop : -2.00 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 538 HIS 0.004 0.001 HIS A 612 PHE 0.018 0.002 PHE B 953 TYR 0.016 0.002 TYR C1122 ARG 0.005 0.001 ARG C 869 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 109 time to evaluate : 2.475 Fit side-chains REVERT: A 826 THR cc_start: 0.8487 (p) cc_final: 0.8156 (t) REVERT: A 842 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: A 907 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7668 (p0) REVERT: B 766 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7159 (mm) REVERT: B 842 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6840 (m-30) REVERT: B 949 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7094 (tmtm) REVERT: C 512 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7038 (m-10) REVERT: C 541 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: C 665 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7838 (mmpt) REVERT: C 908 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7896 (mp) outliers start: 80 outliers final: 32 residues processed: 166 average time/residue: 0.9639 time to fit residues: 193.4353 Evaluate side-chains 142 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 101 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 908 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 232 optimal weight: 0.0040 chunk 188 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 GLN B 400 GLN B 420 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 22272 Z= 0.457 Angle : 0.722 11.738 30222 Z= 0.381 Chirality : 0.051 0.420 3273 Planarity : 0.005 0.063 4041 Dihedral : 15.779 171.977 3609 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.88 % Favored : 88.95 % Rotamer: Outliers : 3.72 % Allowed : 12.08 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.77 (0.16), residues: 2841 helix: -0.64 (0.39), residues: 189 sheet: -0.35 (0.15), residues: 1191 loop : -2.00 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 538 HIS 0.005 0.002 HIS A 612 PHE 0.017 0.002 PHE B 953 TYR 0.017 0.002 TYR B1080 ARG 0.007 0.001 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 105 time to evaluate : 2.401 Fit side-chains REVERT: A 842 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6714 (m-30) REVERT: A 907 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7790 (p0) REVERT: B 415 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7194 (mtt-85) REVERT: B 541 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: B 842 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: B 949 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7044 (tmtm) REVERT: C 541 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: C 623 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: C 665 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7907 (mmpt) outliers start: 81 outliers final: 44 residues processed: 167 average time/residue: 0.9938 time to fit residues: 199.2962 Evaluate side-chains 151 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 98 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 833 LYS Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1029 VAL Chi-restraints excluded: chain C residue 1096 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.5980 chunk 245 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22272 Z= 0.262 Angle : 0.627 11.417 30222 Z= 0.331 Chirality : 0.047 0.363 3273 Planarity : 0.004 0.059 4041 Dihedral : 15.077 175.481 3609 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.52 % Favored : 89.30 % Rotamer: Outliers : 3.76 % Allowed : 13.04 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.70 (0.16), residues: 2841 helix: -0.52 (0.39), residues: 189 sheet: -0.32 (0.15), residues: 1194 loop : -1.94 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 538 HIS 0.003 0.001 HIS A 612 PHE 0.016 0.001 PHE B 953 TYR 0.012 0.002 TYR B 698 ARG 0.006 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 109 time to evaluate : 2.538 Fit side-chains REVERT: A 791 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: A 842 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6743 (m-30) REVERT: A 907 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7661 (p0) REVERT: A 949 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7228 (tmtm) REVERT: B 541 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: B 766 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7165 (mm) REVERT: B 842 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: C 541 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: C 665 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7849 (mmpt) outliers start: 82 outliers final: 42 residues processed: 170 average time/residue: 1.0587 time to fit residues: 214.3524 Evaluate side-chains 151 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 100 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 833 LYS Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1096 ASP Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 1023 THR Chi-restraints excluded: chain C residue 1029 VAL Chi-restraints excluded: chain C residue 1096 ASP Chi-restraints excluded: chain C residue 1131 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 199 optimal weight: 0.4980 chunk 154 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 165 optimal weight: 0.4980 chunk 125 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22272 Z= 0.266 Angle : 0.623 11.255 30222 Z= 0.330 Chirality : 0.047 0.357 3273 Planarity : 0.004 0.058 4041 Dihedral : 14.786 175.488 3609 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.45 % Favored : 89.37 % Rotamer: Outliers : 3.86 % Allowed : 13.31 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2841 helix: -0.50 (0.39), residues: 189 sheet: -0.30 (0.15), residues: 1194 loop : -1.90 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 538 HIS 0.003 0.001 HIS A 612 PHE 0.017 0.001 PHE B 953 TYR 0.012 0.002 TYR A 696 ARG 0.007 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 106 time to evaluate : 2.397 Fit side-chains REVERT: A 262 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8561 (tp) REVERT: A 623 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 681 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.6850 (mtp180) REVERT: A 791 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: A 842 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: A 907 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7625 (p0) REVERT: B 541 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: B 766 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7178 (mm) REVERT: B 842 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: C 541 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: C 665 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7855 (mmpt) REVERT: C 681 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7611 (mtp180) REVERT: C 908 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7910 (mp) outliers start: 84 outliers final: 52 residues processed: 171 average time/residue: 1.0389 time to fit residues: 211.0727 Evaluate side-chains 165 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 100 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 833 LYS Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1096 ASP Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 681 ARG Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 1023 THR Chi-restraints excluded: chain C residue 1029 VAL Chi-restraints excluded: chain C residue 1096 ASP Chi-restraints excluded: chain C residue 1131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN A 707 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN B 818 GLN ** C 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22272 Z= 0.311 Angle : 0.645 11.219 30222 Z= 0.341 Chirality : 0.048 0.369 3273 Planarity : 0.004 0.062 4041 Dihedral : 14.549 173.654 3609 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.84 % Favored : 88.98 % Rotamer: Outliers : 4.09 % Allowed : 13.50 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.66 (0.16), residues: 2841 helix: -0.56 (0.39), residues: 189 sheet: -0.33 (0.15), residues: 1206 loop : -1.88 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 538 HIS 0.004 0.001 HIS A 612 PHE 0.017 0.002 PHE B 953 TYR 0.013 0.002 TYR A 696 ARG 0.006 0.000 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 102 time to evaluate : 2.547 Fit side-chains REVERT: A 262 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8565 (tp) REVERT: A 623 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: A 681 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6934 (mtp180) REVERT: A 842 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: A 907 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7649 (p0) REVERT: B 541 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: B 766 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7192 (mm) REVERT: B 842 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6701 (m-30) REVERT: C 541 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: C 665 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7888 (mmpt) REVERT: C 681 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7532 (mtp180) REVERT: C 842 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6912 (m-30) outliers start: 89 outliers final: 58 residues processed: 169 average time/residue: 1.0532 time to fit residues: 218.2781 Evaluate side-chains 168 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 98 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 833 LYS Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1096 ASP Chi-restraints excluded: chain B residue 1110 ARG Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 681 ARG Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1023 THR Chi-restraints excluded: chain C residue 1029 VAL Chi-restraints excluded: chain C residue 1096 ASP Chi-restraints excluded: chain C residue 1131 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.0060 chunk 237 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 ASN ** C 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22272 Z= 0.213 Angle : 0.594 11.112 30222 Z= 0.315 Chirality : 0.046 0.326 3273 Planarity : 0.004 0.060 4041 Dihedral : 14.107 176.723 3609 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.03 % Favored : 89.83 % Rotamer: Outliers : 3.21 % Allowed : 14.42 % Favored : 82.37 % 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: -1.58 (0.16), residues: 2841 helix: -0.43 (0.39), residues: 189 sheet: -0.28 (0.15), residues: 1194 loop : -1.82 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 538 HIS 0.002 0.001 HIS A 612 PHE 0.015 0.001 PHE B 953 TYR 0.011 0.001 TYR A 837 ARG 0.006 0.000 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 105 time to evaluate : 2.472 Fit side-chains REVERT: A 262 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 623 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: A 681 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.6895 (mtp180) REVERT: A 791 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: A 842 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6754 (m-30) REVERT: A 907 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7537 (p0) REVERT: B 541 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: B 766 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7060 (mm) REVERT: B 842 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: B 907 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7618 (p0) REVERT: C 541 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: C 681 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7560 (mtp180) outliers start: 70 outliers final: 54 residues processed: 162 average time/residue: 1.0137 time to fit residues: 197.7094 Evaluate side-chains 163 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 97 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 833 LYS Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1096 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 681 ARG Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1023 THR Chi-restraints excluded: chain C residue 1029 VAL Chi-restraints excluded: chain C residue 1096 ASP Chi-restraints excluded: chain C residue 1131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 10.0000 chunk 267 optimal weight: 0.3980 chunk 163 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22272 Z= 0.289 Angle : 0.623 11.061 30222 Z= 0.331 Chirality : 0.048 0.347 3273 Planarity : 0.004 0.061 4041 Dihedral : 14.040 173.922 3609 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.49 % Favored : 89.30 % Rotamer: Outliers : 3.49 % Allowed : 14.37 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2841 helix: -0.46 (0.39), residues: 189 sheet: -0.31 (0.15), residues: 1206 loop : -1.81 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 538 HIS 0.003 0.001 HIS A 612 PHE 0.017 0.001 PHE B 953 TYR 0.013 0.002 TYR A 696 ARG 0.006 0.000 ARG B 415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 99 time to evaluate : 2.645 Fit side-chains REVERT: A 262 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8537 (tp) REVERT: A 623 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: A 681 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.6924 (mtp180) REVERT: A 791 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: A 842 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: A 907 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7596 (p0) REVERT: B 541 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: B 766 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7099 (mm) REVERT: B 842 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: B 907 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7709 (p0) REVERT: C 541 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: C 681 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7476 (mtp180) REVERT: C 842 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6910 (m-30) outliers start: 76 outliers final: 56 residues processed: 158 average time/residue: 1.0055 time to fit residues: 190.5106 Evaluate side-chains 166 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 97 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 833 LYS Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1096 ASP Chi-restraints excluded: chain B residue 1110 ARG Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 681 ARG Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1023 THR Chi-restraints excluded: chain C residue 1029 VAL Chi-restraints excluded: chain C residue 1096 ASP Chi-restraints excluded: chain C residue 1131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 0.9980 chunk 238 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 206 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 230 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 420 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.112547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090687 restraints weight = 31137.961| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.15 r_work: 0.3172 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22272 Z= 0.151 Angle : 0.555 11.737 30222 Z= 0.294 Chirality : 0.045 0.306 3273 Planarity : 0.004 0.058 4041 Dihedral : 13.560 179.406 3609 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.26 % Favored : 90.64 % Rotamer: Outliers : 2.57 % Allowed : 15.29 % Favored : 82.14 % 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: -1.50 (0.16), residues: 2841 helix: -0.23 (0.40), residues: 186 sheet: -0.32 (0.15), residues: 1209 loop : -1.70 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 538 HIS 0.002 0.001 HIS C 612 PHE 0.013 0.001 PHE B 953 TYR 0.010 0.001 TYR C1122 ARG 0.008 0.000 ARG B 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6173.64 seconds wall clock time: 112 minutes 5.72 seconds (6725.72 seconds total)