Starting phenix.real_space_refine on Fri Feb 16 00:54:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/02_2024/8j9w_36117_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/02_2024/8j9w_36117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/02_2024/8j9w_36117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/02_2024/8j9w_36117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/02_2024/8j9w_36117_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/02_2024/8j9w_36117_neut_updated.pdb" } resolution = 2.76 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= -0.000 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 8693 2.51 5 N 2373 2.21 5 O 2661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A PHE 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 940": "NH1" <-> "NH2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13841 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6283 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 30, 'TRANS': 744} Chain: "B" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6283 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 30, 'TRANS': 744} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 255 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 334 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 334 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'EVP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.30, per 1000 atoms: 0.60 Number of scatterers: 13841 At special positions: 0 Unit cell: (122.01, 104.58, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 56 15.00 Mg 2 11.99 O 2661 8.00 N 2373 7.00 C 8693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.68 Conformation dependent library (CDL) restraints added in 2.7 seconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 14 sheets defined 43.1% alpha, 8.3% beta 15 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 8.22 Creating SS restraints... Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 497 through 500 No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 622 through 630 Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 657 through 664 removed outlier: 4.322A pdb=" N GLU A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 681 Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.805A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 729 Processing helix chain 'A' and resid 738 through 748 Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 820 Processing helix chain 'A' and resid 843 through 846 No H-bonds generated for 'chain 'A' and resid 843 through 846' Processing helix chain 'A' and resid 867 through 876 Processing helix chain 'A' and resid 883 through 892 Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 954 through 958 Processing helix chain 'A' and resid 985 through 988 No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1028 through 1074 Proline residue: A1037 - end of helix removed outlier: 4.634A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1091 Processing helix chain 'A' and resid 1099 through 1101 No H-bonds generated for 'chain 'A' and resid 1099 through 1101' Processing helix chain 'A' and resid 1110 through 1118 Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1130 through 1133 Processing helix chain 'A' and resid 1135 through 1159 Processing helix chain 'A' and resid 1167 through 1187 removed outlier: 3.611A pdb=" N THR A1187 " --> pdb=" O LYS A1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.710A pdb=" N LEU B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 500 No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 503 through 512 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 622 through 630 Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 657 through 664 removed outlier: 3.879A pdb=" N ARG B 662 " --> pdb=" O GLU B 658 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 681 Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.808A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 728 Processing helix chain 'B' and resid 738 through 748 Processing helix chain 'B' and resid 756 through 766 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 820 Processing helix chain 'B' and resid 843 through 846 No H-bonds generated for 'chain 'B' and resid 843 through 846' Processing helix chain 'B' and resid 867 through 876 Processing helix chain 'B' and resid 883 through 892 Processing helix chain 'B' and resid 943 through 950 Processing helix chain 'B' and resid 954 through 957 No H-bonds generated for 'chain 'B' and resid 954 through 957' Processing helix chain 'B' and resid 985 through 989 Processing helix chain 'B' and resid 998 through 1002 Processing helix chain 'B' and resid 1028 through 1074 Proline residue: B1037 - end of helix removed outlier: 4.462A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1091 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1110 through 1118 Processing helix chain 'B' and resid 1122 through 1126 Processing helix chain 'B' and resid 1130 through 1133 Processing helix chain 'B' and resid 1135 through 1159 Processing helix chain 'B' and resid 1167 through 1186 removed outlier: 3.635A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 434 through 437 removed outlier: 5.442A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 577 through 581 Processing sheet with id= C, first strand: chain 'A' and resid 779 through 782 Processing sheet with id= D, first strand: chain 'A' and resid 850 through 852 Processing sheet with id= E, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.545A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 922 through 926 removed outlier: 3.620A pdb=" N GLU A 936 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP A 924 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE A 934 " --> pdb=" O ASP A 924 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER A 926 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 932 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.509A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 434 through 437 removed outlier: 5.442A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 577 through 580 Processing sheet with id= J, first strand: chain 'B' and resid 779 through 782 Processing sheet with id= K, first strand: chain 'B' and resid 850 through 852 Processing sheet with id= L, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.548A pdb=" N HIS B 909 " --> pdb=" O TYR B 920 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 962 through 965 removed outlier: 3.735A pdb=" N ILE B 931 " --> pdb=" O SER B 926 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 926 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 1014 through 1016 471 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 6.14 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: 2121 1.31 - 1.44: 4227 1.44 - 1.56: 7739 1.56 - 1.68: 112 1.68 - 1.81: 88 Bond restraints: 14287 Sorted by residual: bond pdb=" N VAL B 941 " pdb=" CA VAL B 941 " ideal model delta sigma weight residual 1.456 1.495 -0.038 8.70e-03 1.32e+04 1.94e+01 bond pdb=" CA TRP A1189 " pdb=" C TRP A1189 " ideal model delta sigma weight residual 1.525 1.457 0.068 1.63e-02 3.76e+03 1.72e+01 bond pdb=" C CYS B 545 " pdb=" O CYS B 545 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" CA LEU B 542 " pdb=" C LEU B 542 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.35e-02 5.49e+03 1.36e+01 bond pdb=" C LEU B 542 " pdb=" O LEU B 542 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.18e-02 7.18e+03 1.28e+01 ... (remaining 14282 not shown) Histogram of bond angle deviations from ideal: 94.61 - 102.51: 108 102.51 - 110.40: 3728 110.40 - 118.29: 7367 118.29 - 126.19: 7998 126.19 - 134.08: 366 Bond angle restraints: 19567 Sorted by residual: angle pdb=" N ARG B 940 " pdb=" CA ARG B 940 " pdb=" C ARG B 940 " ideal model delta sigma weight residual 111.52 120.84 -9.32 1.40e+00 5.10e-01 4.43e+01 angle pdb=" C LEU A1047 " pdb=" N MET A1048 " pdb=" CA MET A1048 " ideal model delta sigma weight residual 121.14 109.59 11.55 1.75e+00 3.27e-01 4.36e+01 angle pdb=" N CYS B 545 " pdb=" CA CYS B 545 " pdb=" C CYS B 545 " ideal model delta sigma weight residual 109.46 99.17 10.29 1.66e+00 3.63e-01 3.84e+01 angle pdb=" N GLU B1041 " pdb=" CA GLU B1041 " pdb=" CB GLU B1041 " ideal model delta sigma weight residual 110.39 119.34 -8.95 1.66e+00 3.63e-01 2.91e+01 angle pdb=" N GLU A1041 " pdb=" CA GLU A1041 " pdb=" CB GLU A1041 " ideal model delta sigma weight residual 110.39 119.32 -8.93 1.66e+00 3.63e-01 2.89e+01 ... (remaining 19562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 8170 35.78 - 71.56: 330 71.56 - 107.34: 17 107.34 - 143.12: 6 143.12 - 178.90: 2 Dihedral angle restraints: 8525 sinusoidal: 3981 harmonic: 4544 Sorted by residual: dihedral pdb=" CA PRO A 938 " pdb=" C PRO A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta harmonic sigma weight residual -180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" N HIS A1192 " pdb=" C HIS A1192 " pdb=" CA HIS A1192 " pdb=" CB HIS A1192 " ideal model delta harmonic sigma weight residual 122.80 133.62 -10.82 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA VAL A 941 " pdb=" C VAL A 941 " pdb=" N PRO A 942 " pdb=" CA PRO A 942 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1873 0.074 - 0.148: 239 0.148 - 0.222: 25 0.222 - 0.296: 3 0.296 - 0.370: 3 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA HIS A1192 " pdb=" N HIS A1192 " pdb=" C HIS A1192 " pdb=" CB HIS A1192 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C9 EVP D 101 " pdb=" C10 EVP D 101 " pdb=" C6 EVP D 101 " pdb=" C8 EVP D 101 " both_signs ideal model delta sigma weight residual False 2.49 2.83 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ARG B 940 " pdb=" N ARG B 940 " pdb=" C ARG B 940 " pdb=" CB ARG B 940 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 2140 not shown) Planarity restraints: 2279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1190 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LYS A1190 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS A1190 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A1191 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1044 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" CD GLN A1044 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN A1044 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN A1044 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1169 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C VAL B1169 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL B1169 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP B1170 " -0.014 2.00e-02 2.50e+03 ... (remaining 2276 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 631 2.72 - 3.26: 13625 3.26 - 3.81: 24118 3.81 - 4.35: 29353 4.35 - 4.90: 47233 Nonbonded interactions: 114960 Sorted by model distance: nonbonded pdb=" OD2 ASP B 541 " pdb="MG MG B1201 " model vdw 2.175 2.170 nonbonded pdb=" OD2 ASP A 541 " pdb="MG MG A1201 " model vdw 2.202 2.170 nonbonded pdb=" O PRO A1095 " pdb=" OH TYR A1124 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR B 580 " pdb=" OE1 GLU B 624 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR B 751 " pdb=" OP2 DA E 12 " model vdw 2.286 2.440 ... (remaining 114955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 12 or (resid 13 and (name P or name OP1 or name \ OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' or n \ ame C2' or name C1')))) selection = chain 'E' } ncs_group { reference = (chain 'D' and resid 1 through 17) selection = chain 'F' } 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.930 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 45.300 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.068 14287 Z= 0.286 Angle : 0.839 11.552 19567 Z= 0.454 Chirality : 0.052 0.370 2143 Planarity : 0.006 0.084 2279 Dihedral : 18.058 178.896 5613 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1546 helix: -0.51 (0.19), residues: 714 sheet: -1.17 (0.38), residues: 190 loop : -0.82 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 560 HIS 0.004 0.001 HIS B 680 PHE 0.015 0.002 PHE A1107 TYR 0.031 0.002 TYR B1067 ARG 0.011 0.001 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 601 LYS cc_start: 0.9365 (mmpt) cc_final: 0.9160 (pptt) REVERT: B 966 TYR cc_start: 0.8595 (m-80) cc_final: 0.8311 (m-10) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 1.4618 time to fit residues: 181.8112 Evaluate side-chains 69 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1114 ASN B1186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14287 Z= 0.242 Angle : 0.636 9.009 19567 Z= 0.329 Chirality : 0.043 0.264 2143 Planarity : 0.004 0.049 2279 Dihedral : 18.283 176.038 2515 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.54 % Allowed : 10.29 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1546 helix: 0.16 (0.19), residues: 722 sheet: -1.25 (0.37), residues: 188 loop : -0.64 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.004 0.001 HIS A1099 PHE 0.021 0.001 PHE B1107 TYR 0.020 0.001 TYR A 698 ARG 0.006 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.556 Fit side-chains REVERT: A 799 ARG cc_start: 0.7978 (mpp-170) cc_final: 0.7697 (mtt180) REVERT: A 924 ASP cc_start: 0.8685 (m-30) cc_final: 0.8461 (t0) REVERT: B 593 GLU cc_start: 0.8395 (pm20) cc_final: 0.8004 (pp20) REVERT: B 601 LYS cc_start: 0.9393 (mmpt) cc_final: 0.9160 (pptt) REVERT: B 966 TYR cc_start: 0.8650 (m-80) cc_final: 0.8313 (m-10) REVERT: B 1048 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7564 (mpp) outliers start: 21 outliers final: 5 residues processed: 89 average time/residue: 1.3063 time to fit residues: 128.3877 Evaluate side-chains 69 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1048 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 143 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 128 optimal weight: 0.0060 chunk 142 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 0.0770 overall best weight: 0.1812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 540 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS B 752 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14287 Z= 0.147 Angle : 0.588 10.670 19567 Z= 0.298 Chirality : 0.041 0.229 2143 Planarity : 0.003 0.039 2279 Dihedral : 17.741 178.715 2515 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.76 % Allowed : 13.09 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1546 helix: 0.54 (0.20), residues: 724 sheet: -1.11 (0.36), residues: 190 loop : -0.53 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.002 0.000 HIS A1051 PHE 0.024 0.001 PHE A 596 TYR 0.017 0.001 TYR A 698 ARG 0.006 0.000 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 1.666 Fit side-chains REVERT: A 848 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.5835 (p90) REVERT: A 924 ASP cc_start: 0.8750 (m-30) cc_final: 0.8472 (t0) REVERT: A 1173 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: B 593 GLU cc_start: 0.8351 (pm20) cc_final: 0.8040 (pp20) REVERT: B 601 LYS cc_start: 0.9387 (mmpt) cc_final: 0.9165 (pptt) REVERT: B 966 TYR cc_start: 0.8637 (m-80) cc_final: 0.8290 (m-10) REVERT: B 1048 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7612 (mpp) REVERT: B 1173 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7676 (mp0) outliers start: 24 outliers final: 5 residues processed: 91 average time/residue: 1.2299 time to fit residues: 124.2937 Evaluate side-chains 78 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 800 TYR Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 0.0040 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 740 GLN A1114 ASN B 540 GLN B 804 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14287 Z= 0.304 Angle : 0.650 9.193 19567 Z= 0.336 Chirality : 0.044 0.265 2143 Planarity : 0.004 0.048 2279 Dihedral : 17.839 173.774 2515 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.35 % Allowed : 15.44 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1546 helix: 0.58 (0.20), residues: 722 sheet: -1.20 (0.37), residues: 188 loop : -0.58 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1035 HIS 0.005 0.001 HIS A1099 PHE 0.028 0.002 PHE B1107 TYR 0.026 0.002 TYR A1028 ARG 0.009 0.001 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 593 GLU cc_start: 0.8827 (mp0) cc_final: 0.8604 (pp20) REVERT: A 599 TRP cc_start: 0.8658 (t60) cc_final: 0.8401 (t60) REVERT: A 924 ASP cc_start: 0.8666 (m-30) cc_final: 0.8401 (t0) REVERT: A 1173 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: B 593 GLU cc_start: 0.8413 (pm20) cc_final: 0.8079 (pp20) REVERT: B 601 LYS cc_start: 0.9393 (mmpt) cc_final: 0.9190 (pptt) REVERT: B 966 TYR cc_start: 0.8646 (m-80) cc_final: 0.8346 (m-10) REVERT: B 1048 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7575 (mpp) REVERT: B 1173 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7952 (mt-10) outliers start: 32 outliers final: 8 residues processed: 89 average time/residue: 1.2948 time to fit residues: 127.7419 Evaluate side-chains 75 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 800 TYR Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 740 GLN B 928 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14287 Z= 0.269 Angle : 0.633 8.234 19567 Z= 0.324 Chirality : 0.043 0.257 2143 Planarity : 0.004 0.059 2279 Dihedral : 17.805 175.109 2515 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.65 % Allowed : 16.40 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1546 helix: 0.68 (0.20), residues: 710 sheet: -1.17 (0.37), residues: 188 loop : -0.47 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1170 HIS 0.004 0.001 HIS B1099 PHE 0.022 0.001 PHE B1107 TYR 0.023 0.001 TYR A1028 ARG 0.007 0.001 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 68 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: A 593 GLU cc_start: 0.8780 (mp0) cc_final: 0.8544 (tm-30) REVERT: A 599 TRP cc_start: 0.8573 (t60) cc_final: 0.8313 (t60) REVERT: A 846 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8848 (mpp) REVERT: A 924 ASP cc_start: 0.8673 (m-30) cc_final: 0.8397 (t0) REVERT: A 993 THR cc_start: 0.9642 (OUTLIER) cc_final: 0.9404 (p) REVERT: A 1048 MET cc_start: 0.7925 (ptp) cc_final: 0.7594 (pmm) REVERT: A 1097 LEU cc_start: 0.6666 (pt) cc_final: 0.5734 (tt) REVERT: A 1173 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: B 593 GLU cc_start: 0.8379 (pm20) cc_final: 0.8061 (pp20) REVERT: B 848 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.6107 (p90) REVERT: B 966 TYR cc_start: 0.8646 (m-80) cc_final: 0.8295 (m-10) REVERT: B 1048 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7600 (mpp) REVERT: B 1173 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7627 (mp0) outliers start: 36 outliers final: 16 residues processed: 96 average time/residue: 1.2291 time to fit residues: 131.1595 Evaluate side-chains 84 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 846 MET Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 800 TYR Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.0040 chunk 37 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 740 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14287 Z= 0.198 Angle : 0.606 9.863 19567 Z= 0.308 Chirality : 0.041 0.224 2143 Planarity : 0.004 0.063 2279 Dihedral : 17.454 176.731 2513 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.35 % Allowed : 17.65 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1546 helix: 0.77 (0.20), residues: 710 sheet: -1.08 (0.38), residues: 188 loop : -0.37 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 820 HIS 0.002 0.001 HIS B1099 PHE 0.017 0.001 PHE B1107 TYR 0.018 0.001 TYR A 698 ARG 0.006 0.000 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8713 (m-80) cc_final: 0.8219 (m-80) REVERT: A 586 MET cc_start: 0.8695 (mmp) cc_final: 0.8489 (tpp) REVERT: A 597 ASP cc_start: 0.9391 (m-30) cc_final: 0.9170 (t70) REVERT: A 599 TRP cc_start: 0.8577 (t60) cc_final: 0.8302 (t60) REVERT: A 924 ASP cc_start: 0.8702 (m-30) cc_final: 0.8403 (t0) REVERT: A 993 THR cc_start: 0.9641 (OUTLIER) cc_final: 0.9417 (p) REVERT: B 593 GLU cc_start: 0.8413 (pm20) cc_final: 0.8142 (pp20) REVERT: B 599 TRP cc_start: 0.8533 (t60) cc_final: 0.8260 (t60) REVERT: B 966 TYR cc_start: 0.8646 (m-80) cc_final: 0.8266 (m-10) REVERT: B 1048 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7556 (mpp) REVERT: B 1173 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7594 (mp0) outliers start: 32 outliers final: 13 residues processed: 101 average time/residue: 1.1903 time to fit residues: 134.8879 Evaluate side-chains 78 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 740 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14287 Z= 0.262 Angle : 0.643 9.973 19567 Z= 0.327 Chirality : 0.043 0.245 2143 Planarity : 0.004 0.043 2279 Dihedral : 17.357 174.031 2513 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 2.72 % Allowed : 18.16 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1546 helix: 0.74 (0.20), residues: 708 sheet: -1.14 (0.38), residues: 188 loop : -0.34 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 861 HIS 0.004 0.001 HIS A1099 PHE 0.024 0.001 PHE B1107 TYR 0.019 0.001 TYR A 698 ARG 0.006 0.000 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 62 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8776 (m-80) cc_final: 0.8260 (m-80) REVERT: A 475 MET cc_start: 0.8317 (ptm) cc_final: 0.7477 (ptt) REVERT: A 599 TRP cc_start: 0.8561 (t60) cc_final: 0.8299 (t60) REVERT: A 924 ASP cc_start: 0.8700 (m-30) cc_final: 0.8414 (t0) REVERT: A 993 THR cc_start: 0.9632 (OUTLIER) cc_final: 0.9392 (p) REVERT: A 1048 MET cc_start: 0.7888 (ptp) cc_final: 0.7548 (pmm) REVERT: B 593 GLU cc_start: 0.8435 (pm20) cc_final: 0.8137 (pp20) REVERT: B 599 TRP cc_start: 0.8567 (t60) cc_final: 0.8285 (t60) REVERT: B 848 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.6238 (p90) REVERT: B 966 TYR cc_start: 0.8677 (m-80) cc_final: 0.8274 (m-10) REVERT: B 1048 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7560 (mpp) outliers start: 37 outliers final: 21 residues processed: 93 average time/residue: 1.1762 time to fit residues: 122.5105 Evaluate side-chains 85 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14287 Z= 0.198 Angle : 0.619 10.980 19567 Z= 0.313 Chirality : 0.041 0.205 2143 Planarity : 0.003 0.039 2279 Dihedral : 17.171 175.469 2513 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 2.35 % Allowed : 18.82 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1546 helix: 0.77 (0.20), residues: 710 sheet: -1.08 (0.38), residues: 188 loop : -0.32 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 820 HIS 0.002 0.001 HIS B1099 PHE 0.017 0.001 PHE B1107 TYR 0.018 0.001 TYR A 698 ARG 0.005 0.000 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8757 (m-80) cc_final: 0.8241 (m-80) REVERT: A 475 MET cc_start: 0.8219 (ptm) cc_final: 0.7393 (ptt) REVERT: A 586 MET cc_start: 0.8640 (mmp) cc_final: 0.8429 (tpp) REVERT: A 599 TRP cc_start: 0.8570 (t60) cc_final: 0.8295 (t60) REVERT: A 924 ASP cc_start: 0.8716 (m-30) cc_final: 0.8406 (t0) REVERT: A 993 THR cc_start: 0.9626 (OUTLIER) cc_final: 0.9396 (p) REVERT: B 593 GLU cc_start: 0.8440 (pm20) cc_final: 0.8172 (pp20) REVERT: B 599 TRP cc_start: 0.8564 (t60) cc_final: 0.8275 (t60) REVERT: B 848 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6210 (p90) REVERT: B 966 TYR cc_start: 0.8663 (m-80) cc_final: 0.8250 (m-10) REVERT: B 1048 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7548 (mpp) outliers start: 32 outliers final: 19 residues processed: 97 average time/residue: 1.1811 time to fit residues: 128.2070 Evaluate side-chains 85 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.2980 chunk 133 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14287 Z= 0.225 Angle : 0.636 11.156 19567 Z= 0.323 Chirality : 0.042 0.230 2143 Planarity : 0.004 0.040 2279 Dihedral : 17.151 174.584 2513 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 2.13 % Allowed : 19.49 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1546 helix: 0.76 (0.20), residues: 708 sheet: -1.07 (0.38), residues: 188 loop : -0.26 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 PHE 0.020 0.001 PHE A1107 TYR 0.018 0.001 TYR A 698 ARG 0.005 0.000 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8798 (m-80) cc_final: 0.8254 (m-80) REVERT: A 475 MET cc_start: 0.8257 (ptm) cc_final: 0.7443 (ptt) REVERT: A 586 MET cc_start: 0.8669 (mmp) cc_final: 0.8454 (tpp) REVERT: A 599 TRP cc_start: 0.8557 (t60) cc_final: 0.8289 (t60) REVERT: A 608 ASN cc_start: 0.8826 (t0) cc_final: 0.8463 (t0) REVERT: A 924 ASP cc_start: 0.8717 (m-30) cc_final: 0.8407 (t0) REVERT: A 993 THR cc_start: 0.9623 (OUTLIER) cc_final: 0.9374 (p) REVERT: B 593 GLU cc_start: 0.8423 (pm20) cc_final: 0.8154 (pp20) REVERT: B 599 TRP cc_start: 0.8573 (t60) cc_final: 0.8283 (t60) REVERT: B 848 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.6326 (p90) REVERT: B 966 TYR cc_start: 0.8674 (m-80) cc_final: 0.8297 (m-10) REVERT: B 1048 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7571 (mpp) outliers start: 29 outliers final: 21 residues processed: 88 average time/residue: 1.2614 time to fit residues: 123.2323 Evaluate side-chains 88 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14287 Z= 0.232 Angle : 0.641 11.637 19567 Z= 0.327 Chirality : 0.042 0.243 2143 Planarity : 0.004 0.041 2279 Dihedral : 17.153 174.211 2513 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 2.13 % Allowed : 19.49 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1546 helix: 0.74 (0.20), residues: 708 sheet: -0.95 (0.37), residues: 198 loop : -0.32 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 PHE 0.021 0.001 PHE A1107 TYR 0.018 0.001 TYR A 698 ARG 0.005 0.000 ARG A 799 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8815 (m-80) cc_final: 0.8252 (m-80) REVERT: A 586 MET cc_start: 0.8656 (mmp) cc_final: 0.8434 (tpp) REVERT: A 599 TRP cc_start: 0.8552 (t60) cc_final: 0.8272 (t60) REVERT: A 608 ASN cc_start: 0.8822 (t0) cc_final: 0.8458 (t0) REVERT: A 924 ASP cc_start: 0.8715 (m-30) cc_final: 0.8405 (t0) REVERT: A 993 THR cc_start: 0.9615 (OUTLIER) cc_final: 0.9364 (p) REVERT: A 1048 MET cc_start: 0.7933 (ptp) cc_final: 0.7568 (pmm) REVERT: B 593 GLU cc_start: 0.8428 (pm20) cc_final: 0.8173 (pp20) REVERT: B 599 TRP cc_start: 0.8576 (t60) cc_final: 0.8269 (t60) REVERT: B 739 PHE cc_start: 0.8728 (t80) cc_final: 0.8354 (m-80) REVERT: B 848 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.6399 (p90) REVERT: B 924 ASP cc_start: 0.8809 (m-30) cc_final: 0.8420 (t0) REVERT: B 966 TYR cc_start: 0.8797 (m-80) cc_final: 0.8358 (m-10) REVERT: B 1048 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7565 (mpp) outliers start: 29 outliers final: 19 residues processed: 92 average time/residue: 1.2008 time to fit residues: 123.3862 Evaluate side-chains 88 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 18 optimal weight: 0.0270 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 128 optimal weight: 0.0020 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.4646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 GLN B 903 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.093938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.078049 restraints weight = 52937.103| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.75 r_work: 0.3553 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14287 Z= 0.177 Angle : 0.632 11.631 19567 Z= 0.318 Chirality : 0.041 0.226 2143 Planarity : 0.003 0.038 2279 Dihedral : 16.980 176.677 2513 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 1.99 % Allowed : 19.78 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1546 helix: 0.79 (0.20), residues: 708 sheet: -0.91 (0.38), residues: 190 loop : -0.23 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 820 HIS 0.002 0.001 HIS A1192 PHE 0.013 0.001 PHE B1107 TYR 0.017 0.001 TYR A 698 ARG 0.003 0.000 ARG B1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3682.71 seconds wall clock time: 67 minutes 33.46 seconds (4053.46 seconds total)