Starting phenix.real_space_refine on Thu Feb 15 21:36:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/02_2024/6zy5_11550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/02_2024/6zy5_11550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/02_2024/6zy5_11550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/02_2024/6zy5_11550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/02_2024/6zy5_11550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/02_2024/6zy5_11550_updated.pdb" } resolution = 3.6 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= 0.005 sd= 0.097 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: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 52 5.16 5 C 8418 2.51 5 N 2312 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 870": "NH1" <-> "NH2" Residue "B ARG 1148": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 1148": "NH1" <-> "NH2" 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: 13504 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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: 8.29, per 1000 atoms: 0.61 Number of scatterers: 13504 At special positions: 0 Unit cell: (103.983, 116.039, 119.053, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 56 15.00 O 2666 8.00 N 2312 7.00 C 8418 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: 5.57 Conformation dependent library (CDL) restraints added in 2.3 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 45.4% alpha, 5.5% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 5.98 Creating SS restraints... Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.578A pdb=" N LEU B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 544 through 560 removed outlier: 4.014A pdb=" N ASN B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 removed outlier: 3.576A pdb=" N ARG B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 643 through 653 Processing helix chain 'B' and resid 658 through 678 removed outlier: 3.595A pdb=" N PHE B 668 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 701 Processing helix chain 'B' and resid 703 through 713 Processing helix chain 'B' and resid 724 through 735 removed outlier: 3.547A pdb=" N VAL B 729 " --> pdb=" O GLY B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 754 Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.775A pdb=" N MET B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 817 No H-bonds generated for 'chain 'B' and resid 814 through 817' Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 847 through 851 removed outlier: 4.216A pdb=" N ASN B 851 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 881 removed outlier: 3.726A pdb=" N ASP B 881 " --> pdb=" O ARG B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 944 removed outlier: 4.589A pdb=" N GLU B 941 " --> pdb=" O GLU B 937 " (cutoff:3.500A) Proline residue: B 942 - end of helix Processing helix chain 'B' and resid 974 through 983 Processing helix chain 'B' and resid 985 through 988 No H-bonds generated for 'chain 'B' and resid 985 through 988' Processing helix chain 'B' and resid 1015 through 1060 removed outlier: 3.884A pdb=" N TYR B1029 " --> pdb=" O LEU B1025 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B1030 " --> pdb=" O ARG B1026 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY B1039 " --> pdb=" O GLU B1035 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B1040 " --> pdb=" O TRP B1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY B1042 " --> pdb=" O LEU B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1080 removed outlier: 3.686A pdb=" N ARG B1080 " --> pdb=" O VAL B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1095 Processing helix chain 'B' and resid 1133 through 1136 Processing helix chain 'B' and resid 1138 through 1160 removed outlier: 3.998A pdb=" N GLU B1143 " --> pdb=" O GLU B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1192 removed outlier: 3.696A pdb=" N ALA B1180 " --> pdb=" O GLU B1176 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B1189 " --> pdb=" O GLU B1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.578A pdb=" N LEU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 544 through 560 removed outlier: 4.013A pdb=" N ASN A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.576A pdb=" N ARG A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 658 through 678 removed outlier: 3.596A pdb=" N PHE A 668 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 713 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.547A pdb=" N VAL A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 754 Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.773A pdb=" N MET A 766 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 767 " --> pdb=" O SER A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 817 No H-bonds generated for 'chain 'A' and resid 814 through 817' Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 847 through 851 removed outlier: 4.216A pdb=" N ASN A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 881 removed outlier: 3.726A pdb=" N ASP A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 944 removed outlier: 4.587A pdb=" N GLU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix Processing helix chain 'A' and resid 974 through 983 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 1015 through 1060 removed outlier: 3.885A pdb=" N TYR A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1080 removed outlier: 3.686A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 Processing helix chain 'A' and resid 1133 through 1136 Processing helix chain 'A' and resid 1138 through 1160 removed outlier: 3.998A pdb=" N GLU A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1192 removed outlier: 3.696A pdb=" N ALA A1180 " --> pdb=" O GLU A1176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A1189 " --> pdb=" O GLU A1185 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 483 through 485 removed outlier: 8.576A pdb=" N PHE B 484 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 458 " --> pdb=" O PHE B 484 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS B 535 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU B 459 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET B 537 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 853 through 856 Processing sheet with id= C, first strand: chain 'B' and resid 898 through 901 Processing sheet with id= D, first strand: chain 'B' and resid 956 through 959 removed outlier: 6.340A pdb=" N GLU B 912 " --> pdb=" O SER B 924 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 483 through 485 removed outlier: 8.574A pdb=" N PHE A 484 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 458 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS A 535 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 459 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET A 537 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 853 through 856 Processing sheet with id= G, first strand: chain 'A' and resid 898 through 901 Processing sheet with id= H, first strand: chain 'A' and resid 956 through 959 removed outlier: 6.342A pdb=" N GLU A 912 " --> pdb=" O SER A 924 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2331 1.32 - 1.44: 3733 1.44 - 1.57: 7640 1.57 - 1.69: 112 1.69 - 1.82: 92 Bond restraints: 13908 Sorted by residual: bond pdb=" C LYS B1071 " pdb=" O LYS B1071 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.16e-02 7.43e+03 1.89e+01 bond pdb=" C LYS A1071 " pdb=" O LYS A1071 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.16e-02 7.43e+03 1.88e+01 bond pdb=" C ILE B1074 " pdb=" O ILE B1074 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.87e+01 bond pdb=" C ILE A1074 " pdb=" O ILE A1074 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.17e-02 7.31e+03 1.80e+01 bond pdb=" CA SER B 861 " pdb=" CB SER B 861 " ideal model delta sigma weight residual 1.534 1.469 0.066 1.77e-02 3.19e+03 1.38e+01 ... (remaining 13903 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.12: 652 106.12 - 113.20: 7527 113.20 - 120.29: 6633 120.29 - 127.37: 4032 127.37 - 134.45: 186 Bond angle restraints: 19030 Sorted by residual: angle pdb=" CA SER A 861 " pdb=" C SER A 861 " pdb=" O SER A 861 " ideal model delta sigma weight residual 121.51 116.15 5.36 1.12e+00 7.97e-01 2.29e+01 angle pdb=" CA SER B 861 " pdb=" C SER B 861 " pdb=" O SER B 861 " ideal model delta sigma weight residual 121.51 116.29 5.22 1.12e+00 7.97e-01 2.17e+01 angle pdb=" N LEU B1166 " pdb=" CA LEU B1166 " pdb=" C LEU B1166 " ideal model delta sigma weight residual 112.23 106.62 5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N LEU A1166 " pdb=" CA LEU A1166 " pdb=" C LEU A1166 " ideal model delta sigma weight residual 112.23 106.63 5.60 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N ILE B1065 " pdb=" CA ILE B1065 " pdb=" C ILE B1065 " ideal model delta sigma weight residual 112.43 108.58 3.85 9.20e-01 1.18e+00 1.75e+01 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 8028 28.12 - 56.24: 307 56.24 - 84.36: 45 84.36 - 112.48: 2 112.48 - 140.60: 2 Dihedral angle restraints: 8384 sinusoidal: 3964 harmonic: 4420 Sorted by residual: dihedral pdb=" C4' DC E 9 " pdb=" C3' DC E 9 " pdb=" O3' DC E 9 " pdb=" P DG E 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.40 140.60 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DC C 9 " pdb=" C3' DC C 9 " pdb=" O3' DC C 9 " pdb=" P DG C 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.49 140.51 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C TYR A 830 " pdb=" N TYR A 830 " pdb=" CA TYR A 830 " pdb=" CB TYR A 830 " ideal model delta harmonic sigma weight residual -122.60 -131.77 9.17 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 8381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1060 0.058 - 0.115: 634 0.115 - 0.173: 308 0.173 - 0.230: 82 0.230 - 0.288: 10 Chirality restraints: 2094 Sorted by residual: chirality pdb=" CA ILE B 915 " pdb=" N ILE B 915 " pdb=" C ILE B 915 " pdb=" CB ILE B 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA ILE A 915 " pdb=" N ILE A 915 " pdb=" C ILE A 915 " pdb=" CB ILE A 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE A 864 " pdb=" N ILE A 864 " pdb=" C ILE A 864 " pdb=" CB ILE A 864 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2091 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 824 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C HIS B 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS B 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 824 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C HIS A 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS A 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 936 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C LYS A 936 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS A 936 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 937 " -0.014 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1629 2.76 - 3.29: 13232 3.29 - 3.83: 20997 3.83 - 4.36: 25401 4.36 - 4.90: 41092 Nonbonded interactions: 102351 Sorted by model distance: nonbonded pdb=" O6 DG E 13 " pdb=" O13 EVP F 101 " model vdw 2.219 2.440 nonbonded pdb=" OE1 GLN B1094 " pdb=" NE2 GLN B1095 " model vdw 2.348 2.520 nonbonded pdb=" OE1 GLN A1094 " pdb=" NE2 GLN A1095 " model vdw 2.348 2.520 nonbonded pdb=" NH2 ARG A 870 " pdb=" OE1 GLU A1182 " model vdw 2.348 2.520 nonbonded pdb=" NH2 ARG B 870 " pdb=" OE1 GLU B1182 " model vdw 2.349 2.520 ... (remaining 102346 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' selection = chain 'E' } ncs_group { reference = chain 'D' 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 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: 0.010 Normalize map: mean=0, sd=1: 0.690 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: 2.930 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 42.050 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.011 0.066 13908 Z= 0.697 Angle : 1.165 7.628 19030 Z= 0.866 Chirality : 0.086 0.288 2094 Planarity : 0.007 0.039 2220 Dihedral : 13.851 140.604 5536 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.15 % Allowed : 0.90 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1512 helix: 1.50 (0.19), residues: 678 sheet: -1.37 (0.37), residues: 198 loop : -2.35 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B1090 HIS 0.004 0.001 HIS B 986 PHE 0.010 0.002 PHE A 818 TYR 0.022 0.002 TYR B 830 ARG 0.006 0.001 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 471 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 498 HIS cc_start: 0.5973 (t70) cc_final: 0.5327 (t-170) REVERT: B 530 THR cc_start: 0.8648 (m) cc_final: 0.8420 (p) REVERT: B 657 GLN cc_start: 0.7537 (mt0) cc_final: 0.7252 (mm-40) REVERT: B 714 SER cc_start: 0.8491 (m) cc_final: 0.8194 (t) REVERT: B 766 MET cc_start: 0.7498 (ttm) cc_final: 0.7254 (ttm) REVERT: B 774 ASN cc_start: 0.8606 (p0) cc_final: 0.8332 (p0) REVERT: B 805 TYR cc_start: 0.7935 (m-10) cc_final: 0.7621 (m-10) REVERT: B 856 ILE cc_start: 0.9163 (mt) cc_final: 0.8945 (mt) REVERT: B 916 LEU cc_start: 0.8902 (mt) cc_final: 0.7892 (tt) REVERT: B 1053 ARG cc_start: 0.6470 (mmm160) cc_final: 0.6143 (ttp80) REVERT: A 498 HIS cc_start: 0.5993 (t70) cc_final: 0.5645 (t-170) REVERT: A 529 LYS cc_start: 0.7905 (tttt) cc_final: 0.7598 (mtpt) REVERT: A 530 THR cc_start: 0.8655 (m) cc_final: 0.8421 (p) REVERT: A 657 GLN cc_start: 0.7518 (mt0) cc_final: 0.7242 (mm-40) REVERT: A 714 SER cc_start: 0.8492 (m) cc_final: 0.8146 (t) REVERT: A 766 MET cc_start: 0.7446 (ttm) cc_final: 0.7180 (ttm) REVERT: A 774 ASN cc_start: 0.8616 (p0) cc_final: 0.8343 (p0) REVERT: A 805 TYR cc_start: 0.7925 (m-10) cc_final: 0.7614 (m-10) REVERT: A 856 ILE cc_start: 0.9244 (mt) cc_final: 0.9040 (mt) REVERT: A 916 LEU cc_start: 0.8896 (mt) cc_final: 0.7880 (tt) REVERT: A 1053 ARG cc_start: 0.6472 (mmm160) cc_final: 0.6138 (ttp80) outliers start: 2 outliers final: 2 residues processed: 473 average time/residue: 0.3276 time to fit residues: 208.3911 Evaluate side-chains 223 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain A residue 1078 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 559 HIS B 634 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 ASN B 875 ASN A 559 HIS A 634 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN A 875 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13908 Z= 0.229 Angle : 0.542 5.011 19030 Z= 0.286 Chirality : 0.040 0.190 2094 Planarity : 0.004 0.037 2220 Dihedral : 17.746 137.197 2424 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.56 % Allowed : 11.22 % Favored : 86.22 % 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: -0.21 (0.22), residues: 1512 helix: 1.95 (0.20), residues: 672 sheet: -1.51 (0.36), residues: 216 loop : -2.06 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 664 HIS 0.005 0.001 HIS B 605 PHE 0.014 0.001 PHE A 807 TYR 0.016 0.001 TYR A 957 ARG 0.007 0.001 ARG B1146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 THR cc_start: 0.8752 (m) cc_final: 0.8476 (p) REVERT: B 657 GLN cc_start: 0.7579 (mt0) cc_final: 0.7268 (mm-40) REVERT: B 737 ASN cc_start: 0.8058 (t0) cc_final: 0.7772 (t0) REVERT: B 774 ASN cc_start: 0.8704 (p0) cc_final: 0.8386 (p0) REVERT: B 778 SER cc_start: 0.8737 (t) cc_final: 0.8472 (t) REVERT: B 805 TYR cc_start: 0.8111 (m-10) cc_final: 0.7752 (m-80) REVERT: B 1134 TRP cc_start: 0.7600 (m100) cc_final: 0.7285 (m100) REVERT: B 1153 GLN cc_start: 0.6391 (mm-40) cc_final: 0.5953 (mt0) REVERT: A 530 THR cc_start: 0.8762 (m) cc_final: 0.8472 (p) REVERT: A 657 GLN cc_start: 0.7542 (mt0) cc_final: 0.7258 (mm-40) REVERT: A 737 ASN cc_start: 0.8073 (t0) cc_final: 0.7791 (t0) REVERT: A 774 ASN cc_start: 0.8721 (p0) cc_final: 0.8410 (p0) REVERT: A 778 SER cc_start: 0.8743 (t) cc_final: 0.8469 (t) REVERT: A 805 TYR cc_start: 0.8107 (m-10) cc_final: 0.7779 (m-80) REVERT: A 1134 TRP cc_start: 0.7604 (m100) cc_final: 0.7286 (m100) REVERT: A 1153 GLN cc_start: 0.6401 (mm-40) cc_final: 0.5965 (mt0) outliers start: 34 outliers final: 20 residues processed: 223 average time/residue: 0.2549 time to fit residues: 84.5841 Evaluate side-chains 167 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 821 LYS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1145 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1145 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 ASN B 558 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 ASN A 508 ASN A 558 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13908 Z= 0.197 Angle : 0.498 6.258 19030 Z= 0.265 Chirality : 0.039 0.149 2094 Planarity : 0.004 0.031 2220 Dihedral : 17.691 136.210 2420 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.86 % Allowed : 13.03 % Favored : 84.11 % 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: 0.15 (0.23), residues: 1512 helix: 2.17 (0.20), residues: 676 sheet: -0.40 (0.50), residues: 134 loop : -2.02 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1090 HIS 0.007 0.001 HIS B 605 PHE 0.010 0.001 PHE A 706 TYR 0.016 0.001 TYR B1029 ARG 0.004 0.000 ARG B 835 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 493 VAL cc_start: 0.9465 (m) cc_final: 0.9212 (p) REVERT: B 530 THR cc_start: 0.8734 (m) cc_final: 0.8443 (p) REVERT: B 657 GLN cc_start: 0.7618 (mt0) cc_final: 0.7340 (mm110) REVERT: B 751 VAL cc_start: 0.8946 (t) cc_final: 0.8702 (t) REVERT: B 755 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8226 (t) REVERT: B 778 SER cc_start: 0.8683 (t) cc_final: 0.8415 (t) REVERT: B 917 ASN cc_start: 0.7667 (m-40) cc_final: 0.6672 (p0) REVERT: B 1134 TRP cc_start: 0.7566 (m100) cc_final: 0.7364 (m100) REVERT: B 1153 GLN cc_start: 0.6345 (mm-40) cc_final: 0.5943 (mt0) REVERT: A 493 VAL cc_start: 0.9497 (m) cc_final: 0.9283 (p) REVERT: A 529 LYS cc_start: 0.8180 (mttp) cc_final: 0.7856 (mtpt) REVERT: A 530 THR cc_start: 0.8825 (m) cc_final: 0.8526 (p) REVERT: A 657 GLN cc_start: 0.7578 (mt0) cc_final: 0.7321 (mm110) REVERT: A 751 VAL cc_start: 0.8933 (t) cc_final: 0.8690 (t) REVERT: A 755 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8228 (t) REVERT: A 778 SER cc_start: 0.8690 (t) cc_final: 0.8421 (t) REVERT: A 917 ASN cc_start: 0.7665 (m-40) cc_final: 0.6661 (p0) REVERT: A 1153 GLN cc_start: 0.6357 (mm-40) cc_final: 0.5967 (mt0) outliers start: 38 outliers final: 15 residues processed: 202 average time/residue: 0.2464 time to fit residues: 73.7089 Evaluate side-chains 157 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 ASN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN B 833 ASN A 508 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN A 833 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13908 Z= 0.261 Angle : 0.561 5.480 19030 Z= 0.295 Chirality : 0.041 0.155 2094 Planarity : 0.004 0.032 2220 Dihedral : 17.928 134.785 2420 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.79 % Allowed : 14.98 % Favored : 82.23 % 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: -0.00 (0.22), residues: 1512 helix: 1.89 (0.20), residues: 700 sheet: -0.69 (0.48), residues: 136 loop : -2.01 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1090 HIS 0.006 0.001 HIS B 605 PHE 0.013 0.002 PHE A 706 TYR 0.012 0.002 TYR A 957 ARG 0.005 0.001 ARG B 713 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: B 530 THR cc_start: 0.8838 (m) cc_final: 0.8495 (p) REVERT: B 751 VAL cc_start: 0.8997 (t) cc_final: 0.8639 (t) REVERT: B 755 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8322 (t) REVERT: B 778 SER cc_start: 0.8682 (t) cc_final: 0.8419 (t) REVERT: B 1030 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7447 (m-10) REVERT: B 1153 GLN cc_start: 0.6495 (mm-40) cc_final: 0.6082 (mt0) REVERT: A 530 THR cc_start: 0.8884 (m) cc_final: 0.8570 (p) REVERT: A 751 VAL cc_start: 0.8985 (t) cc_final: 0.8628 (t) REVERT: A 755 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8308 (t) REVERT: A 778 SER cc_start: 0.8691 (t) cc_final: 0.8420 (t) REVERT: A 1030 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7453 (m-10) REVERT: A 1134 TRP cc_start: 0.7487 (m100) cc_final: 0.6931 (m100) REVERT: A 1153 GLN cc_start: 0.6510 (mm-40) cc_final: 0.6105 (mt0) outliers start: 37 outliers final: 20 residues processed: 184 average time/residue: 0.2099 time to fit residues: 60.2725 Evaluate side-chains 154 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1177 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0050 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN B 795 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN A 795 HIS A 833 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13908 Z= 0.210 Angle : 0.508 5.759 19030 Z= 0.269 Chirality : 0.039 0.155 2094 Planarity : 0.003 0.033 2220 Dihedral : 17.854 136.142 2420 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.18 % Allowed : 16.04 % Favored : 81.78 % 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: 0.25 (0.22), residues: 1512 helix: 2.10 (0.20), residues: 686 sheet: -0.60 (0.44), residues: 162 loop : -1.83 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 664 HIS 0.005 0.001 HIS B 605 PHE 0.012 0.001 PHE A 706 TYR 0.010 0.001 TYR A 640 ARG 0.003 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: B 506 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: B 530 THR cc_start: 0.8719 (m) cc_final: 0.8404 (p) REVERT: B 751 VAL cc_start: 0.9003 (t) cc_final: 0.8637 (t) REVERT: B 755 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8258 (t) REVERT: B 762 MET cc_start: 0.8190 (tmm) cc_final: 0.7522 (tmm) REVERT: B 778 SER cc_start: 0.8809 (t) cc_final: 0.8524 (t) REVERT: B 1030 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7176 (m-10) REVERT: B 1134 TRP cc_start: 0.7594 (m100) cc_final: 0.6982 (m100) REVERT: B 1153 GLN cc_start: 0.6469 (mm-40) cc_final: 0.6043 (mt0) REVERT: A 506 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: A 530 THR cc_start: 0.8802 (m) cc_final: 0.8479 (p) REVERT: A 669 MET cc_start: 0.8658 (mtp) cc_final: 0.8217 (mtp) REVERT: A 751 VAL cc_start: 0.8992 (t) cc_final: 0.8624 (t) REVERT: A 755 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8240 (t) REVERT: A 762 MET cc_start: 0.8161 (tmm) cc_final: 0.7480 (tmm) REVERT: A 778 SER cc_start: 0.8810 (t) cc_final: 0.8518 (t) REVERT: A 1030 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7181 (m-10) REVERT: A 1134 TRP cc_start: 0.7578 (m100) cc_final: 0.6999 (m100) REVERT: A 1153 GLN cc_start: 0.6484 (mm-40) cc_final: 0.6066 (mt0) outliers start: 29 outliers final: 21 residues processed: 169 average time/residue: 0.2280 time to fit residues: 59.2136 Evaluate side-chains 161 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1177 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 chunk 150 optimal weight: 0.0030 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13908 Z= 0.139 Angle : 0.461 5.817 19030 Z= 0.247 Chirality : 0.037 0.147 2094 Planarity : 0.003 0.030 2220 Dihedral : 17.717 136.962 2420 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.96 % Allowed : 16.27 % Favored : 81.78 % 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: 0.41 (0.22), residues: 1512 helix: 2.27 (0.20), residues: 674 sheet: -0.52 (0.44), residues: 162 loop : -1.72 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 664 HIS 0.005 0.001 HIS B 605 PHE 0.022 0.001 PHE A 807 TYR 0.008 0.001 TYR A 957 ARG 0.002 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: B 530 THR cc_start: 0.8664 (m) cc_final: 0.8353 (p) REVERT: B 669 MET cc_start: 0.8705 (mtp) cc_final: 0.8333 (mtp) REVERT: B 751 VAL cc_start: 0.8997 (t) cc_final: 0.8729 (t) REVERT: B 762 MET cc_start: 0.8128 (tmm) cc_final: 0.7514 (tmm) REVERT: B 778 SER cc_start: 0.8789 (t) cc_final: 0.8508 (t) REVERT: B 1033 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6297 (tpp80) REVERT: B 1134 TRP cc_start: 0.7532 (m100) cc_final: 0.6870 (m100) REVERT: B 1153 GLN cc_start: 0.6569 (mm-40) cc_final: 0.6134 (mt0) REVERT: A 530 THR cc_start: 0.8735 (m) cc_final: 0.8411 (p) REVERT: A 669 MET cc_start: 0.8730 (mtp) cc_final: 0.8316 (mtp) REVERT: A 751 VAL cc_start: 0.8983 (t) cc_final: 0.8719 (t) REVERT: A 762 MET cc_start: 0.8105 (tmm) cc_final: 0.7500 (tmm) REVERT: A 778 SER cc_start: 0.8797 (t) cc_final: 0.8506 (t) REVERT: A 1033 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6254 (tpp80) REVERT: A 1134 TRP cc_start: 0.7451 (m100) cc_final: 0.6985 (m100) REVERT: A 1153 GLN cc_start: 0.6580 (mm-40) cc_final: 0.6153 (mt0) outliers start: 26 outliers final: 20 residues processed: 175 average time/residue: 0.2262 time to fit residues: 60.8599 Evaluate side-chains 157 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1177 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13908 Z= 0.195 Angle : 0.492 6.509 19030 Z= 0.263 Chirality : 0.038 0.148 2094 Planarity : 0.004 0.030 2220 Dihedral : 17.780 137.266 2420 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.56 % Allowed : 16.72 % Favored : 80.72 % 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: 0.41 (0.23), residues: 1512 helix: 2.27 (0.21), residues: 674 sheet: -0.51 (0.45), residues: 162 loop : -1.71 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 664 HIS 0.005 0.001 HIS B 605 PHE 0.010 0.001 PHE A 706 TYR 0.009 0.001 TYR A 640 ARG 0.004 0.000 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.628 Fit side-chains revert: symmetry clash REVERT: B 506 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6612 (pm20) REVERT: B 530 THR cc_start: 0.8755 (m) cc_final: 0.8422 (p) REVERT: B 737 ASN cc_start: 0.8112 (t0) cc_final: 0.7761 (t0) REVERT: B 751 VAL cc_start: 0.9013 (t) cc_final: 0.8742 (t) REVERT: B 755 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8184 (t) REVERT: B 762 MET cc_start: 0.8225 (tmm) cc_final: 0.7571 (tmm) REVERT: B 778 SER cc_start: 0.8784 (t) cc_final: 0.8507 (t) REVERT: B 1033 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.6325 (tpp80) REVERT: B 1134 TRP cc_start: 0.7489 (m100) cc_final: 0.6939 (m100) REVERT: B 1153 GLN cc_start: 0.6622 (mm-40) cc_final: 0.6177 (mt0) REVERT: A 506 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6594 (pm20) REVERT: A 530 THR cc_start: 0.8787 (m) cc_final: 0.8453 (p) REVERT: A 751 VAL cc_start: 0.8990 (t) cc_final: 0.8700 (t) REVERT: A 762 MET cc_start: 0.8207 (tmm) cc_final: 0.7558 (tmm) REVERT: A 778 SER cc_start: 0.8790 (t) cc_final: 0.8508 (t) REVERT: A 1033 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6328 (tpp80) REVERT: A 1134 TRP cc_start: 0.7517 (m100) cc_final: 0.7030 (m100) REVERT: A 1153 GLN cc_start: 0.6632 (mm-40) cc_final: 0.6199 (mt0) outliers start: 34 outliers final: 25 residues processed: 164 average time/residue: 0.2294 time to fit residues: 57.2611 Evaluate side-chains 156 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1177 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13908 Z= 0.202 Angle : 0.501 7.522 19030 Z= 0.266 Chirality : 0.038 0.149 2094 Planarity : 0.004 0.031 2220 Dihedral : 17.851 136.926 2420 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.56 % Allowed : 16.49 % Favored : 80.95 % 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: 0.40 (0.23), residues: 1512 helix: 2.25 (0.21), residues: 684 sheet: -0.58 (0.44), residues: 162 loop : -1.75 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 664 HIS 0.004 0.001 HIS B 605 PHE 0.010 0.001 PHE A 706 TYR 0.010 0.001 TYR A1030 ARG 0.003 0.000 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: B 506 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6690 (pm20) REVERT: B 530 THR cc_start: 0.8729 (m) cc_final: 0.8396 (p) REVERT: B 751 VAL cc_start: 0.8998 (t) cc_final: 0.8725 (t) REVERT: B 755 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8308 (t) REVERT: B 762 MET cc_start: 0.8229 (tmm) cc_final: 0.7540 (tmm) REVERT: B 778 SER cc_start: 0.8782 (t) cc_final: 0.8502 (t) REVERT: B 1033 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.6335 (tpp80) REVERT: B 1134 TRP cc_start: 0.7452 (m100) cc_final: 0.6932 (m100) REVERT: B 1153 GLN cc_start: 0.6533 (mm-40) cc_final: 0.6146 (mt0) REVERT: A 506 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: A 530 THR cc_start: 0.8769 (m) cc_final: 0.8432 (p) REVERT: A 669 MET cc_start: 0.8738 (mtp) cc_final: 0.8400 (mtp) REVERT: A 751 VAL cc_start: 0.8991 (t) cc_final: 0.8698 (t) REVERT: A 755 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8279 (t) REVERT: A 762 MET cc_start: 0.8213 (tmm) cc_final: 0.7556 (tmm) REVERT: A 778 SER cc_start: 0.8789 (t) cc_final: 0.8502 (t) REVERT: A 1033 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6340 (tpp80) REVERT: A 1134 TRP cc_start: 0.7479 (m100) cc_final: 0.7039 (m100) REVERT: A 1153 GLN cc_start: 0.6545 (mm-40) cc_final: 0.6168 (mt0) outliers start: 34 outliers final: 24 residues processed: 159 average time/residue: 0.2096 time to fit residues: 52.4780 Evaluate side-chains 158 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1177 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0670 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13908 Z= 0.183 Angle : 0.493 8.308 19030 Z= 0.263 Chirality : 0.038 0.148 2094 Planarity : 0.004 0.033 2220 Dihedral : 17.879 137.812 2420 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.71 % Allowed : 17.02 % Favored : 80.27 % 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: 0.40 (0.23), residues: 1512 helix: 2.29 (0.21), residues: 672 sheet: -0.64 (0.44), residues: 162 loop : -1.70 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 664 HIS 0.004 0.001 HIS B 605 PHE 0.009 0.001 PHE A 706 TYR 0.008 0.001 TYR B 640 ARG 0.003 0.000 ARG A 736 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: B 506 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6776 (mm-30) REVERT: B 530 THR cc_start: 0.8715 (m) cc_final: 0.8384 (p) REVERT: B 737 ASN cc_start: 0.8193 (t0) cc_final: 0.7929 (t0) REVERT: B 751 VAL cc_start: 0.9004 (t) cc_final: 0.8733 (t) REVERT: B 762 MET cc_start: 0.8217 (tmm) cc_final: 0.7525 (tmm) REVERT: B 778 SER cc_start: 0.8771 (t) cc_final: 0.8489 (t) REVERT: B 831 ASP cc_start: 0.7665 (t0) cc_final: 0.7304 (t0) REVERT: B 1033 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6339 (tpp80) REVERT: B 1134 TRP cc_start: 0.7443 (m100) cc_final: 0.6931 (m100) REVERT: B 1153 GLN cc_start: 0.6533 (mm-40) cc_final: 0.6145 (mt0) REVERT: A 506 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6797 (mm-30) REVERT: A 530 THR cc_start: 0.8764 (m) cc_final: 0.8426 (p) REVERT: A 669 MET cc_start: 0.8728 (mtp) cc_final: 0.8355 (mtp) REVERT: A 751 VAL cc_start: 0.9076 (t) cc_final: 0.8804 (t) REVERT: A 755 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8161 (t) REVERT: A 762 MET cc_start: 0.8208 (tmm) cc_final: 0.7535 (tmm) REVERT: A 778 SER cc_start: 0.8776 (t) cc_final: 0.8474 (t) REVERT: A 831 ASP cc_start: 0.7571 (t0) cc_final: 0.7212 (t0) REVERT: A 1033 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6343 (tpp80) REVERT: A 1134 TRP cc_start: 0.7327 (m100) cc_final: 0.6890 (m100) REVERT: A 1153 GLN cc_start: 0.6544 (mm-40) cc_final: 0.6166 (mt0) outliers start: 36 outliers final: 24 residues processed: 168 average time/residue: 0.2261 time to fit residues: 58.3540 Evaluate side-chains 163 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1177 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 674 GLN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13908 Z= 0.300 Angle : 0.577 8.276 19030 Z= 0.305 Chirality : 0.041 0.149 2094 Planarity : 0.004 0.034 2220 Dihedral : 18.130 136.674 2420 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.33 % Allowed : 17.47 % Favored : 80.20 % 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: 1512 helix: 1.90 (0.20), residues: 696 sheet: -0.82 (0.43), residues: 162 loop : -1.93 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 664 HIS 0.005 0.001 HIS B 605 PHE 0.028 0.002 PHE A 807 TYR 0.012 0.002 TYR A1030 ARG 0.003 0.000 ARG A 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: B 506 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6852 (mm-30) REVERT: B 530 THR cc_start: 0.8774 (m) cc_final: 0.8441 (p) REVERT: B 751 VAL cc_start: 0.9022 (t) cc_final: 0.8728 (t) REVERT: B 754 MET cc_start: 0.7660 (ttm) cc_final: 0.7454 (ttm) REVERT: B 762 MET cc_start: 0.8085 (tmm) cc_final: 0.7445 (tmm) REVERT: B 778 SER cc_start: 0.8839 (t) cc_final: 0.8561 (t) REVERT: B 831 ASP cc_start: 0.7514 (t0) cc_final: 0.7163 (t0) REVERT: B 1033 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6596 (tpp80) REVERT: B 1134 TRP cc_start: 0.7242 (m100) cc_final: 0.6756 (m100) REVERT: B 1153 GLN cc_start: 0.6460 (mm-40) cc_final: 0.6074 (mt0) REVERT: A 506 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6887 (mm-30) REVERT: A 530 THR cc_start: 0.8829 (m) cc_final: 0.8474 (p) REVERT: A 751 VAL cc_start: 0.9012 (t) cc_final: 0.8706 (t) REVERT: A 755 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8370 (t) REVERT: A 762 MET cc_start: 0.8086 (tmm) cc_final: 0.7462 (tmm) REVERT: A 778 SER cc_start: 0.8838 (t) cc_final: 0.8560 (t) REVERT: A 831 ASP cc_start: 0.7482 (t0) cc_final: 0.7145 (t0) REVERT: A 1033 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6743 (tpp80) REVERT: A 1134 TRP cc_start: 0.7288 (m100) cc_final: 0.6878 (m100) REVERT: A 1153 GLN cc_start: 0.6472 (mm-40) cc_final: 0.6096 (mt0) outliers start: 31 outliers final: 25 residues processed: 167 average time/residue: 0.2321 time to fit residues: 59.2617 Evaluate side-chains 159 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1177 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.5980 chunk 37 optimal weight: 0.0040 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110835 restraints weight = 23260.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114236 restraints weight = 12541.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116561 restraints weight = 8358.108| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13908 Z= 0.171 Angle : 0.505 8.335 19030 Z= 0.269 Chirality : 0.038 0.147 2094 Planarity : 0.004 0.032 2220 Dihedral : 18.051 137.276 2420 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.48 % Allowed : 17.92 % Favored : 79.59 % 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: 0.33 (0.23), residues: 1512 helix: 2.20 (0.21), residues: 684 sheet: -0.81 (0.43), residues: 162 loop : -1.73 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 664 HIS 0.004 0.001 HIS B 605 PHE 0.016 0.001 PHE A 807 TYR 0.011 0.001 TYR B 627 ARG 0.003 0.000 ARG B 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.61 seconds wall clock time: 46 minutes 36.36 seconds (2796.36 seconds total)