Starting phenix.real_space_refine on Thu Feb 15 18:15:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq8_34022/02_2024/7yq8_34022_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq8_34022/02_2024/7yq8_34022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq8_34022/02_2024/7yq8_34022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq8_34022/02_2024/7yq8_34022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq8_34022/02_2024/7yq8_34022_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq8_34022/02_2024/7yq8_34022_updated.pdb" } resolution = 3.9 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= 0.003 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 48 5.16 5 C 8123 2.51 5 N 2247 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B ASP 680": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13036 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5901 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 25, 'TRANS': 704} Chain breaks: 1 Chain: "B" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5901 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 25, 'TRANS': 704} Chain breaks: 1 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.24, per 1000 atoms: 0.56 Number of scatterers: 13036 At special positions: 0 Unit cell: (103.335, 123.255, 117.03, 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 48 16.00 P 56 15.00 Mg 2 11.99 O 2560 8.00 N 2247 7.00 C 8123 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: 5.69 Conformation dependent library (CDL) restraints added in 2.2 seconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 15 sheets defined 48.2% alpha, 10.3% beta 28 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.844A pdb=" N GLY A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.953A pdb=" N THR A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 588 Proline residue: A 583 - end of helix removed outlier: 4.617A pdb=" N LEU A 586 " --> pdb=" O TRP A 582 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 622 removed outlier: 3.621A pdb=" N HIS A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.631A pdb=" N LYS A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 674 Processing helix chain 'A' and resid 676 through 699 removed outlier: 3.703A pdb=" N ILE A 679 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP A 680 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 681 " --> pdb=" O LYS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 722 Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 745 through 757 Processing helix chain 'A' and resid 765 through 775 Processing helix chain 'A' and resid 782 through 792 Processing helix chain 'A' and resid 833 through 838 removed outlier: 3.706A pdb=" N LEU A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 869 through 872 No H-bonds generated for 'chain 'A' and resid 869 through 872' Processing helix chain 'A' and resid 890 through 901 Processing helix chain 'A' and resid 953 through 965 removed outlier: 4.846A pdb=" N GLU A 962 " --> pdb=" O GLU A 958 " (cutoff:3.500A) Proline residue: A 963 - end of helix Processing helix chain 'A' and resid 995 through 1004 Processing helix chain 'A' and resid 1006 through 1010 Processing helix chain 'A' and resid 1036 through 1081 Processing helix chain 'A' and resid 1091 through 1101 Processing helix chain 'A' and resid 1107 through 1117 removed outlier: 3.548A pdb=" N ALA A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A1115 " --> pdb=" O TRP A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1147 No H-bonds generated for 'chain 'A' and resid 1144 through 1147' Processing helix chain 'A' and resid 1151 through 1154 Processing helix chain 'A' and resid 1156 through 1177 removed outlier: 3.830A pdb=" N ASN A1174 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1205 removed outlier: 3.696A pdb=" N LYS A1186 " --> pdb=" O SER A1182 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A1187 " --> pdb=" O ASP A1183 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1195 " --> pdb=" O ALA A1191 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A1197 " --> pdb=" O VAL A1193 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS A1198 " --> pdb=" O GLU A1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.747A pdb=" N GLY B 495 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 526 through 535 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.758A pdb=" N THR B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 581 Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 613 through 622 removed outlier: 3.647A pdb=" N HIS B 622 " --> pdb=" O GLU B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 642 through 650 removed outlier: 3.555A pdb=" N LYS B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 647 " --> pdb=" O LYS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 674 Processing helix chain 'B' and resid 676 through 699 removed outlier: 3.722A pdb=" N ILE B 679 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP B 680 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 681 " --> pdb=" O LYS B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 722 Processing helix chain 'B' and resid 724 through 735 Processing helix chain 'B' and resid 745 through 757 Processing helix chain 'B' and resid 765 through 775 Processing helix chain 'B' and resid 782 through 792 Processing helix chain 'B' and resid 833 through 838 removed outlier: 3.765A pdb=" N LEU B 837 " --> pdb=" O THR B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 868 through 872 removed outlier: 4.178A pdb=" N ASN B 872 " --> pdb=" O VAL B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 901 Processing helix chain 'B' and resid 953 through 965 removed outlier: 4.681A pdb=" N GLU B 962 " --> pdb=" O GLU B 958 " (cutoff:3.500A) Proline residue: B 963 - end of helix Processing helix chain 'B' and resid 995 through 1004 Processing helix chain 'B' and resid 1006 through 1010 Processing helix chain 'B' and resid 1036 through 1081 Processing helix chain 'B' and resid 1091 through 1101 Processing helix chain 'B' and resid 1107 through 1117 Processing helix chain 'B' and resid 1151 through 1154 Processing helix chain 'B' and resid 1156 through 1177 removed outlier: 3.810A pdb=" N ASN B1174 " --> pdb=" O GLY B1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1205 removed outlier: 3.537A pdb=" N TRP B1185 " --> pdb=" O PRO B1181 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B1186 " --> pdb=" O SER B1182 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B1187 " --> pdb=" O ASP B1183 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B1188 " --> pdb=" O LEU B1184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B1195 " --> pdb=" O ALA B1191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B1197 " --> pdb=" O VAL B1193 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS B1198 " --> pdb=" O GLU B1194 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B1199 " --> pdb=" O GLU B1195 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 502 through 507 removed outlier: 6.607A pdb=" N THR A 477 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N PHE A 505 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 479 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU A 507 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR A 481 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS A 556 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 480 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET A 558 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLU A 482 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET A 560 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 606 through 610 Processing sheet with id= C, first strand: chain 'A' and resid 874 through 877 Processing sheet with id= D, first strand: chain 'A' and resid 1013 through 1017 removed outlier: 6.257A pdb=" N ALA A 929 " --> pdb=" O GLU A 922 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU A 922 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER A 931 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE A 920 " --> pdb=" O SER A 931 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 933 through 935 removed outlier: 3.624A pdb=" N GLU A 946 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 935 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE A 944 " --> pdb=" O PHE A 935 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1021 through 1024 removed outlier: 4.111A pdb=" N MET A1021 " --> pdb=" O TYR A1033 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 849 through 851 removed outlier: 5.017A pdb=" N GLU A 858 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 502 through 507 removed outlier: 6.557A pdb=" N THR B 477 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N PHE B 505 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE B 479 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 507 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR B 481 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS B 556 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU B 480 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET B 558 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLU B 482 " --> pdb=" O MET B 558 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET B 560 " --> pdb=" O GLU B 482 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 606 through 610 Processing sheet with id= J, first strand: chain 'B' and resid 805 through 808 removed outlier: 3.996A pdb=" N MET B 830 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 874 through 876 Processing sheet with id= L, first strand: chain 'B' and resid 1013 through 1017 removed outlier: 6.234A pdb=" N ALA B 929 " --> pdb=" O GLU B 922 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU B 922 " --> pdb=" O ALA B 929 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER B 931 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE B 920 " --> pdb=" O SER B 931 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 933 through 935 removed outlier: 3.590A pdb=" N GLU B 946 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B 935 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE B 944 " --> pdb=" O PHE B 935 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 1021 through 1024 removed outlier: 4.094A pdb=" N MET B1021 " --> pdb=" O TYR B1033 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 849 through 851 removed outlier: 5.011A pdb=" N GLU B 858 " --> pdb=" O LEU B 850 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 6.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3928 1.34 - 1.46: 2544 1.46 - 1.58: 6754 1.58 - 1.70: 108 1.70 - 1.82: 86 Bond restraints: 13420 Sorted by residual: bond pdb=" C7 EVP D 101 " pdb=" O4 EVP D 101 " ideal model delta sigma weight residual 1.200 1.296 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C7 EVP F 101 " pdb=" O4 EVP F 101 " ideal model delta sigma weight residual 1.200 1.295 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C14 EVP F 101 " pdb=" C5 EVP F 101 " ideal model delta sigma weight residual 1.518 1.575 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C13 EVP D 101 " pdb=" C2 EVP D 101 " ideal model delta sigma weight residual 1.388 1.440 -0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" C13 EVP F 101 " pdb=" C2 EVP F 101 " ideal model delta sigma weight residual 1.388 1.440 -0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 13415 not shown) Histogram of bond angle deviations from ideal: 98.45 - 106.03: 536 106.03 - 113.60: 7514 113.60 - 121.18: 6897 121.18 - 128.76: 3269 128.76 - 136.33: 126 Bond angle restraints: 18342 Sorted by residual: angle pdb=" CB ARG B 939 " pdb=" CG ARG B 939 " pdb=" CD ARG B 939 " ideal model delta sigma weight residual 111.30 120.39 -9.09 2.30e+00 1.89e-01 1.56e+01 angle pdb=" CB ARG A 939 " pdb=" CG ARG A 939 " pdb=" CD ARG A 939 " ideal model delta sigma weight residual 111.30 120.24 -8.94 2.30e+00 1.89e-01 1.51e+01 angle pdb=" CA GLU B 723 " pdb=" CB GLU B 723 " pdb=" CG GLU B 723 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C11 EVP F 101 " pdb=" C10 EVP F 101 " pdb=" O8 EVP F 101 " ideal model delta sigma weight residual 107.62 116.67 -9.05 3.00e+00 1.11e-01 9.10e+00 angle pdb=" C ASN B 721 " pdb=" N LYS B 722 " pdb=" CA LYS B 722 " ideal model delta sigma weight residual 121.52 116.44 5.08 1.74e+00 3.30e-01 8.53e+00 ... (remaining 18337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6893 17.65 - 35.29: 819 35.29 - 52.94: 262 52.94 - 70.59: 53 70.59 - 88.23: 19 Dihedral angle restraints: 8046 sinusoidal: 3802 harmonic: 4244 Sorted by residual: dihedral pdb=" CA ALA A 673 " pdb=" C ALA A 673 " pdb=" N PHE A 674 " pdb=" CA PHE A 674 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.77e+00 dihedral pdb=" CA ALA B 673 " pdb=" C ALA B 673 " pdb=" N PHE B 674 " pdb=" CA PHE B 674 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.74e+00 dihedral pdb=" N LYS B 540 " pdb=" CA LYS B 540 " pdb=" CB LYS B 540 " pdb=" CG LYS B 540 " ideal model delta sinusoidal sigma weight residual -60.00 -118.10 58.10 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 8043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1963 0.110 - 0.220: 41 0.220 - 0.330: 2 0.330 - 0.441: 0 0.441 - 0.551: 2 Chirality restraints: 2008 Sorted by residual: chirality pdb=" C6 EVP D 101 " pdb=" C5 EVP D 101 " pdb=" C7 EVP D 101 " pdb=" C9 EVP D 101 " both_signs ideal model delta sigma weight residual False -2.41 -1.86 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" C6 EVP F 101 " pdb=" C5 EVP F 101 " pdb=" C7 EVP F 101 " pdb=" C9 EVP F 101 " both_signs ideal model delta sigma weight residual False -2.41 -1.87 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA GLU B 723 " pdb=" N GLU B 723 " pdb=" C GLU B 723 " pdb=" CB GLU B 723 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2005 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 723 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.73e+00 pdb=" CD GLU B 723 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU B 723 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 723 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1051 " 0.019 2.00e-02 2.50e+03 1.15e-02 2.62e+00 pdb=" CG TYR B1051 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B1051 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B1051 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B1051 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B1051 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B1051 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1051 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 482 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C GLU A 482 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU A 482 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY A 483 " -0.009 2.00e-02 2.50e+03 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 198 2.61 - 3.18: 11493 3.18 - 3.76: 21778 3.76 - 4.33: 29233 4.33 - 4.90: 45763 Nonbonded interactions: 108465 Sorted by model distance: nonbonded pdb=" OD2 ASP A 564 " pdb="MG MG A1701 " model vdw 2.038 2.170 nonbonded pdb=" OD2 ASP B 564 " pdb="MG MG B1701 " model vdw 2.045 2.170 nonbonded pdb=" OD2 ASP A 562 " pdb="MG MG A1701 " model vdw 2.053 2.170 nonbonded pdb=" OD2 ASP B 562 " pdb="MG MG B1701 " model vdw 2.056 2.170 nonbonded pdb=" O VAL B 772 " pdb=" OG SER B 776 " model vdw 2.205 2.440 ... (remaining 108460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.350 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: 2.410 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 42.120 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 13420 Z= 0.234 Angle : 0.649 9.090 18342 Z= 0.314 Chirality : 0.045 0.551 2008 Planarity : 0.003 0.032 2148 Dihedral : 17.079 88.235 5310 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.76 (0.24), residues: 1452 helix: 1.92 (0.20), residues: 678 sheet: -1.08 (0.43), residues: 166 loop : -0.63 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 582 HIS 0.002 0.000 HIS B 569 PHE 0.026 0.002 PHE A 674 TYR 0.025 0.001 TYR B1051 ARG 0.006 0.000 ARG B1047 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.500 Fit side-chains REVERT: A 900 MET cc_start: 0.8665 (mtp) cc_final: 0.8413 (mtp) REVERT: B 463 ASP cc_start: 0.8325 (m-30) cc_final: 0.8078 (m-30) REVERT: B 830 MET cc_start: 0.7527 (ppp) cc_final: 0.7260 (ppp) REVERT: B 900 MET cc_start: 0.8725 (mtp) cc_final: 0.8480 (mtp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2367 time to fit residues: 36.8537 Evaluate side-chains 81 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 20.0000 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 60 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 806 GLN B1165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13420 Z= 0.186 Angle : 0.517 6.941 18342 Z= 0.278 Chirality : 0.038 0.178 2008 Planarity : 0.004 0.031 2148 Dihedral : 16.390 65.296 2306 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.31 % Allowed : 6.80 % Favored : 92.89 % 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: 0.60 (0.23), residues: 1452 helix: 1.65 (0.20), residues: 680 sheet: -1.00 (0.43), residues: 166 loop : -0.59 (0.28), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1111 HIS 0.002 0.000 HIS A 579 PHE 0.019 0.002 PHE A 674 TYR 0.018 0.001 TYR A 978 ARG 0.004 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 1.524 Fit side-chains REVERT: A 900 MET cc_start: 0.8707 (mtp) cc_final: 0.8458 (mtp) REVERT: A 1154 LEU cc_start: 0.8978 (mm) cc_final: 0.8313 (tp) REVERT: A 1186 LYS cc_start: 0.9663 (mttt) cc_final: 0.9204 (mmmt) REVERT: B 900 MET cc_start: 0.8728 (mtp) cc_final: 0.8482 (mtp) REVERT: B 1149 MET cc_start: 0.8652 (mpp) cc_final: 0.8435 (mpp) outliers start: 4 outliers final: 2 residues processed: 92 average time/residue: 0.2582 time to fit residues: 37.2030 Evaluate side-chains 85 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 0.3980 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 0.2980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13420 Z= 0.133 Angle : 0.485 7.681 18342 Z= 0.258 Chirality : 0.036 0.165 2008 Planarity : 0.003 0.032 2148 Dihedral : 16.371 68.608 2306 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.39 % Allowed : 9.30 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1452 helix: 1.78 (0.20), residues: 678 sheet: -0.94 (0.43), residues: 166 loop : -0.52 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 582 HIS 0.001 0.000 HIS A 579 PHE 0.018 0.001 PHE A 674 TYR 0.016 0.001 TYR A 978 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.549 Fit side-chains REVERT: A 1154 LEU cc_start: 0.8954 (mm) cc_final: 0.8282 (tp) REVERT: A 1186 LYS cc_start: 0.9669 (mttt) cc_final: 0.9197 (mmmt) REVERT: A 1195 GLU cc_start: 0.8761 (pm20) cc_final: 0.8345 (mp0) REVERT: B 872 ASN cc_start: 0.7633 (m-40) cc_final: 0.7418 (m-40) REVERT: B 900 MET cc_start: 0.8782 (mtp) cc_final: 0.8538 (mtp) REVERT: B 1149 MET cc_start: 0.8644 (mpp) cc_final: 0.8308 (mpp) REVERT: B 1154 LEU cc_start: 0.8894 (mm) cc_final: 0.8251 (tp) REVERT: B 1195 GLU cc_start: 0.8581 (pm20) cc_final: 0.8246 (mp0) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 0.2161 time to fit residues: 35.4690 Evaluate side-chains 94 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 591 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 0.0270 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 0.0170 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13420 Z= 0.196 Angle : 0.512 7.579 18342 Z= 0.274 Chirality : 0.037 0.171 2008 Planarity : 0.003 0.032 2148 Dihedral : 16.459 68.707 2306 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.70 % Allowed : 11.72 % Favored : 87.58 % 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: 0.76 (0.24), residues: 1452 helix: 1.79 (0.20), residues: 672 sheet: -1.14 (0.42), residues: 172 loop : -0.40 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.002 0.000 HIS A 579 PHE 0.022 0.002 PHE B 674 TYR 0.017 0.001 TYR A 978 ARG 0.002 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 2.151 Fit side-chains REVERT: A 571 LYS cc_start: 0.8576 (mttm) cc_final: 0.8160 (mttm) REVERT: A 1051 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6232 (m-10) REVERT: A 1154 LEU cc_start: 0.8875 (mm) cc_final: 0.8229 (tp) REVERT: A 1186 LYS cc_start: 0.9684 (mttt) cc_final: 0.9264 (mmmt) REVERT: A 1195 GLU cc_start: 0.8778 (pm20) cc_final: 0.8349 (mp0) REVERT: B 872 ASN cc_start: 0.7632 (m-40) cc_final: 0.7397 (m-40) REVERT: B 900 MET cc_start: 0.8728 (mtp) cc_final: 0.8487 (mtp) REVERT: B 1051 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.5817 (m-10) REVERT: B 1154 LEU cc_start: 0.8959 (mm) cc_final: 0.8263 (tp) REVERT: B 1195 GLU cc_start: 0.8552 (pm20) cc_final: 0.8228 (mp0) outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.2360 time to fit residues: 37.4150 Evaluate side-chains 95 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13420 Z= 0.201 Angle : 0.512 7.020 18342 Z= 0.273 Chirality : 0.037 0.170 2008 Planarity : 0.003 0.030 2148 Dihedral : 16.518 70.174 2306 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.17 % Allowed : 12.50 % Favored : 86.33 % 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: 0.68 (0.24), residues: 1452 helix: 1.74 (0.20), residues: 674 sheet: -1.23 (0.41), residues: 176 loop : -0.44 (0.28), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 582 HIS 0.001 0.000 HIS B 569 PHE 0.022 0.002 PHE B 674 TYR 0.018 0.001 TYR A 978 ARG 0.003 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 571 LYS cc_start: 0.8543 (mttm) cc_final: 0.8340 (mttm) REVERT: A 775 MET cc_start: 0.7592 (ptm) cc_final: 0.7390 (ptm) REVERT: A 1027 MET cc_start: 0.7668 (ppp) cc_final: 0.7081 (ppp) REVERT: A 1051 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.6535 (m-10) REVERT: A 1154 LEU cc_start: 0.8894 (mm) cc_final: 0.8236 (tp) REVERT: A 1186 LYS cc_start: 0.9692 (mttt) cc_final: 0.9209 (mmtp) REVERT: A 1195 GLU cc_start: 0.8764 (pm20) cc_final: 0.8411 (mp0) REVERT: B 775 MET cc_start: 0.7390 (ptm) cc_final: 0.7108 (ptm) REVERT: B 872 ASN cc_start: 0.7625 (m-40) cc_final: 0.7388 (m-40) REVERT: B 900 MET cc_start: 0.8729 (mtp) cc_final: 0.8494 (mtp) REVERT: B 1051 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.5949 (m-10) REVERT: B 1149 MET cc_start: 0.8596 (mpp) cc_final: 0.8269 (mpp) REVERT: B 1195 GLU cc_start: 0.8657 (pm20) cc_final: 0.8341 (mp0) outliers start: 15 outliers final: 8 residues processed: 100 average time/residue: 0.2393 time to fit residues: 37.4800 Evaluate side-chains 100 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13420 Z= 0.350 Angle : 0.630 8.037 18342 Z= 0.332 Chirality : 0.041 0.201 2008 Planarity : 0.004 0.028 2148 Dihedral : 16.842 70.274 2306 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.09 % Allowed : 14.84 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1452 helix: 1.23 (0.20), residues: 668 sheet: -1.34 (0.41), residues: 174 loop : -0.75 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1185 HIS 0.003 0.001 HIS B 569 PHE 0.032 0.002 PHE A 674 TYR 0.014 0.002 TYR A 978 ARG 0.005 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.382 Fit side-chains REVERT: A 571 LYS cc_start: 0.8478 (mttm) cc_final: 0.8227 (mttm) REVERT: A 830 MET cc_start: 0.7712 (ppp) cc_final: 0.7465 (ppp) REVERT: A 1051 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.6952 (m-10) REVERT: A 1195 GLU cc_start: 0.8858 (pm20) cc_final: 0.8511 (mp0) REVERT: B 900 MET cc_start: 0.8726 (mtp) cc_final: 0.8477 (mtp) REVERT: B 1051 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: B 1061 MET cc_start: 0.8061 (tmm) cc_final: 0.7827 (tmm) REVERT: B 1195 GLU cc_start: 0.8782 (pm20) cc_final: 0.8414 (mp0) outliers start: 14 outliers final: 8 residues processed: 95 average time/residue: 0.2025 time to fit residues: 31.3062 Evaluate side-chains 94 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 89 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN A1072 GLN ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13420 Z= 0.191 Angle : 0.547 11.007 18342 Z= 0.284 Chirality : 0.038 0.168 2008 Planarity : 0.003 0.028 2148 Dihedral : 16.683 71.801 2306 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.02 % Allowed : 16.17 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1452 helix: 1.37 (0.21), residues: 680 sheet: -1.37 (0.41), residues: 176 loop : -0.48 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 582 HIS 0.002 0.000 HIS B 569 PHE 0.027 0.001 PHE A 674 TYR 0.013 0.001 TYR A 978 ARG 0.002 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: A 830 MET cc_start: 0.7633 (ppp) cc_final: 0.7365 (ppp) REVERT: A 1051 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6769 (m-10) REVERT: A 1154 LEU cc_start: 0.9038 (mm) cc_final: 0.8370 (tp) REVERT: A 1195 GLU cc_start: 0.8774 (pm20) cc_final: 0.8446 (mp0) REVERT: B 900 MET cc_start: 0.8744 (mtp) cc_final: 0.8521 (mtp) REVERT: B 1051 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.6395 (m-10) REVERT: B 1061 MET cc_start: 0.8049 (tmm) cc_final: 0.7840 (tmm) REVERT: B 1149 MET cc_start: 0.8601 (mpp) cc_final: 0.8301 (mpp) REVERT: B 1195 GLU cc_start: 0.8741 (pm20) cc_final: 0.8365 (mp0) outliers start: 13 outliers final: 11 residues processed: 102 average time/residue: 0.2180 time to fit residues: 35.5665 Evaluate side-chains 100 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13420 Z= 0.262 Angle : 0.584 10.837 18342 Z= 0.304 Chirality : 0.039 0.170 2008 Planarity : 0.003 0.028 2148 Dihedral : 16.735 71.179 2306 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.09 % Allowed : 17.50 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1452 helix: 1.17 (0.20), residues: 694 sheet: -1.36 (0.41), residues: 174 loop : -0.81 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.002 0.001 HIS B 569 PHE 0.031 0.002 PHE A 674 TYR 0.014 0.001 TYR B 928 ARG 0.003 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 1051 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.6859 (m-10) REVERT: A 1149 MET cc_start: 0.8916 (ptp) cc_final: 0.8435 (mpp) REVERT: A 1195 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: B 900 MET cc_start: 0.8744 (mtp) cc_final: 0.8520 (mtp) REVERT: B 1051 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6585 (m-10) REVERT: B 1061 MET cc_start: 0.8069 (tmm) cc_final: 0.7852 (tmm) REVERT: B 1149 MET cc_start: 0.8646 (mpp) cc_final: 0.8349 (mpp) REVERT: B 1154 LEU cc_start: 0.8878 (mm) cc_final: 0.8226 (tp) REVERT: B 1195 GLU cc_start: 0.8777 (pm20) cc_final: 0.8407 (mp0) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 0.2131 time to fit residues: 33.7322 Evaluate side-chains 101 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 121 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13420 Z= 0.195 Angle : 0.551 7.898 18342 Z= 0.286 Chirality : 0.038 0.161 2008 Planarity : 0.003 0.029 2148 Dihedral : 16.691 71.577 2306 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.33 % Allowed : 17.58 % Favored : 81.09 % 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: 0.14 (0.23), residues: 1452 helix: 1.24 (0.20), residues: 706 sheet: -1.36 (0.41), residues: 174 loop : -0.82 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 582 HIS 0.002 0.000 HIS B 579 PHE 0.028 0.002 PHE A 674 TYR 0.013 0.001 TYR B 928 ARG 0.002 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 830 MET cc_start: 0.7806 (ppp) cc_final: 0.7509 (ppp) REVERT: A 1051 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.6800 (m-10) REVERT: A 1149 MET cc_start: 0.8878 (ptp) cc_final: 0.8336 (mpp) REVERT: A 1154 LEU cc_start: 0.8962 (mm) cc_final: 0.8293 (tp) REVERT: A 1195 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: B 900 MET cc_start: 0.8743 (mtp) cc_final: 0.8528 (mtp) REVERT: B 1051 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6561 (m-10) REVERT: B 1149 MET cc_start: 0.8615 (mpp) cc_final: 0.8302 (mpp) REVERT: B 1154 LEU cc_start: 0.8892 (mm) cc_final: 0.8276 (tp) REVERT: B 1195 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8374 (mp0) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.2273 time to fit residues: 37.1850 Evaluate side-chains 105 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13420 Z= 0.182 Angle : 0.551 8.940 18342 Z= 0.284 Chirality : 0.038 0.161 2008 Planarity : 0.003 0.029 2148 Dihedral : 16.614 71.357 2306 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.48 % Allowed : 17.73 % Favored : 80.78 % 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: 0.51 (0.24), residues: 1452 helix: 1.51 (0.21), residues: 678 sheet: -1.24 (0.42), residues: 170 loop : -0.45 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 582 HIS 0.002 0.000 HIS B 780 PHE 0.025 0.001 PHE A 674 TYR 0.013 0.001 TYR B 928 ARG 0.002 0.000 ARG B 939 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 830 MET cc_start: 0.7810 (ppp) cc_final: 0.7516 (ppp) REVERT: A 1051 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6697 (m-10) REVERT: A 1154 LEU cc_start: 0.8931 (mm) cc_final: 0.8262 (tp) REVERT: A 1186 LYS cc_start: 0.9654 (mttt) cc_final: 0.9262 (mmmt) REVERT: A 1195 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: B 900 MET cc_start: 0.8735 (mtp) cc_final: 0.8522 (mtp) REVERT: B 993 MET cc_start: 0.7374 (pmm) cc_final: 0.7167 (pmm) REVERT: B 1051 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.6395 (m-10) REVERT: B 1149 MET cc_start: 0.8598 (mpp) cc_final: 0.8290 (mpp) REVERT: B 1154 LEU cc_start: 0.8818 (mm) cc_final: 0.8237 (tp) REVERT: B 1195 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8355 (mp0) outliers start: 19 outliers final: 9 residues processed: 106 average time/residue: 0.2216 time to fit residues: 36.6998 Evaluate side-chains 104 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** A1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.060693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049614 restraints weight = 59006.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.051233 restraints weight = 30743.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052380 restraints weight = 19553.328| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13420 Z= 0.319 Angle : 0.634 10.032 18342 Z= 0.330 Chirality : 0.040 0.167 2008 Planarity : 0.004 0.029 2148 Dihedral : 16.830 71.819 2306 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.17 % Allowed : 17.73 % Favored : 81.09 % 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 (0.23), residues: 1452 helix: 1.08 (0.20), residues: 694 sheet: -1.42 (0.41), residues: 174 loop : -0.82 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.003 0.001 HIS B 569 PHE 0.033 0.002 PHE A 674 TYR 0.011 0.001 TYR B 543 ARG 0.005 0.000 ARG A 682 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2026.99 seconds wall clock time: 38 minutes 49.17 seconds (2329.17 seconds total)