Starting phenix.real_space_refine on Fri Mar 15 16:55:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/03_2024/8j89_36064.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/03_2024/8j89_36064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/03_2024/8j89_36064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/03_2024/8j89_36064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/03_2024/8j89_36064.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/03_2024/8j89_36064.pdb" } resolution = 2.31 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7855 2.51 5 N 2097 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "B ASP 633": "OD1" <-> "OD2" Residue "B ASP 701": "OD1" <-> "OD2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "B GLU 835": "OE1" <-> "OE2" Residue "B TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 997": "OD1" <-> "OD2" Residue "B GLU 1050": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12222 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6105 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 30, 'TRANS': 720} Chain breaks: 1 Chain: "B" Number of atoms: 6117 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 751, 6105 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 30, 'TRANS': 720} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 751, 6105 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 30, 'TRANS': 720} Chain breaks: 1 bond proxies already assigned to first conformer: 6237 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR B1029 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B1029 " occ=0.50 Time building chain proxies: 9.31, per 1000 atoms: 0.76 Number of scatterers: 12222 At special positions: 0 Unit cell: (115.37, 103.75, 111.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2220 8.00 N 2097 7.00 C 7855 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: 4.64 Conformation dependent library (CDL) restraints added in 3.2 seconds 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 51.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.923A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.709A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.566A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 659 through 664 removed outlier: 3.707A pdb=" N GLU A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 removed outlier: 3.523A pdb=" N VAL A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.524A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 765 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.676A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 removed outlier: 3.505A pdb=" N MET A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 847' Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 882 through 891 removed outlier: 3.839A pdb=" N LYS A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.718A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1071 removed outlier: 3.735A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix Processing helix chain 'A' and resid 1075 through 1079 Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1118 removed outlier: 4.541A pdb=" N LEU A1118 " --> pdb=" O ASN A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1166 through 1187 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.927A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.757A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.607A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.596A pdb=" N HIS B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.517A pdb=" N GLU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 removed outlier: 3.518A pdb=" N VAL B 682 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 705 Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 754 through 765 Processing helix chain 'B' and resid 806 through 814 removed outlier: 3.669A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.545A pdb=" N MET B 846 " --> pdb=" O PRO B 842 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 842 through 847' Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 882 through 891 removed outlier: 3.860A pdb=" N LYS B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 982 through 991 removed outlier: 3.684A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 988 " --> pdb=" O ASN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1071 removed outlier: 3.721A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix Processing helix chain 'B' and resid 1075 through 1079 Processing helix chain 'B' and resid 1081 through 1092 Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1118 removed outlier: 4.554A pdb=" N LEU B1118 " --> pdb=" O ASN B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 Processing helix chain 'B' and resid 1134 through 1160 Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.279A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.514A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 926 removed outlier: 5.876A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 962 " --> pdb=" O LYS A 977 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.454A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 465 through 469 removed outlier: 6.170A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB2, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.487A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB4, first strand: chain 'B' and resid 922 through 926 removed outlier: 5.867A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 962 " --> pdb=" O LYS B 977 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1014 through 1016 566 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3943 1.35 - 1.46: 2969 1.46 - 1.58: 5526 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 12516 Sorted by residual: bond pdb=" CB ILE A 801 " pdb=" CG2 ILE A 801 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CB ILE B 801 " pdb=" CG2 ILE B 801 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CA THR A 895 " pdb=" CB THR A 895 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.61e-02 3.86e+03 6.12e-01 bond pdb=" CG LEU B 843 " pdb=" CD2 LEU B 843 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.84e-01 bond pdb=" CA THR B 895 " pdb=" CB THR B 895 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.61e-02 3.86e+03 5.71e-01 ... (remaining 12511 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.89: 341 106.89 - 113.66: 6836 113.66 - 120.42: 4752 120.42 - 127.19: 4842 127.19 - 133.95: 140 Bond angle restraints: 16911 Sorted by residual: angle pdb=" C GLU B1106 " pdb=" CA GLU B1106 " pdb=" CB GLU B1106 " ideal model delta sigma weight residual 116.54 110.48 6.06 1.15e+00 7.56e-01 2.78e+01 angle pdb=" N ILE A 845 " pdb=" CA ILE A 845 " pdb=" C ILE A 845 " ideal model delta sigma weight residual 112.96 109.42 3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" N ILE B 845 " pdb=" CA ILE B 845 " pdb=" C ILE B 845 " ideal model delta sigma weight residual 112.96 109.42 3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" CA GLU B1106 " pdb=" C GLU B1106 " pdb=" N PHE B1107 " ideal model delta sigma weight residual 119.52 117.00 2.52 7.90e-01 1.60e+00 1.02e+01 angle pdb=" C SER B 657 " pdb=" N GLU B 658 " pdb=" CA GLU B 658 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.73e+00 ... (remaining 16906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 6968 15.88 - 31.77: 441 31.77 - 47.65: 86 47.65 - 63.53: 13 63.53 - 79.41: 5 Dihedral angle restraints: 7513 sinusoidal: 3102 harmonic: 4411 Sorted by residual: dihedral pdb=" CA GLU B1073 " pdb=" C GLU B1073 " pdb=" N LEU B1074 " pdb=" CA LEU B1074 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO B 938 " pdb=" C PRO B 938 " pdb=" N LEU B 939 " pdb=" CA LEU B 939 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PRO A 938 " pdb=" C PRO A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 7510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1036 0.026 - 0.053: 467 0.053 - 0.079: 204 0.079 - 0.105: 82 0.105 - 0.132: 38 Chirality restraints: 1827 Sorted by residual: chirality pdb=" CA THR B 895 " pdb=" N THR B 895 " pdb=" C THR B 895 " pdb=" CB THR B 895 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA THR A 895 " pdb=" N THR A 895 " pdb=" C THR A 895 " pdb=" CB THR A 895 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL A 669 " pdb=" N VAL A 669 " pdb=" C VAL A 669 " pdb=" CB VAL A 669 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1824 not shown) Planarity restraints: 2157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 938 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 937 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 938 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 938 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 938 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 858 " 0.014 2.00e-02 2.50e+03 8.40e-03 1.41e+00 pdb=" CG TYR B 858 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 858 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 858 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 858 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 858 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 858 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 858 " 0.001 2.00e-02 2.50e+03 ... (remaining 2154 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1623 2.75 - 3.29: 11801 3.29 - 3.83: 20557 3.83 - 4.36: 26228 4.36 - 4.90: 43818 Nonbonded interactions: 104027 Sorted by model distance: nonbonded pdb=" OH TYR B1043 " pdb=" OE1 GLU B1173 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR B 923 " pdb=" OD2 ASP B 997 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.225 2.440 nonbonded pdb=" O ARG A 447 " pdb=" OG1 THR A 451 " model vdw 2.261 2.440 nonbonded pdb=" O PRO A1095 " pdb=" OH TYR A1124 " model vdw 2.274 2.440 ... (remaining 104022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 414 through 1028 or resid 1030 through 1192)) selection = (chain 'B' and (resid 414 through 1028 or resid 1030 through 1192)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 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: 15.560 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 37.760 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.003 0.037 12516 Z= 0.180 Angle : 0.458 6.059 16911 Z= 0.253 Chirality : 0.040 0.132 1827 Planarity : 0.003 0.046 2157 Dihedral : 10.981 79.413 4687 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % 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 (0.22), residues: 1497 helix: 1.05 (0.20), residues: 659 sheet: -0.49 (0.40), residues: 182 loop : -0.01 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.003 0.001 HIS B1192 PHE 0.008 0.001 PHE A 990 TYR 0.018 0.001 TYR B 858 ARG 0.002 0.000 ARG A 736 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.615 Fit side-chains REVERT: A 756 MET cc_start: 0.8055 (tpp) cc_final: 0.7755 (tpt) REVERT: A 970 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 970 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 1111 GLU cc_start: 0.8266 (pm20) cc_final: 0.8039 (pm20) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 1.7494 time to fit residues: 155.5782 Evaluate side-chains 60 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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: 3.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS A1092 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12516 Z= 0.193 Angle : 0.484 6.337 16911 Z= 0.260 Chirality : 0.041 0.147 1827 Planarity : 0.004 0.046 2157 Dihedral : 4.124 25.328 1671 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.68 % Allowed : 3.79 % Favored : 95.53 % 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: 0.86 (0.22), residues: 1497 helix: 1.49 (0.20), residues: 687 sheet: -0.39 (0.38), residues: 212 loop : -0.02 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 599 HIS 0.016 0.001 HIS A1078 PHE 0.011 0.001 PHE A 990 TYR 0.019 0.001 TYR B 858 ARG 0.007 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.827 Fit side-chains REVERT: A 929 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7794 (ptm-80) REVERT: A 970 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 977 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8342 (mmmt) REVERT: B 756 MET cc_start: 0.7878 (tpp) cc_final: 0.7563 (tpp) REVERT: B 970 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7816 (mt-10) outliers start: 9 outliers final: 2 residues processed: 74 average time/residue: 1.6050 time to fit residues: 128.2626 Evaluate side-chains 66 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 977 LYS Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12516 Z= 0.215 Angle : 0.476 5.820 16911 Z= 0.255 Chirality : 0.041 0.143 1827 Planarity : 0.004 0.048 2157 Dihedral : 4.157 25.848 1671 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.53 % Allowed : 5.76 % Favored : 93.71 % 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: 0.96 (0.22), residues: 1497 helix: 1.65 (0.20), residues: 687 sheet: -0.43 (0.38), residues: 212 loop : -0.03 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1189 HIS 0.003 0.001 HIS B1078 PHE 0.012 0.001 PHE A 990 TYR 0.020 0.001 TYR B 858 ARG 0.008 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.493 Fit side-chains REVERT: A 929 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7756 (ptm-80) REVERT: A 970 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 926 SER cc_start: 0.8865 (m) cc_final: 0.8438 (p) REVERT: B 929 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7426 (ptm-80) REVERT: B 970 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7854 (mt-10) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 1.6043 time to fit residues: 121.4667 Evaluate side-chains 68 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 HIS B1092 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12516 Z= 0.213 Angle : 0.471 5.707 16911 Z= 0.252 Chirality : 0.041 0.139 1827 Planarity : 0.004 0.047 2157 Dihedral : 4.156 25.792 1671 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.99 % Allowed : 5.76 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1497 helix: 1.70 (0.20), residues: 693 sheet: -0.40 (0.38), residues: 202 loop : -0.07 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 820 HIS 0.017 0.001 HIS B1078 PHE 0.012 0.001 PHE A 990 TYR 0.020 0.001 TYR B 858 ARG 0.008 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.377 Fit side-chains REVERT: B 926 SER cc_start: 0.8881 (m) cc_final: 0.8472 (p) REVERT: B 929 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7408 (ptm-80) REVERT: B 970 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 983 LEU cc_start: 0.9050 (tm) cc_final: 0.8740 (tp) outliers start: 13 outliers final: 3 residues processed: 71 average time/residue: 1.4429 time to fit residues: 111.5474 Evaluate side-chains 68 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS B1078 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12516 Z= 0.195 Angle : 0.456 5.600 16911 Z= 0.244 Chirality : 0.041 0.139 1827 Planarity : 0.003 0.047 2157 Dihedral : 4.099 25.439 1671 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.99 % Allowed : 6.22 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1497 helix: 1.76 (0.20), residues: 693 sheet: -0.35 (0.40), residues: 182 loop : -0.14 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1189 HIS 0.014 0.001 HIS B1078 PHE 0.012 0.001 PHE A 990 TYR 0.020 0.001 TYR B 858 ARG 0.008 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.518 Fit side-chains REVERT: A 929 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7605 (ptm-80) REVERT: B 926 SER cc_start: 0.8905 (m) cc_final: 0.8491 (p) REVERT: B 929 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7411 (ptm-80) REVERT: B 970 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 983 LEU cc_start: 0.9033 (tm) cc_final: 0.8724 (tp) outliers start: 13 outliers final: 6 residues processed: 70 average time/residue: 1.5416 time to fit residues: 117.0078 Evaluate side-chains 72 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12516 Z= 0.226 Angle : 0.467 5.776 16911 Z= 0.250 Chirality : 0.041 0.138 1827 Planarity : 0.004 0.048 2157 Dihedral : 4.155 25.949 1671 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.29 % Allowed : 6.90 % Favored : 91.81 % 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: 1.00 (0.22), residues: 1497 helix: 1.74 (0.20), residues: 693 sheet: -0.38 (0.39), residues: 182 loop : -0.16 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 820 HIS 0.003 0.001 HIS B1192 PHE 0.013 0.001 PHE A 990 TYR 0.021 0.001 TYR B 858 ARG 0.008 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 1.535 Fit side-chains REVERT: A 929 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7527 (ptm-80) REVERT: B 926 SER cc_start: 0.8923 (m) cc_final: 0.8502 (p) REVERT: B 929 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7410 (ptm-80) REVERT: B 970 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 983 LEU cc_start: 0.9063 (tm) cc_final: 0.8764 (tp) outliers start: 17 outliers final: 9 residues processed: 71 average time/residue: 1.5523 time to fit residues: 119.3477 Evaluate side-chains 75 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12516 Z= 0.272 Angle : 0.488 6.131 16911 Z= 0.261 Chirality : 0.042 0.140 1827 Planarity : 0.004 0.048 2157 Dihedral : 4.293 26.867 1671 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.06 % Allowed : 7.58 % Favored : 91.36 % 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: 0.92 (0.22), residues: 1497 helix: 1.69 (0.20), residues: 693 sheet: -0.49 (0.39), residues: 192 loop : -0.19 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 820 HIS 0.004 0.001 HIS B1192 PHE 0.013 0.001 PHE A 990 TYR 0.023 0.001 TYR B 858 ARG 0.009 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 1.480 Fit side-chains REVERT: A 929 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7447 (ptm-80) REVERT: B 926 SER cc_start: 0.8918 (m) cc_final: 0.8547 (p) REVERT: B 929 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7466 (ptm-80) REVERT: B 970 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 983 LEU cc_start: 0.9067 (tm) cc_final: 0.8765 (tp) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 1.5323 time to fit residues: 113.1101 Evaluate side-chains 77 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 1112 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12516 Z= 0.183 Angle : 0.453 5.838 16911 Z= 0.242 Chirality : 0.040 0.137 1827 Planarity : 0.003 0.047 2157 Dihedral : 4.101 25.632 1671 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.99 % Allowed : 7.88 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1497 helix: 1.76 (0.20), residues: 693 sheet: -0.38 (0.40), residues: 182 loop : -0.14 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS B1192 PHE 0.011 0.001 PHE A 990 TYR 0.019 0.001 TYR B 858 ARG 0.009 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 1.549 Fit side-chains REVERT: A 929 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7421 (ptm-80) REVERT: B 970 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7779 (mt-10) REVERT: B 983 LEU cc_start: 0.9058 (tm) cc_final: 0.8765 (tp) outliers start: 13 outliers final: 7 residues processed: 69 average time/residue: 1.5251 time to fit residues: 114.1929 Evaluate side-chains 71 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12516 Z= 0.172 Angle : 0.444 5.524 16911 Z= 0.237 Chirality : 0.040 0.137 1827 Planarity : 0.003 0.048 2157 Dihedral : 4.033 25.031 1671 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.83 % Allowed : 8.19 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1497 helix: 1.80 (0.20), residues: 693 sheet: -0.38 (0.40), residues: 182 loop : -0.12 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.002 0.001 HIS B1192 PHE 0.012 0.001 PHE A 990 TYR 0.019 0.001 TYR B 858 ARG 0.009 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.487 Fit side-chains REVERT: A 929 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7402 (ptm-80) REVERT: B 970 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 983 LEU cc_start: 0.9048 (tm) cc_final: 0.8758 (tp) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 1.5201 time to fit residues: 110.6568 Evaluate side-chains 72 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 72 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12516 Z= 0.175 Angle : 0.446 5.704 16911 Z= 0.237 Chirality : 0.040 0.136 1827 Planarity : 0.003 0.047 2157 Dihedral : 4.014 24.728 1671 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.76 % Allowed : 8.42 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.22), residues: 1497 helix: 1.81 (0.20), residues: 693 sheet: -0.36 (0.40), residues: 182 loop : -0.12 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1189 HIS 0.003 0.001 HIS B1192 PHE 0.012 0.001 PHE A 990 TYR 0.019 0.001 TYR B 858 ARG 0.010 0.000 ARG A 985 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 1.592 Fit side-chains REVERT: A 929 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7383 (ptm-80) REVERT: B 970 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7759 (mt-10) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 1.6026 time to fit residues: 116.6346 Evaluate side-chains 72 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.0010 chunk 119 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 0.0570 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 ASN ** 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 = 0.3214 r_free = 0.3214 target = 0.081645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.060735 restraints weight = 37670.503| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.18 r_work: 0.2680 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12516 Z= 0.121 Angle : 0.419 5.087 16911 Z= 0.222 Chirality : 0.039 0.135 1827 Planarity : 0.003 0.047 2157 Dihedral : 3.785 23.084 1671 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.38 % Allowed : 8.87 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1497 helix: 1.91 (0.20), residues: 693 sheet: -0.25 (0.40), residues: 182 loop : -0.08 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1189 HIS 0.002 0.000 HIS B1051 PHE 0.011 0.001 PHE A 990 TYR 0.016 0.001 TYR B 858 ARG 0.009 0.000 ARG B 985 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3510.13 seconds wall clock time: 63 minutes 30.05 seconds (3810.05 seconds total)