Starting phenix.real_space_refine on Sun Nov 17 00:21:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/11_2024/8j8a_36065.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/11_2024/8j8a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/11_2024/8j8a_36065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/11_2024/8j8a_36065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/11_2024/8j8a_36065.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/11_2024/8j8a_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.44, per 1000 atoms: 0.85 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: 3.01 Conformation dependent library (CDL) restraints added in 2.2 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: 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: 1.44 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: 4.23 Time building geometry restraints manager: 3.35 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: 2.840 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.400 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.360 ------------------------------------------------------------------------------- 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= 0.176 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 *********************** 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 : 1.523 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: 1.3557 time to fit residues: 187.2495 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 : 1.357 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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= 0.201 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 *********************** 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 : 1.435 Fit side-chains REVERT: A 433 MET cc_start: 0.7931 (ptp) cc_final: 0.7683 (ptp) REVERT: A 916 TYR cc_start: 0.8143 (m-80) cc_final: 0.7689 (m-80) REVERT: A 957 MET cc_start: 0.8897 (tpt) cc_final: 0.8588 (tpt) REVERT: B 433 MET cc_start: 0.7905 (ptp) cc_final: 0.7668 (ptp) REVERT: B 503 LYS cc_start: 0.9193 (tttm) cc_final: 0.8974 (tptp) REVERT: B 916 TYR cc_start: 0.7712 (m-80) cc_final: 0.7226 (m-80) REVERT: B 973 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7919 (tm-30) outliers start: 14 outliers final: 4 residues processed: 98 average time/residue: 1.3930 time to fit residues: 148.7630 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 : 1.548 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12516 Z= 0.238 Angle : 0.519 6.415 16911 Z= 0.277 Chirality : 0.042 0.168 1827 Planarity : 0.004 0.046 2157 Dihedral : 4.130 21.298 1671 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.21 % Allowed : 7.43 % 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: 0.95 (0.22), residues: 1497 helix: 1.72 (0.20), residues: 677 sheet: -0.37 (0.39), residues: 198 loop : -0.16 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1170 HIS 0.003 0.001 HIS A 752 PHE 0.016 0.001 PHE B 990 TYR 0.016 0.001 TYR B 858 ARG 0.011 0.001 ARG B 929 *********************** 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 100 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 433 MET cc_start: 0.7916 (ptp) cc_final: 0.7642 (ptp) REVERT: A 684 ARG cc_start: 0.6077 (mtp85) cc_final: 0.5754 (mtp180) REVERT: A 957 MET cc_start: 0.8967 (tpt) cc_final: 0.8734 (tpt) REVERT: A 985 ARG cc_start: 0.7934 (tpp80) cc_final: 0.7608 (tpp80) REVERT: A 988 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: B 433 MET cc_start: 0.7817 (ptp) cc_final: 0.7502 (ptp) REVERT: B 503 LYS cc_start: 0.9163 (tttm) cc_final: 0.8783 (tppt) REVERT: B 673 GLU cc_start: 0.7435 (pm20) cc_final: 0.7201 (pm20) REVERT: B 684 ARG cc_start: 0.6070 (mtp85) cc_final: 0.5795 (mtp180) REVERT: B 916 TYR cc_start: 0.7714 (m-80) cc_final: 0.7286 (m-80) REVERT: B 973 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7852 (tm-30) outliers start: 16 outliers final: 7 residues processed: 90 average time/residue: 1.5645 time to fit residues: 152.3988 Evaluate side-chains 88 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 931 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1153 ASP 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 134 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12516 Z= 0.189 Angle : 0.491 7.561 16911 Z= 0.260 Chirality : 0.041 0.164 1827 Planarity : 0.004 0.045 2157 Dihedral : 4.010 19.723 1671 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.82 % Allowed : 8.11 % Favored : 90.07 % 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: 1.74 (0.20), residues: 677 sheet: -0.30 (0.37), residues: 218 loop : -0.25 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1170 HIS 0.003 0.001 HIS A 887 PHE 0.010 0.001 PHE A 990 TYR 0.015 0.001 TYR B 858 ARG 0.010 0.001 ARG B 929 *********************** 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 109 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.551 Fit side-chains REVERT: A 433 MET cc_start: 0.7856 (ptp) cc_final: 0.7600 (ptp) REVERT: A 454 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8448 (mmmm) REVERT: A 684 ARG cc_start: 0.6131 (mtp85) cc_final: 0.5829 (mtp180) REVERT: A 957 MET cc_start: 0.8998 (tpt) cc_final: 0.8746 (tpt) REVERT: A 985 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7379 (tpp80) REVERT: B 433 MET cc_start: 0.7750 (ptp) cc_final: 0.7450 (ptp) REVERT: B 503 LYS cc_start: 0.9179 (tttm) cc_final: 0.8910 (tptp) REVERT: B 673 GLU cc_start: 0.7474 (pm20) cc_final: 0.7250 (pm20) REVERT: B 684 ARG cc_start: 0.5970 (mtp85) cc_final: 0.5669 (mtp180) REVERT: B 916 TYR cc_start: 0.7730 (m-80) cc_final: 0.7316 (m-80) REVERT: B 973 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7845 (tm-30) outliers start: 24 outliers final: 14 residues processed: 96 average time/residue: 1.4299 time to fit residues: 149.4233 Evaluate side-chains 95 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 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 801 ILE 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 120 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12516 Z= 0.282 Angle : 0.534 7.946 16911 Z= 0.282 Chirality : 0.043 0.172 1827 Planarity : 0.004 0.052 2157 Dihedral : 4.208 23.210 1671 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.90 % Allowed : 8.64 % Favored : 89.46 % 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: 0.80 (0.22), residues: 1497 helix: 1.65 (0.20), residues: 675 sheet: -0.47 (0.37), residues: 218 loop : -0.28 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1170 HIS 0.005 0.001 HIS A 752 PHE 0.012 0.001 PHE A 990 TYR 0.018 0.001 TYR B 858 ARG 0.011 0.001 ARG B 929 *********************** 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 111 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.401 Fit side-chains REVERT: A 433 MET cc_start: 0.7915 (ptp) cc_final: 0.7673 (ptp) REVERT: A 454 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8615 (mmmt) REVERT: A 684 ARG cc_start: 0.6276 (mtp85) cc_final: 0.5934 (mtp180) REVERT: A 916 TYR cc_start: 0.8028 (m-80) cc_final: 0.7286 (m-80) REVERT: A 957 MET cc_start: 0.9018 (tpt) cc_final: 0.8656 (tpt) REVERT: B 433 MET cc_start: 0.7844 (ptp) cc_final: 0.7513 (ptp) REVERT: B 454 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8686 (mmmm) REVERT: B 503 LYS cc_start: 0.9171 (tttm) cc_final: 0.8905 (tptp) REVERT: B 673 GLU cc_start: 0.7514 (pm20) cc_final: 0.7285 (pm20) REVERT: B 684 ARG cc_start: 0.6215 (mtp85) cc_final: 0.5963 (mtp180) REVERT: B 916 TYR cc_start: 0.7782 (m-80) cc_final: 0.7012 (m-80) REVERT: B 973 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7788 (tm-30) outliers start: 25 outliers final: 11 residues processed: 98 average time/residue: 1.4313 time to fit residues: 152.7601 Evaluate side-chains 95 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1112 GLU 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 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 48 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 0.0570 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2324 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= 0.213 Angle : 0.504 9.192 16911 Z= 0.266 Chirality : 0.041 0.162 1827 Planarity : 0.004 0.052 2157 Dihedral : 4.104 21.164 1671 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.67 % Allowed : 9.55 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1497 helix: 1.68 (0.20), residues: 675 sheet: -0.50 (0.37), residues: 218 loop : -0.32 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS A 887 PHE 0.012 0.001 PHE A 559 TYR 0.016 0.001 TYR B 858 ARG 0.013 0.001 ARG A 929 *********************** 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: 22 poor density : 86 time to evaluate : 1.536 Fit side-chains REVERT: A 433 MET cc_start: 0.7859 (ptp) cc_final: 0.7613 (ptp) REVERT: A 684 ARG cc_start: 0.6150 (mtp85) cc_final: 0.5832 (mtp180) REVERT: A 929 ARG cc_start: 0.8434 (ttp-110) cc_final: 0.8139 (mtp180) REVERT: A 957 MET cc_start: 0.9026 (tpt) cc_final: 0.8650 (tpt) REVERT: A 973 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 985 ARG cc_start: 0.7400 (tpp80) cc_final: 0.7100 (mtm-85) REVERT: B 433 MET cc_start: 0.7760 (ptp) cc_final: 0.7489 (ptp) REVERT: B 503 LYS cc_start: 0.9166 (tttm) cc_final: 0.8903 (tptp) REVERT: B 673 GLU cc_start: 0.7502 (pm20) cc_final: 0.7268 (pm20) REVERT: B 684 ARG cc_start: 0.6072 (mtp85) cc_final: 0.5842 (mtp180) REVERT: B 916 TYR cc_start: 0.7857 (m-80) cc_final: 0.7077 (m-80) REVERT: B 973 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 1040 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7938 (ttm-80) outliers start: 22 outliers final: 15 residues processed: 97 average time/residue: 1.4651 time to fit residues: 154.2524 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 : 1.594 ------------------------------------------------------------------------------- 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 1112 GLU 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 16 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 144 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 89 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2421 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= 0.167 Angle : 0.493 8.731 16911 Z= 0.258 Chirality : 0.040 0.160 1827 Planarity : 0.004 0.054 2157 Dihedral : 3.944 20.206 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 : 1.29 % Allowed : 10.54 % Favored : 88.17 % 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: 0.88 (0.22), residues: 1497 helix: 1.78 (0.20), residues: 675 sheet: -0.45 (0.38), residues: 218 loop : -0.33 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS B 887 PHE 0.009 0.001 PHE B 990 TYR 0.015 0.001 TYR B 858 ARG 0.014 0.001 ARG B 929 *********************** 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 105 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.416 Fit side-chains REVERT: A 433 MET cc_start: 0.7799 (ptp) cc_final: 0.7554 (ptp) REVERT: A 454 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8796 (mmmm) REVERT: A 684 ARG cc_start: 0.6166 (mtp85) cc_final: 0.5810 (mtp180) REVERT: A 916 TYR cc_start: 0.7862 (m-80) cc_final: 0.7591 (m-80) REVERT: A 957 MET cc_start: 0.9033 (tpt) cc_final: 0.8685 (tpt) REVERT: A 973 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 985 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7168 (mtm-85) REVERT: A 1040 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7882 (ttm-80) REVERT: B 433 MET cc_start: 0.7731 (ptp) cc_final: 0.7419 (ptp) REVERT: B 454 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8760 (mmmm) REVERT: B 503 LYS cc_start: 0.9167 (tttm) cc_final: 0.8918 (tptp) REVERT: B 673 GLU cc_start: 0.7502 (pm20) cc_final: 0.7267 (pm20) REVERT: B 684 ARG cc_start: 0.5930 (mtp85) cc_final: 0.5719 (mtp180) REVERT: B 916 TYR cc_start: 0.7875 (m-80) cc_final: 0.7123 (m-80) REVERT: B 973 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 1040 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7893 (ttm-80) outliers start: 17 outliers final: 13 residues processed: 97 average time/residue: 1.4335 time to fit residues: 151.1871 Evaluate side-chains 94 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 0.0970 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8304 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12516 Z= 0.234 Angle : 0.524 9.635 16911 Z= 0.271 Chirality : 0.042 0.236 1827 Planarity : 0.004 0.058 2157 Dihedral : 4.043 21.107 1671 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.52 % Allowed : 10.99 % Favored : 87.49 % 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: 0.84 (0.22), residues: 1497 helix: 1.75 (0.20), residues: 675 sheet: -0.49 (0.37), residues: 218 loop : -0.34 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS B 752 PHE 0.016 0.001 PHE A 559 TYR 0.016 0.001 TYR B 858 ARG 0.014 0.001 ARG B 929 *********************** 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: 20 poor density : 84 time to evaluate : 1.652 Fit side-chains REVERT: A 433 MET cc_start: 0.7873 (ptp) cc_final: 0.7606 (ptp) REVERT: A 454 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8796 (mmmm) REVERT: A 673 GLU cc_start: 0.7361 (pm20) cc_final: 0.7111 (pm20) REVERT: A 684 ARG cc_start: 0.6192 (mtp85) cc_final: 0.5935 (mtp180) REVERT: A 916 TYR cc_start: 0.7880 (m-80) cc_final: 0.7222 (m-80) REVERT: A 973 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7650 (tm-30) REVERT: A 985 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7196 (mtm-85) REVERT: B 433 MET cc_start: 0.7796 (ptp) cc_final: 0.7536 (ptp) REVERT: B 454 LYS cc_start: 0.9200 (mmmt) cc_final: 0.8800 (mmtp) REVERT: B 503 LYS cc_start: 0.9164 (tttm) cc_final: 0.8937 (tptp) REVERT: B 684 ARG cc_start: 0.6122 (mtp85) cc_final: 0.5894 (mtp180) REVERT: B 801 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8231 (tp) REVERT: B 916 TYR cc_start: 0.7887 (m-80) cc_final: 0.7120 (m-80) REVERT: B 973 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 1040 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7938 (ttm-80) outliers start: 20 outliers final: 14 residues processed: 94 average time/residue: 1.4579 time to fit residues: 150.3311 Evaluate side-chains 96 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 1112 GLU 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 701 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.0050 chunk 121 optimal weight: 0.0980 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.8282 moved from start: 0.2540 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= 0.174 Angle : 0.505 9.049 16911 Z= 0.262 Chirality : 0.041 0.203 1827 Planarity : 0.004 0.060 2157 Dihedral : 3.941 20.434 1671 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.14 % Allowed : 11.30 % Favored : 87.57 % 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: 0.91 (0.22), residues: 1497 helix: 1.80 (0.20), residues: 675 sheet: -0.43 (0.38), residues: 218 loop : -0.30 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS B 887 PHE 0.011 0.001 PHE A 559 TYR 0.015 0.001 TYR B 858 ARG 0.014 0.001 ARG B 929 *********************** 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 97 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.681 Fit side-chains REVERT: A 433 MET cc_start: 0.7823 (ptp) cc_final: 0.7556 (ptp) REVERT: A 454 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8798 (mmmm) REVERT: A 673 GLU cc_start: 0.7368 (pm20) cc_final: 0.7119 (pm20) REVERT: A 684 ARG cc_start: 0.6155 (mtp85) cc_final: 0.5912 (mtp180) REVERT: A 916 TYR cc_start: 0.7832 (m-80) cc_final: 0.7617 (m-80) REVERT: A 973 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 985 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7195 (mtm-85) REVERT: A 1040 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7865 (ttm-80) REVERT: B 433 MET cc_start: 0.7745 (ptp) cc_final: 0.7405 (ptp) REVERT: B 454 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8819 (mmtp) REVERT: B 503 LYS cc_start: 0.9162 (tttm) cc_final: 0.8949 (tptp) REVERT: B 684 ARG cc_start: 0.5966 (mtp85) cc_final: 0.5758 (mtp180) REVERT: B 916 TYR cc_start: 0.7872 (m-80) cc_final: 0.7503 (m-80) REVERT: B 973 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 1040 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7863 (ttm-80) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 1.3036 time to fit residues: 127.3661 Evaluate side-chains 92 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL 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 522 THR Chi-restraints excluded: chain B residue 701 ASP Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 137 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2599 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= 0.172 Angle : 0.498 8.968 16911 Z= 0.258 Chirality : 0.041 0.210 1827 Planarity : 0.004 0.061 2157 Dihedral : 3.890 20.057 1671 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.99 % Allowed : 11.52 % Favored : 87.49 % 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: 1.82 (0.20), residues: 675 sheet: -0.44 (0.38), residues: 218 loop : -0.29 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS B 887 PHE 0.010 0.001 PHE A 990 TYR 0.015 0.001 TYR B 858 ARG 0.015 0.001 ARG A 929 ********************** 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 94 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.453 Fit side-chains REVERT: A 433 MET cc_start: 0.7839 (ptp) cc_final: 0.7570 (ptp) REVERT: A 454 LYS cc_start: 0.9200 (mmmt) cc_final: 0.8881 (mmmt) REVERT: A 673 GLU cc_start: 0.7404 (pm20) cc_final: 0.7147 (pm20) REVERT: A 684 ARG cc_start: 0.6149 (mtp85) cc_final: 0.5904 (mtp180) REVERT: A 916 TYR cc_start: 0.7840 (m-80) cc_final: 0.7620 (m-80) REVERT: A 929 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.8048 (mtp180) REVERT: A 985 ARG cc_start: 0.7538 (tpp80) cc_final: 0.7250 (mtm-85) REVERT: A 1040 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7847 (ttm-80) REVERT: B 433 MET cc_start: 0.7719 (ptp) cc_final: 0.7402 (ptp) REVERT: B 454 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8811 (mmtt) REVERT: B 503 LYS cc_start: 0.9176 (tttm) cc_final: 0.8962 (tptp) REVERT: B 684 ARG cc_start: 0.5960 (mtp85) cc_final: 0.5751 (mtp180) REVERT: B 916 TYR cc_start: 0.7868 (m-80) cc_final: 0.7507 (m-80) REVERT: B 973 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 1040 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7848 (ttm-80) outliers start: 13 outliers final: 11 residues processed: 88 average time/residue: 1.4621 time to fit residues: 139.3664 Evaluate side-chains 88 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL 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 522 THR Chi-restraints excluded: chain B residue 701 ASP Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1153 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 119 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.096624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.070112 restraints weight = 40248.551| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.37 r_work: 0.2874 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2620 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= 0.190 Angle : 0.507 8.746 16911 Z= 0.263 Chirality : 0.041 0.244 1827 Planarity : 0.004 0.063 2157 Dihedral : 3.919 20.230 1671 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.91 % Allowed : 11.60 % Favored : 87.49 % 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: 0.90 (0.22), residues: 1497 helix: 1.80 (0.20), residues: 675 sheet: -0.46 (0.38), residues: 218 loop : -0.30 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS B 887 PHE 0.011 0.001 PHE A 559 TYR 0.015 0.001 TYR B 858 ARG 0.015 0.001 ARG B 929 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.82 seconds wall clock time: 78 minutes 35.92 seconds (4715.92 seconds total)