Starting phenix.real_space_refine on Wed May 14 23:01:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8a_36065/05_2025/8j8a_36065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8a_36065/05_2025/8j8a_36065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8a_36065/05_2025/8j8a_36065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8a_36065/05_2025/8j8a_36065.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8a_36065/05_2025/8j8a_36065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8a_36065/05_2025/8j8a_36065.cif" } resolution = 2.51 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= 0.009 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. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.65, per 1000 atoms: 0.79 Number of scatterers: 12222 At special positions: 0 Unit cell: (117.03, 105.41, 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 - 3.00 Amino acid : True - 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: 2.75 Conformation dependent library (CDL) restraints added in 2.1 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: 68 helices and 14 sheets defined 52.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... 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 528 removed outlier: 3.871A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 566 removed outlier: 4.283A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 604 removed outlier: 3.505A pdb=" N THR A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.783A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.655A 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 642 through 653 removed outlier: 4.066A pdb=" N LYS A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 687 through 707 removed outlier: 4.797A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 732 removed outlier: 4.376A pdb=" N SER A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN A 732 " --> pdb=" O CYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.626A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 882 through 891 removed outlier: 3.989A pdb=" N LYS A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 984 through 990 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1070 removed outlier: 3.702A 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 removed outlier: 4.023A pdb=" N HIS A1078 " --> pdb=" O ASN A1075 " (cutoff:3.500A) 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: 4.189A 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 removed outlier: 3.585A pdb=" N GLN A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1187 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 528 removed outlier: 3.889A pdb=" N LYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.562A pdb=" N PHE B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.965A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 604 removed outlier: 3.505A pdb=" N THR B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.801A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.661A 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 642 through 653 removed outlier: 3.926A pdb=" N LYS B 646 " --> pdb=" O ASP B 642 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 647 " --> pdb=" O ASP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 665 removed outlier: 3.613A pdb=" N GLU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 687 through 707 removed outlier: 4.756A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 706 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 732 removed outlier: 4.355A pdb=" N SER B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN B 732 " --> pdb=" O CYS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 750 Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 806 through 814 removed outlier: 4.105A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix 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: 3.962A 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: 3.609A pdb=" N ILE B 986 " --> pdb=" O SER B 982 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1070 removed outlier: 3.831A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix 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 1116 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 removed outlier: 3.527A pdb=" N GLN B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.699A pdb=" N GLU B1172 " --> pdb=" O SER B1168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 removed outlier: 5.890A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (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: 4.373A 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 removed outlier: 4.300A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 926 removed outlier: 6.059A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 977 " --> pdb=" O GLU A 962 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 962 " --> pdb=" O LYS A 977 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AA8, first strand: chain 'B' and resid 465 through 469 removed outlier: 5.955A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.133A 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: 4.479A 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 removed outlier: 4.589A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.046A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 4.116A 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 583 hydrogen bonds defined for protein. 1656 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: 4.08 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3943 1.34 - 1.46: 2701 1.46 - 1.58: 5794 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12516 Sorted by residual: bond pdb=" CB ILE B 801 " pdb=" CG2 ILE B 801 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CB ILE A 801 " pdb=" CG2 ILE A 801 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 bond pdb=" CG LEU A 549 " pdb=" CD1 LEU A 549 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.25e-01 bond pdb=" C PHE A 785 " pdb=" N GLY A 786 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 7.23e-01 bond pdb=" CB ASP B 416 " pdb=" CG ASP B 416 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.11e-01 ... (remaining 12511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 16508 1.42 - 2.83: 328 2.83 - 4.25: 63 4.25 - 5.66: 11 5.66 - 7.08: 1 Bond angle restraints: 16911 Sorted by residual: angle pdb=" C LYS B1190 " pdb=" N PHE B1191 " pdb=" CA PHE B1191 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.37e+01 angle pdb=" N VAL A 415 " pdb=" CA VAL A 415 " pdb=" C VAL A 415 " ideal model delta sigma weight residual 109.46 105.00 4.46 1.38e+00 5.25e-01 1.04e+01 angle pdb=" N ILE A 845 " pdb=" CA ILE A 845 " pdb=" C ILE A 845 " ideal model delta sigma weight residual 113.39 108.97 4.42 1.47e+00 4.63e-01 9.02e+00 angle pdb=" CA ILE A 845 " pdb=" C ILE A 845 " pdb=" N MET A 846 " ideal model delta sigma weight residual 118.55 116.15 2.40 8.60e-01 1.35e+00 7.79e+00 angle pdb=" N GLU B1173 " pdb=" CA GLU B1173 " pdb=" C GLU B1173 " ideal model delta sigma weight residual 111.36 108.37 2.99 1.09e+00 8.42e-01 7.54e+00 ... (remaining 16906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 6848 17.29 - 34.58: 550 34.58 - 51.87: 86 51.87 - 69.16: 19 69.16 - 86.45: 10 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 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA GLU A1073 " pdb=" C GLU A1073 " pdb=" N LEU A1074 " pdb=" CA LEU A1074 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+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 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 7510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1201 0.034 - 0.067: 455 0.067 - 0.100: 116 0.100 - 0.134: 54 0.134 - 0.167: 1 Chirality restraints: 1827 Sorted by residual: chirality pdb=" CA VAL A 415 " pdb=" N VAL A 415 " pdb=" C VAL A 415 " pdb=" CB VAL A 415 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA PRO B 980 " pdb=" N PRO B 980 " pdb=" C PRO B 980 " pdb=" CB PRO B 980 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA LYS B 991 " pdb=" N LYS B 991 " pdb=" C LYS B 991 " pdb=" CB LYS B 991 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1824 not shown) Planarity restraints: 2157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 937 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 938 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 938 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 938 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 938 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 979 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 980 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 980 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 980 " 0.024 5.00e-02 4.00e+02 ... (remaining 2154 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 765 2.74 - 3.28: 12320 3.28 - 3.82: 20341 3.82 - 4.36: 25397 4.36 - 4.90: 43225 Nonbonded interactions: 102048 Sorted by model distance: nonbonded pdb=" OG SER A 919 " pdb=" OD1 ASN A1007 " model vdw 2.197 3.040 nonbonded pdb=" O GLY B 781 " pdb=" NZ LYS B1190 " model vdw 2.211 3.120 nonbonded pdb=" OH TYR B 923 " pdb=" OD2 ASP B 997 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 923 " pdb=" OD2 ASP A 997 " model vdw 2.277 3.040 nonbonded pdb=" NH2 ARG B1049 " pdb=" O GLU B1106 " model vdw 2.279 3.120 ... (remaining 102043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.030 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 0.039 12516 Z= 0.116 Angle : 0.499 7.078 16911 Z= 0.271 Chirality : 0.041 0.167 1827 Planarity : 0.004 0.048 2157 Dihedral : 12.916 86.447 4687 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.55 % 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 (0.21), residues: 1497 helix: 1.81 (0.20), residues: 645 sheet: -0.07 (0.38), residues: 196 loop : -0.14 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 820 HIS 0.004 0.001 HIS B 566 PHE 0.013 0.001 PHE A1107 TYR 0.015 0.001 TYR B 858 ARG 0.009 0.001 ARG B 526 Details of bonding type rmsd hydrogen bonds : bond 0.21221 ( 583) hydrogen bonds : angle 6.61479 ( 1656) covalent geometry : bond 0.00268 (12516) covalent geometry : angle 0.49906 (16911) *********************** 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 128 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.363 Fit side-chains REVERT: A 433 MET cc_start: 0.8026 (ptp) cc_final: 0.7823 (ptp) REVERT: A 970 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 999 ILE cc_start: 0.8550 (mm) cc_final: 0.8274 (mm) REVERT: B 433 MET cc_start: 0.7978 (ptp) cc_final: 0.7758 (ptp) REVERT: B 503 LYS cc_start: 0.9235 (tttm) cc_final: 0.8994 (tptp) REVERT: B 916 TYR cc_start: 0.7797 (m-80) cc_final: 0.7315 (m-80) REVERT: B 973 GLU cc_start: 0.8215 (tm-30) cc_final: 0.8006 (tm-30) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 1.3074 time to fit residues: 180.5189 Evaluate side-chains 84 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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: 0.4980 chunk 113 optimal weight: 0.0030 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN B 733 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.074756 restraints weight = 26534.232| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.83 r_work: 0.2969 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12516 Z= 0.136 Angle : 0.535 6.586 16911 Z= 0.289 Chirality : 0.042 0.175 1827 Planarity : 0.004 0.046 2157 Dihedral : 4.055 21.316 1671 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.06 % Allowed : 5.69 % 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: 1.13 (0.22), residues: 1497 helix: 1.84 (0.20), residues: 677 sheet: 0.01 (0.37), residues: 214 loop : -0.14 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1170 HIS 0.003 0.001 HIS B1051 PHE 0.018 0.001 PHE A 559 TYR 0.015 0.001 TYR A 920 ARG 0.011 0.001 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.05106 ( 583) hydrogen bonds : angle 4.63234 ( 1656) covalent geometry : bond 0.00301 (12516) covalent geometry : angle 0.53469 (16911) *********************** 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 107 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.414 Fit side-chains REVERT: A 433 MET cc_start: 0.7717 (ptp) cc_final: 0.7484 (ptp) REVERT: A 916 TYR cc_start: 0.8301 (m-80) cc_final: 0.7826 (m-80) REVERT: A 957 MET cc_start: 0.8813 (tpt) cc_final: 0.8514 (tpt) REVERT: B 433 MET cc_start: 0.7680 (ptp) cc_final: 0.7463 (ptp) REVERT: B 503 LYS cc_start: 0.9159 (tttm) cc_final: 0.8866 (tptp) REVERT: B 916 TYR cc_start: 0.7751 (m-80) cc_final: 0.7234 (m-80) REVERT: B 973 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8058 (tm-30) outliers start: 14 outliers final: 4 residues processed: 98 average time/residue: 1.2975 time to fit residues: 138.8714 Evaluate side-chains 87 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 108 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 127 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.071399 restraints weight = 30280.337| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.00 r_work: 0.2898 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12516 Z= 0.155 Angle : 0.522 6.626 16911 Z= 0.278 Chirality : 0.042 0.171 1827 Planarity : 0.004 0.046 2157 Dihedral : 4.144 21.539 1671 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.29 % Allowed : 7.43 % Favored : 91.28 % 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: 0.94 (0.22), residues: 1497 helix: 1.72 (0.20), residues: 677 sheet: -0.38 (0.39), residues: 198 loop : -0.17 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1170 HIS 0.004 0.001 HIS A 752 PHE 0.015 0.001 PHE B 990 TYR 0.016 0.001 TYR B 858 ARG 0.012 0.001 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 583) hydrogen bonds : angle 4.28014 ( 1656) covalent geometry : bond 0.00367 (12516) covalent geometry : angle 0.52159 (16911) *********************** 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 101 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 433 MET cc_start: 0.7779 (ptp) cc_final: 0.7517 (ptp) REVERT: A 684 ARG cc_start: 0.6179 (mtp85) cc_final: 0.5837 (mtp180) REVERT: A 957 MET cc_start: 0.8927 (tpt) cc_final: 0.8638 (tpt) REVERT: A 985 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7520 (tpp80) REVERT: A 988 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: B 433 MET cc_start: 0.7654 (ptp) cc_final: 0.7384 (ptp) REVERT: B 503 LYS cc_start: 0.9124 (tttm) cc_final: 0.8687 (tppt) REVERT: B 684 ARG cc_start: 0.6035 (mtp85) cc_final: 0.5755 (mtp180) REVERT: B 916 TYR cc_start: 0.7808 (m-80) cc_final: 0.7329 (m-80) REVERT: B 973 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8042 (tm-30) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 1.4899 time to fit residues: 146.6995 Evaluate side-chains 91 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1024 GLU Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 140 optimal weight: 0.0050 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 113 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 ASN A1010 HIS B 981 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.071556 restraints weight = 40102.038| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.41 r_work: 0.2891 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12516 Z= 0.121 Angle : 0.488 7.245 16911 Z= 0.259 Chirality : 0.041 0.164 1827 Planarity : 0.004 0.045 2157 Dihedral : 3.988 19.423 1671 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.74 % Allowed : 8.26 % Favored : 89.99 % 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: 0.93 (0.22), residues: 1497 helix: 1.75 (0.20), residues: 677 sheet: -0.31 (0.37), residues: 218 loop : -0.25 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1170 HIS 0.003 0.001 HIS B 887 PHE 0.010 0.001 PHE A 990 TYR 0.014 0.001 TYR B 858 ARG 0.010 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 583) hydrogen bonds : angle 4.16500 ( 1656) covalent geometry : bond 0.00278 (12516) covalent geometry : angle 0.48836 (16911) *********************** 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 111 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.522 Fit side-chains REVERT: A 433 MET cc_start: 0.7718 (ptp) cc_final: 0.7491 (ptp) REVERT: A 454 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8617 (mmmm) REVERT: A 684 ARG cc_start: 0.6045 (mtp85) cc_final: 0.5726 (mtp180) REVERT: A 957 MET cc_start: 0.8954 (tpt) cc_final: 0.8713 (tpt) REVERT: A 985 ARG cc_start: 0.7934 (tpp80) cc_final: 0.7319 (tpp80) REVERT: B 433 MET cc_start: 0.7603 (ptp) cc_final: 0.7322 (ptp) REVERT: B 503 LYS cc_start: 0.9121 (tttm) cc_final: 0.8788 (tptp) REVERT: B 684 ARG cc_start: 0.5912 (mtp85) cc_final: 0.5643 (mtp180) REVERT: B 916 TYR cc_start: 0.7840 (m-80) cc_final: 0.7396 (m-80) REVERT: B 973 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8048 (tm-30) REVERT: B 1040 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8043 (ttm-80) outliers start: 23 outliers final: 12 residues processed: 98 average time/residue: 1.3955 time to fit residues: 148.7040 Evaluate side-chains 96 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.070650 restraints weight = 39442.639| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.37 r_work: 0.2878 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12516 Z= 0.131 Angle : 0.495 7.901 16911 Z= 0.261 Chirality : 0.041 0.167 1827 Planarity : 0.004 0.045 2157 Dihedral : 3.980 20.081 1671 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.82 % Allowed : 8.95 % Favored : 89.23 % 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: 0.92 (0.22), residues: 1497 helix: 1.76 (0.20), residues: 675 sheet: -0.37 (0.37), residues: 218 loop : -0.25 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1170 HIS 0.003 0.001 HIS B 887 PHE 0.010 0.001 PHE B 990 TYR 0.015 0.001 TYR B 858 ARG 0.011 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 583) hydrogen bonds : angle 4.10313 ( 1656) covalent geometry : bond 0.00307 (12516) covalent geometry : angle 0.49512 (16911) *********************** 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 109 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.348 Fit side-chains REVERT: A 433 MET cc_start: 0.7760 (ptp) cc_final: 0.7519 (ptp) REVERT: A 454 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8693 (mmmt) REVERT: A 684 ARG cc_start: 0.6180 (mtp85) cc_final: 0.5843 (mtp180) REVERT: A 929 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8221 (mtp180) REVERT: A 957 MET cc_start: 0.8963 (tpt) cc_final: 0.8714 (tpt) REVERT: A 973 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 1040 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8074 (ttm-80) REVERT: B 433 MET cc_start: 0.7625 (ptp) cc_final: 0.7340 (ptp) REVERT: B 454 LYS cc_start: 0.9304 (mmmt) cc_final: 0.8760 (mmmm) REVERT: B 503 LYS cc_start: 0.9114 (tttm) cc_final: 0.8781 (tptp) REVERT: B 684 ARG cc_start: 0.5938 (mtp85) cc_final: 0.5714 (mtp180) REVERT: B 916 TYR cc_start: 0.7854 (m-80) cc_final: 0.7068 (m-80) REVERT: B 973 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8026 (tm-30) REVERT: B 1040 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8072 (ttm-80) outliers start: 24 outliers final: 11 residues processed: 99 average time/residue: 1.3441 time to fit residues: 144.6301 Evaluate side-chains 96 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 0.8980 chunk 129 optimal weight: 0.0870 chunk 66 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.098005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.071050 restraints weight = 40151.690| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.41 r_work: 0.2923 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2275 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= 0.118 Angle : 0.490 8.889 16911 Z= 0.257 Chirality : 0.041 0.161 1827 Planarity : 0.004 0.045 2157 Dihedral : 3.936 19.752 1671 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.59 % Allowed : 9.93 % Favored : 88.48 % 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: 0.93 (0.22), residues: 1497 helix: 1.79 (0.20), residues: 675 sheet: -0.40 (0.38), residues: 218 loop : -0.27 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS A 887 PHE 0.009 0.001 PHE A 990 TYR 0.015 0.001 TYR B 858 ARG 0.011 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 583) hydrogen bonds : angle 4.06210 ( 1656) covalent geometry : bond 0.00273 (12516) covalent geometry : angle 0.48975 (16911) *********************** 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 108 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.368 Fit side-chains REVERT: A 433 MET cc_start: 0.7573 (ptp) cc_final: 0.7339 (ptp) REVERT: A 684 ARG cc_start: 0.6076 (mtp85) cc_final: 0.5747 (mtp180) REVERT: A 756 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7774 (tpt) REVERT: A 916 TYR cc_start: 0.7879 (m-80) cc_final: 0.7096 (m-80) REVERT: A 957 MET cc_start: 0.8891 (tpt) cc_final: 0.8652 (tpt) REVERT: A 973 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 1040 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7926 (ttm-80) REVERT: B 433 MET cc_start: 0.7470 (ptp) cc_final: 0.7191 (ptp) REVERT: B 454 LYS cc_start: 0.9315 (mmmt) cc_final: 0.8847 (mmtt) REVERT: B 503 LYS cc_start: 0.9095 (tttm) cc_final: 0.8753 (tptp) REVERT: B 684 ARG cc_start: 0.5888 (mtp85) cc_final: 0.5664 (mtp180) REVERT: B 916 TYR cc_start: 0.7855 (m-80) cc_final: 0.7021 (m-80) REVERT: B 973 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 1040 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7930 (ttm-80) outliers start: 21 outliers final: 14 residues processed: 97 average time/residue: 1.3858 time to fit residues: 145.9577 Evaluate side-chains 100 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 10 optimal weight: 0.1980 chunk 76 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070736 restraints weight = 47499.100| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.67 r_work: 0.2903 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12516 Z= 0.117 Angle : 0.493 7.902 16911 Z= 0.258 Chirality : 0.040 0.162 1827 Planarity : 0.004 0.051 2157 Dihedral : 3.904 19.635 1671 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.67 % Allowed : 10.54 % Favored : 87.79 % 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: 0.93 (0.22), residues: 1497 helix: 1.81 (0.20), residues: 675 sheet: -0.41 (0.38), residues: 218 loop : -0.29 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS B 887 PHE 0.012 0.001 PHE A 559 TYR 0.015 0.001 TYR B 858 ARG 0.012 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 583) hydrogen bonds : angle 4.03500 ( 1656) covalent geometry : bond 0.00273 (12516) covalent geometry : angle 0.49309 (16911) *********************** 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 110 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.315 Fit side-chains REVERT: A 433 MET cc_start: 0.7588 (ptp) cc_final: 0.7348 (ptp) REVERT: A 454 LYS cc_start: 0.9315 (mmmt) cc_final: 0.8867 (mmmm) REVERT: A 523 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7409 (mm-40) REVERT: A 684 ARG cc_start: 0.6080 (mtp85) cc_final: 0.5710 (mtp180) REVERT: A 916 TYR cc_start: 0.7881 (m-80) cc_final: 0.7129 (m-80) REVERT: A 957 MET cc_start: 0.8890 (tpt) cc_final: 0.8649 (tpt) REVERT: A 973 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 985 ARG cc_start: 0.7258 (tpp80) cc_final: 0.6897 (mtm-85) REVERT: A 1040 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7912 (ttm-80) REVERT: B 433 MET cc_start: 0.7522 (ptp) cc_final: 0.7233 (ptp) REVERT: B 503 LYS cc_start: 0.9094 (tttm) cc_final: 0.8755 (tptp) REVERT: B 683 ARG cc_start: 0.6888 (mtm-85) cc_final: 0.6622 (mtm-85) REVERT: B 684 ARG cc_start: 0.5883 (mtp85) cc_final: 0.5661 (mtp180) REVERT: B 801 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8211 (tp) REVERT: B 916 TYR cc_start: 0.7867 (m-80) cc_final: 0.7034 (m-80) REVERT: B 973 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 1040 ARG cc_start: 0.8350 (ttp80) cc_final: 0.7892 (ttm-80) outliers start: 22 outliers final: 13 residues processed: 99 average time/residue: 1.3701 time to fit residues: 147.5444 Evaluate side-chains 100 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 64 optimal weight: 0.0470 chunk 129 optimal weight: 0.0770 chunk 106 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.072746 restraints weight = 30263.963| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.96 r_work: 0.2930 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12516 Z= 0.104 Angle : 0.480 8.889 16911 Z= 0.251 Chirality : 0.040 0.207 1827 Planarity : 0.004 0.057 2157 Dihedral : 3.815 19.063 1671 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.29 % Allowed : 10.99 % Favored : 87.72 % 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: 1.00 (0.22), residues: 1497 helix: 1.86 (0.20), residues: 675 sheet: -0.35 (0.38), residues: 220 loop : -0.25 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.002 0.000 HIS B 887 PHE 0.009 0.001 PHE A 990 TYR 0.014 0.001 TYR B 858 ARG 0.014 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 583) hydrogen bonds : angle 3.99484 ( 1656) covalent geometry : bond 0.00234 (12516) covalent geometry : angle 0.48037 (16911) *********************** 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 104 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.358 Fit side-chains REVERT: A 433 MET cc_start: 0.7473 (ptp) cc_final: 0.7247 (ptp) REVERT: A 454 LYS cc_start: 0.9322 (mmmt) cc_final: 0.8891 (mmmm) REVERT: A 673 GLU cc_start: 0.7184 (pm20) cc_final: 0.6980 (pm20) REVERT: A 684 ARG cc_start: 0.6078 (mtp85) cc_final: 0.5746 (mtp180) REVERT: A 916 TYR cc_start: 0.7878 (m-80) cc_final: 0.7544 (m-80) REVERT: A 973 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 985 ARG cc_start: 0.7297 (tpp80) cc_final: 0.6943 (mtm-85) REVERT: A 1040 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7863 (ttm-80) REVERT: B 433 MET cc_start: 0.7405 (ptp) cc_final: 0.7157 (ptp) REVERT: B 454 LYS cc_start: 0.9333 (mmmt) cc_final: 0.8824 (mmmm) REVERT: B 503 LYS cc_start: 0.9108 (tttm) cc_final: 0.8769 (tptp) REVERT: B 684 ARG cc_start: 0.5829 (mtp85) cc_final: 0.5616 (mtp180) REVERT: B 916 TYR cc_start: 0.7868 (m-80) cc_final: 0.7386 (m-80) REVERT: B 973 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 1040 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7838 (ttm-80) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 1.3900 time to fit residues: 143.1148 Evaluate side-chains 93 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 0.0020 chunk 44 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 129 optimal weight: 0.0060 chunk 93 optimal weight: 0.7980 overall best weight: 0.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074435 restraints weight = 39792.742| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.40 r_work: 0.2948 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12516 Z= 0.095 Angle : 0.480 10.885 16911 Z= 0.246 Chirality : 0.040 0.191 1827 Planarity : 0.004 0.054 2157 Dihedral : 3.645 17.877 1671 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.91 % Allowed : 11.68 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1497 helix: 1.87 (0.20), residues: 679 sheet: -0.46 (0.40), residues: 200 loop : -0.13 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.004 0.000 HIS A 557 PHE 0.009 0.001 PHE A 990 TYR 0.012 0.001 TYR A 920 ARG 0.013 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 583) hydrogen bonds : angle 3.92347 ( 1656) covalent geometry : bond 0.00207 (12516) covalent geometry : angle 0.47958 (16911) *********************** 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 100 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.428 Fit side-chains REVERT: A 433 MET cc_start: 0.7390 (ptp) cc_final: 0.7177 (ptp) REVERT: A 454 LYS cc_start: 0.9288 (mmmt) cc_final: 0.8918 (mmmm) REVERT: A 523 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7505 (mm-40) REVERT: A 673 GLU cc_start: 0.7216 (pm20) cc_final: 0.7003 (pm20) REVERT: A 916 TYR cc_start: 0.7948 (m-80) cc_final: 0.7603 (m-80) REVERT: A 973 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 985 ARG cc_start: 0.7324 (tpp80) cc_final: 0.6990 (mtm-85) REVERT: A 1040 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7877 (ttm-80) REVERT: B 433 MET cc_start: 0.7338 (ptp) cc_final: 0.7111 (ptp) REVERT: B 454 LYS cc_start: 0.9360 (mmmt) cc_final: 0.8849 (mmmm) REVERT: B 503 LYS cc_start: 0.9101 (tttm) cc_final: 0.8791 (tptp) REVERT: B 684 ARG cc_start: 0.5785 (mtp85) cc_final: 0.5576 (mtp180) REVERT: B 916 TYR cc_start: 0.7895 (m-80) cc_final: 0.7379 (m-80) REVERT: B 973 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 1040 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7836 (ttm-80) outliers start: 12 outliers final: 10 residues processed: 95 average time/residue: 1.4652 time to fit residues: 150.5765 Evaluate side-chains 88 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 964 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.0470 chunk 137 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.0070 chunk 103 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072788 restraints weight = 33084.176| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.12 r_work: 0.2921 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12516 Z= 0.114 Angle : 0.483 8.156 16911 Z= 0.253 Chirality : 0.041 0.250 1827 Planarity : 0.004 0.058 2157 Dihedral : 3.733 18.794 1671 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.83 % Allowed : 11.83 % Favored : 87.34 % 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: 1.85 (0.20), residues: 679 sheet: -0.39 (0.38), residues: 218 loop : -0.18 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1170 HIS 0.002 0.001 HIS B 887 PHE 0.017 0.001 PHE A 559 TYR 0.013 0.001 TYR B 858 ARG 0.015 0.000 ARG A 929 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 583) hydrogen bonds : angle 3.93745 ( 1656) covalent geometry : bond 0.00266 (12516) covalent geometry : angle 0.48327 (16911) ********************** 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 91 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.484 Fit side-chains REVERT: A 433 MET cc_start: 0.7442 (ptp) cc_final: 0.7213 (ptp) REVERT: A 454 LYS cc_start: 0.9325 (mmmt) cc_final: 0.8979 (mmmt) REVERT: A 523 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7519 (mm-40) REVERT: A 673 GLU cc_start: 0.7231 (pm20) cc_final: 0.7021 (pm20) REVERT: A 916 TYR cc_start: 0.7929 (m-80) cc_final: 0.7612 (m-80) REVERT: A 985 ARG cc_start: 0.7343 (tpp80) cc_final: 0.7024 (mtm-85) REVERT: A 1040 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7914 (ttm-80) REVERT: B 433 MET cc_start: 0.7442 (ptp) cc_final: 0.7169 (ptp) REVERT: B 454 LYS cc_start: 0.9363 (mmmt) cc_final: 0.8930 (mmtp) REVERT: B 503 LYS cc_start: 0.9105 (tttm) cc_final: 0.8816 (tptp) REVERT: B 684 ARG cc_start: 0.5749 (mtp85) cc_final: 0.5524 (mtp180) REVERT: B 916 TYR cc_start: 0.7940 (m-80) cc_final: 0.7459 (m-80) REVERT: B 973 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 1040 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7896 (ttm-80) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 1.4097 time to fit residues: 135.1647 Evaluate side-chains 86 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 964 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 90 optimal weight: 0.8980 chunk 143 optimal weight: 0.0970 chunk 132 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 133 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.098089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.071621 restraints weight = 32638.269| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.11 r_work: 0.2947 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2566 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= 0.123 Angle : 0.495 10.696 16911 Z= 0.257 Chirality : 0.041 0.233 1827 Planarity : 0.004 0.059 2157 Dihedral : 3.822 19.537 1671 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.83 % Allowed : 11.83 % Favored : 87.34 % 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: 0.99 (0.22), residues: 1497 helix: 1.82 (0.20), residues: 677 sheet: -0.40 (0.38), residues: 218 loop : -0.20 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1170 HIS 0.003 0.001 HIS B 887 PHE 0.010 0.001 PHE A 990 TYR 0.014 0.001 TYR B 858 ARG 0.015 0.001 ARG A 929 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 583) hydrogen bonds : angle 3.95806 ( 1656) covalent geometry : bond 0.00288 (12516) covalent geometry : angle 0.49480 (16911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8838.95 seconds wall clock time: 152 minutes 59.69 seconds (9179.69 seconds total)