Starting phenix.real_space_refine on Mon Apr 8 02:23:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/04_2024/8j8a_36065.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/04_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_36065/04_2024/8j8a_36065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/04_2024/8j8a_36065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/04_2024/8j8a_36065.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8a_36065/04_2024/8j8a_36065.pdb" } 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 Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1024": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.18, per 1000 atoms: 0.75 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 3.2 seconds 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... Secondary structure from input PDB file: 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: 1.41 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: 3.72 Time building geometry restraints manager: 4.90 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: 100.22 - 106.97: 329 106.97 - 113.73: 6864 113.73 - 120.48: 4842 120.48 - 127.23: 4744 127.23 - 133.99: 132 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 2.440 nonbonded pdb=" O GLY B 781 " pdb=" NZ LYS B1190 " model vdw 2.211 2.520 nonbonded pdb=" OH TYR B 923 " pdb=" OD2 ASP B 997 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR A 923 " pdb=" OD2 ASP A 997 " model vdw 2.277 2.440 nonbonded pdb=" NH2 ARG B1049 " pdb=" O GLU B1106 " model vdw 2.279 2.520 ... (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 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: 3.590 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: 13.700 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.820 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.870 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.488 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: 1.5252 time to fit residues: 210.2826 Evaluate side-chains 84 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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: 1.9990 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8243 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12516 Z= 0.254 Angle : 0.539 6.813 16911 Z= 0.288 Chirality : 0.042 0.178 1827 Planarity : 0.004 0.046 2157 Dihedral : 4.147 21.233 1671 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.14 % Allowed : 6.29 % Favored : 92.57 % 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: 1.08 (0.22), residues: 1497 helix: 1.77 (0.20), residues: 677 sheet: 0.01 (0.37), residues: 214 loop : -0.13 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1170 HIS 0.004 0.001 HIS B1051 PHE 0.018 0.001 PHE A 559 TYR 0.014 0.001 TYR B 858 ARG 0.012 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 fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.467 Fit side-chains REVERT: A 433 MET cc_start: 0.8019 (ptp) cc_final: 0.7779 (ptp) REVERT: A 916 TYR cc_start: 0.8136 (m-80) cc_final: 0.7916 (m-80) REVERT: A 957 MET cc_start: 0.8907 (tpt) cc_final: 0.8625 (tpt) REVERT: B 433 MET cc_start: 0.7920 (ptp) cc_final: 0.7624 (ptp) REVERT: B 503 LYS cc_start: 0.9187 (tttm) cc_final: 0.8956 (tptp) REVERT: B 684 ARG cc_start: 0.6011 (mtp85) cc_final: 0.5807 (mtp180) REVERT: B 916 TYR cc_start: 0.7724 (m-80) cc_final: 0.7307 (m-80) REVERT: B 973 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7888 (tm-30) outliers start: 15 outliers final: 6 residues processed: 99 average time/residue: 1.4199 time to fit residues: 152.7709 Evaluate side-chains 88 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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 522 THR Chi-restraints excluded: chain B residue 642 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: 0.8980 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 121 optimal weight: 0.0070 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 109 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12516 Z= 0.162 Angle : 0.477 6.550 16911 Z= 0.254 Chirality : 0.040 0.168 1827 Planarity : 0.004 0.044 2157 Dihedral : 3.967 19.706 1671 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.36 % Allowed : 7.35 % 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: 1.07 (0.22), residues: 1497 helix: 1.82 (0.20), residues: 677 sheet: -0.14 (0.37), residues: 218 loop : -0.16 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1170 HIS 0.002 0.001 HIS B 887 PHE 0.013 0.001 PHE A 559 TYR 0.013 0.001 TYR B 858 ARG 0.011 0.000 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 104 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: A 433 MET cc_start: 0.7942 (ptp) cc_final: 0.7687 (ptp) REVERT: A 916 TYR cc_start: 0.8064 (m-80) cc_final: 0.7862 (m-80) REVERT: A 957 MET cc_start: 0.8952 (tpt) cc_final: 0.8717 (tpt) REVERT: A 988 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: B 433 MET cc_start: 0.7849 (ptp) cc_final: 0.7567 (ptp) REVERT: B 503 LYS cc_start: 0.9169 (tttm) cc_final: 0.8936 (tptp) REVERT: B 684 ARG cc_start: 0.5926 (mtp85) cc_final: 0.5612 (mtp180) REVERT: B 916 TYR cc_start: 0.7705 (m-80) cc_final: 0.7286 (m-80) REVERT: B 973 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7839 (tm-30) outliers start: 18 outliers final: 8 residues processed: 92 average time/residue: 1.4852 time to fit residues: 148.7454 Evaluate side-chains 89 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 988 GLU Chi-restraints excluded: chain A residue 1112 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: 0.5980 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12516 Z= 0.292 Angle : 0.535 6.988 16911 Z= 0.282 Chirality : 0.043 0.170 1827 Planarity : 0.004 0.046 2157 Dihedral : 4.207 23.630 1671 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.82 % Allowed : 8.19 % 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: 0.90 (0.22), residues: 1497 helix: 1.68 (0.20), residues: 675 sheet: -0.34 (0.37), residues: 218 loop : -0.19 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B1170 HIS 0.005 0.001 HIS A 752 PHE 0.013 0.001 PHE A 990 TYR 0.018 0.001 TYR B 858 ARG 0.011 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 108 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 433 MET cc_start: 0.7999 (ptp) cc_final: 0.7756 (ptp) REVERT: A 454 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8537 (mmtp) REVERT: A 684 ARG cc_start: 0.6256 (mtp85) cc_final: 0.5923 (mtp180) REVERT: A 957 MET cc_start: 0.9019 (tpt) cc_final: 0.8742 (tpt) REVERT: A 985 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7556 (tpp80) REVERT: A 988 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: B 433 MET cc_start: 0.7896 (ptp) cc_final: 0.7589 (ptp) REVERT: B 454 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8752 (mmtp) REVERT: B 503 LYS cc_start: 0.9165 (tttm) cc_final: 0.8902 (tptp) REVERT: B 684 ARG cc_start: 0.6211 (mtp85) cc_final: 0.5794 (mtp180) REVERT: B 916 TYR cc_start: 0.7715 (m-80) cc_final: 0.6937 (m-80) REVERT: B 973 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7812 (tm-30) outliers start: 24 outliers final: 14 residues processed: 98 average time/residue: 1.4952 time to fit residues: 159.6837 Evaluate side-chains 96 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 988 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS B 981 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2107 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= 0.202 Angle : 0.482 7.579 16911 Z= 0.255 Chirality : 0.041 0.165 1827 Planarity : 0.004 0.043 2157 Dihedral : 4.045 20.885 1671 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.82 % Allowed : 8.79 % Favored : 89.39 % 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: 1.75 (0.20), residues: 675 sheet: -0.43 (0.37), residues: 218 loop : -0.24 (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 0.011 0.001 PHE A 990 TYR 0.016 0.001 TYR B 858 ARG 0.013 0.000 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 107 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.532 Fit side-chains REVERT: A 433 MET cc_start: 0.7913 (ptp) cc_final: 0.7639 (ptp) REVERT: A 454 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8535 (mmmm) REVERT: A 684 ARG cc_start: 0.6275 (mtp85) cc_final: 0.5918 (mtp180) REVERT: A 957 MET cc_start: 0.9039 (tpt) cc_final: 0.8685 (tpt) REVERT: A 973 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 985 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7491 (tpp80) REVERT: A 988 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: B 433 MET cc_start: 0.7845 (ptp) cc_final: 0.7510 (ptp) REVERT: B 454 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8775 (mmtp) REVERT: B 503 LYS cc_start: 0.9167 (tttm) cc_final: 0.8913 (tptp) REVERT: B 684 ARG cc_start: 0.6241 (mtp85) cc_final: 0.5804 (mtp180) REVERT: B 916 TYR cc_start: 0.7851 (m-80) cc_final: 0.7090 (m-80) REVERT: B 973 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7803 (tm-30) outliers start: 24 outliers final: 12 residues processed: 96 average time/residue: 1.4571 time to fit residues: 152.3087 Evaluate side-chains 94 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 803 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 988 GLU 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 801 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: 0.9990 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12516 Z= 0.240 Angle : 0.502 9.256 16911 Z= 0.264 Chirality : 0.041 0.168 1827 Planarity : 0.004 0.049 2157 Dihedral : 4.076 21.636 1671 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.90 % Allowed : 9.40 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1497 helix: 1.76 (0.20), residues: 675 sheet: -0.52 (0.37), residues: 218 loop : -0.22 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1170 HIS 0.003 0.001 HIS A 887 PHE 0.013 0.001 PHE A 559 TYR 0.016 0.001 TYR B 858 ARG 0.012 0.001 ARG B 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 104 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 1.454 Fit side-chains REVERT: A 433 MET cc_start: 0.7920 (ptp) cc_final: 0.7663 (ptp) REVERT: A 684 ARG cc_start: 0.6233 (mtp85) cc_final: 0.5966 (mtp180) REVERT: A 916 TYR cc_start: 0.8045 (m-80) cc_final: 0.7845 (m-80) REVERT: A 929 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8163 (mtp180) REVERT: A 957 MET cc_start: 0.9049 (tpt) cc_final: 0.8709 (tpt) REVERT: A 985 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7455 (tpp80) REVERT: B 433 MET cc_start: 0.7854 (ptp) cc_final: 0.7546 (ptp) REVERT: B 454 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8792 (mmmt) REVERT: B 503 LYS cc_start: 0.9160 (tttm) cc_final: 0.8909 (tptp) REVERT: B 684 ARG cc_start: 0.6255 (mtp85) cc_final: 0.5916 (mtp180) REVERT: B 916 TYR cc_start: 0.7877 (m-80) cc_final: 0.7105 (m-80) REVERT: B 973 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7799 (tm-30) outliers start: 25 outliers final: 13 residues processed: 92 average time/residue: 1.3706 time to fit residues: 137.6917 Evaluate side-chains 90 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 1022 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 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: 0.8980 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12516 Z= 0.231 Angle : 0.509 8.900 16911 Z= 0.264 Chirality : 0.041 0.166 1827 Planarity : 0.004 0.053 2157 Dihedral : 4.071 21.544 1671 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.52 % Allowed : 10.24 % Favored : 88.25 % 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: 0.89 (0.22), residues: 1497 helix: 1.77 (0.20), residues: 675 sheet: -0.55 (0.37), residues: 218 loop : -0.23 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1170 HIS 0.003 0.001 HIS B 887 PHE 0.015 0.001 PHE A 559 TYR 0.017 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 101 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.191 Fit side-chains REVERT: A 433 MET cc_start: 0.7891 (ptp) cc_final: 0.7635 (ptp) REVERT: A 454 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8422 (mmmm) REVERT: A 684 ARG cc_start: 0.6302 (mtp85) cc_final: 0.5953 (mtp180) REVERT: A 973 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 985 ARG cc_start: 0.7600 (tpp80) cc_final: 0.7385 (mpp80) REVERT: B 433 MET cc_start: 0.7869 (ptp) cc_final: 0.7539 (ptp) REVERT: B 503 LYS cc_start: 0.9170 (tttm) cc_final: 0.8922 (tptp) REVERT: B 684 ARG cc_start: 0.6286 (mtp85) cc_final: 0.5918 (mtp180) REVERT: B 916 TYR cc_start: 0.7877 (m-80) cc_final: 0.7115 (m-80) REVERT: B 973 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7776 (tm-30) outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 1.3842 time to fit residues: 140.6991 Evaluate side-chains 93 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 1022 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 801 ILE Chi-restraints excluded: chain B residue 807 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: 0.9980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** A1078 HIS B 981 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12516 Z= 0.251 Angle : 0.521 8.520 16911 Z= 0.271 Chirality : 0.041 0.165 1827 Planarity : 0.004 0.056 2157 Dihedral : 4.117 21.963 1671 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.59 % Allowed : 10.24 % 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: 0.86 (0.22), residues: 1497 helix: 1.74 (0.20), residues: 675 sheet: -0.59 (0.37), residues: 218 loop : -0.25 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 820 HIS 0.004 0.001 HIS B 752 PHE 0.011 0.001 PHE A 990 TYR 0.017 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 102 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.533 Fit side-chains REVERT: A 433 MET cc_start: 0.7886 (ptp) cc_final: 0.7639 (ptp) REVERT: A 454 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8473 (mmmm) REVERT: A 684 ARG cc_start: 0.6346 (mtp85) cc_final: 0.6084 (mtp180) REVERT: A 916 TYR cc_start: 0.7976 (m-80) cc_final: 0.7728 (m-80) REVERT: A 929 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8065 (mtp180) REVERT: B 433 MET cc_start: 0.7880 (ptp) cc_final: 0.7528 (ptp) REVERT: B 454 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8759 (mmmm) REVERT: B 503 LYS cc_start: 0.9177 (tttm) cc_final: 0.8967 (tptp) REVERT: B 684 ARG cc_start: 0.6350 (mtp85) cc_final: 0.6004 (mtp180) REVERT: B 916 TYR cc_start: 0.7835 (m-80) cc_final: 0.7095 (m-80) REVERT: B 973 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7762 (tm-30) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 1.3350 time to fit residues: 137.3231 Evaluate side-chains 93 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 1022 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 801 ILE Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 807 SER 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: 0.9990 chunk 138 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 0.0060 chunk 121 optimal weight: 0.5980 chunk 127 optimal weight: 0.0050 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.4610 ------------------------------------------------------------------------------- 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** A1078 HIS B 981 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2532 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= 0.166 Angle : 0.486 8.688 16911 Z= 0.252 Chirality : 0.040 0.163 1827 Planarity : 0.004 0.059 2157 Dihedral : 3.920 20.722 1671 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.21 % Allowed : 10.84 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1497 helix: 1.86 (0.20), residues: 675 sheet: -0.50 (0.38), residues: 218 loop : -0.21 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.000 HIS B 887 PHE 0.009 0.001 PHE A 559 TYR 0.014 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 98 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.480 Fit side-chains REVERT: A 433 MET cc_start: 0.7823 (ptp) cc_final: 0.7550 (ptp) REVERT: A 454 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8491 (mmmm) REVERT: A 683 ARG cc_start: 0.7259 (mtm-85) cc_final: 0.6968 (mtm-85) REVERT: A 684 ARG cc_start: 0.6298 (mtp85) cc_final: 0.6018 (mtp180) REVERT: A 916 TYR cc_start: 0.7983 (m-80) cc_final: 0.7772 (m-80) REVERT: A 973 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7640 (tm-30) REVERT: B 433 MET cc_start: 0.7786 (ptp) cc_final: 0.7455 (ptp) REVERT: B 454 LYS cc_start: 0.9188 (mmmt) cc_final: 0.8752 (mmmm) REVERT: B 503 LYS cc_start: 0.9182 (tttm) cc_final: 0.8974 (tptp) REVERT: B 684 ARG cc_start: 0.6346 (mtp85) cc_final: 0.6001 (mtp180) REVERT: B 801 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8225 (tp) REVERT: B 916 TYR cc_start: 0.7847 (m-80) cc_final: 0.7501 (m-80) REVERT: B 973 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7771 (tm-30) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 1.4061 time to fit residues: 140.9023 Evaluate side-chains 89 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 1153 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 803 VAL 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: 3.9990 chunk 99 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 0.0470 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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** A1078 HIS B 981 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2573 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= 0.187 Angle : 0.499 8.337 16911 Z= 0.258 Chirality : 0.041 0.252 1827 Planarity : 0.004 0.063 2157 Dihedral : 3.915 20.757 1671 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.99 % Allowed : 11.37 % Favored : 87.64 % 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: 1.75 (0.20), residues: 687 sheet: -0.51 (0.37), residues: 218 loop : -0.15 (0.25), residues: 592 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 B 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 91 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.583 Fit side-chains REVERT: A 433 MET cc_start: 0.7874 (ptp) cc_final: 0.7594 (ptp) REVERT: A 454 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8489 (mmmm) REVERT: A 683 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: A 684 ARG cc_start: 0.6240 (mtp85) cc_final: 0.6021 (mtp180) REVERT: A 916 TYR cc_start: 0.7996 (m-80) cc_final: 0.7781 (m-80) REVERT: B 433 MET cc_start: 0.7817 (ptp) cc_final: 0.7490 (ptp) REVERT: B 454 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8753 (mmmm) REVERT: B 503 LYS cc_start: 0.9178 (tttm) cc_final: 0.8974 (tptp) REVERT: B 683 ARG cc_start: 0.6756 (mtm-85) cc_final: 0.6538 (mtm-85) REVERT: B 684 ARG cc_start: 0.6337 (mtp85) cc_final: 0.6001 (mtp180) REVERT: B 916 TYR cc_start: 0.7841 (m-80) cc_final: 0.7499 (m-80) REVERT: B 973 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7821 (tm-30) outliers start: 13 outliers final: 11 residues processed: 88 average time/residue: 1.3979 time to fit residues: 134.2357 Evaluate side-chains 88 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 1153 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 803 VAL 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: 0.7980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 119 optimal weight: 0.0870 chunk 49 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.2274 ------------------------------------------------------------------------------- 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** B 981 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.071810 restraints weight = 39783.545| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.30 r_work: 0.2879 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12516 Z= 0.137 Angle : 0.474 8.543 16911 Z= 0.244 Chirality : 0.040 0.215 1827 Planarity : 0.004 0.059 2157 Dihedral : 3.722 18.890 1671 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.99 % Allowed : 11.30 % 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: 1.07 (0.22), residues: 1497 helix: 1.95 (0.20), residues: 675 sheet: -0.43 (0.38), residues: 218 loop : -0.20 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.003 0.000 HIS B 887 PHE 0.008 0.001 PHE A 559 TYR 0.011 0.001 TYR B 858 ARG 0.014 0.000 ARG B 929 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.93 seconds wall clock time: 73 minutes 15.04 seconds (4395.04 seconds total)