Starting phenix.real_space_refine on Sat Aug 23 13:07:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9z_36120/08_2025/8j9z_36120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9z_36120/08_2025/8j9z_36120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j9z_36120/08_2025/8j9z_36120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9z_36120/08_2025/8j9z_36120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j9z_36120/08_2025/8j9z_36120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9z_36120/08_2025/8j9z_36120.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.046 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 7818 2.51 5 N 2086 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12154 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Chain: "B" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Time building chain proxies: 2.46, per 1000 atoms: 0.20 Number of scatterers: 12154 At special positions: 0 Unit cell: (124.45, 116.85, 114, 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 2200 8.00 N 2086 7.00 C 7818 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: 0.74 Conformation dependent library (CDL) restraints added in 476.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 52.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.859A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.904A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.617A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.566A pdb=" N ARG A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.820A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 806 through 814 removed outlier: 4.215A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.627A pdb=" N TRP A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 959 removed outlier: 4.114A pdb=" N PHE A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.623A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.828A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1081 through 1093 removed outlier: 3.626A pdb=" N ALA A1085 " --> pdb=" O ASP A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1117 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.793A pdb=" N LEU A1126 " --> pdb=" O TYR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1133 Processing helix chain 'A' and resid 1134 through 1160 removed outlier: 3.536A 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 428 through 431 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.859A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.904A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.616A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 656 through 664 removed outlier: 3.566A pdb=" N ARG B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.820A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 806 through 814 removed outlier: 4.216A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 removed outlier: 3.626A pdb=" N TRP B 820 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 953 through 959 removed outlier: 4.113A pdb=" N PHE B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.623A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.829A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1093 removed outlier: 3.625A pdb=" N ALA B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1117 Processing helix chain 'B' and resid 1122 through 1127 removed outlier: 3.793A pdb=" N LEU B1126 " --> pdb=" O TYR B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1133 Processing helix chain 'B' and resid 1134 through 1160 removed outlier: 3.536A pdb=" N GLN B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 419 removed outlier: 5.392A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.752A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.010A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.503A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 418 through 419 removed outlier: 5.392A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.752A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 849 through 850 Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB6, first strand: chain 'B' and resid 922 through 925 removed outlier: 6.011A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1013 through 1016 removed outlier: 4.503A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1728 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: 1.82 Time building geometry restraints manager: 0.96 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: 3916 1.34 - 1.46: 2499 1.46 - 1.58: 5953 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12446 Sorted by residual: bond pdb=" CB PRO A1096 " pdb=" CG PRO A1096 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.67e+00 bond pdb=" CB PRO B1096 " pdb=" CG PRO B1096 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.62e+00 bond pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.11e-01 bond pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.84e-01 bond pdb=" CA LEU A1036 " pdb=" C LEU A1036 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.26e-01 ... (remaining 12441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 16452 1.10 - 2.19: 257 2.19 - 3.29: 87 3.29 - 4.39: 13 4.39 - 5.48: 7 Bond angle restraints: 16816 Sorted by residual: angle pdb=" CA GLU B 524 " pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " ideal model delta sigma weight residual 114.10 118.92 -4.82 2.00e+00 2.50e-01 5.82e+00 angle pdb=" CA GLU A 524 " pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " ideal model delta sigma weight residual 114.10 118.90 -4.80 2.00e+00 2.50e-01 5.75e+00 angle pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " pdb=" CD GLU A 524 " ideal model delta sigma weight residual 112.60 116.21 -3.61 1.70e+00 3.46e-01 4.51e+00 angle pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " pdb=" CD GLU B 524 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.70e+00 3.46e-01 4.45e+00 angle pdb=" CA PRO A1096 " pdb=" N PRO A1096 " pdb=" CD PRO A1096 " ideal model delta sigma weight residual 112.00 109.52 2.48 1.40e+00 5.10e-01 3.15e+00 ... (remaining 16811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6476 17.85 - 35.71: 732 35.71 - 53.56: 222 53.56 - 71.42: 26 71.42 - 89.27: 18 Dihedral angle restraints: 7474 sinusoidal: 3088 harmonic: 4386 Sorted by residual: dihedral pdb=" CB GLU B 658 " pdb=" CG GLU B 658 " pdb=" CD GLU B 658 " pdb=" OE1 GLU B 658 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 658 " pdb=" CG GLU A 658 " pdb=" CD GLU A 658 " pdb=" OE1 GLU A 658 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 970 " pdb=" CG GLU B 970 " pdb=" CD GLU B 970 " pdb=" OE1 GLU B 970 " ideal model delta sinusoidal sigma weight residual 0.00 -88.51 88.51 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1105 0.026 - 0.053: 463 0.053 - 0.079: 158 0.079 - 0.105: 65 0.105 - 0.132: 29 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA ILE B 707 " pdb=" N ILE B 707 " pdb=" C ILE B 707 " pdb=" CB ILE B 707 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 707 " pdb=" N ILE A 707 " pdb=" C ILE A 707 " pdb=" CB ILE A 707 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE A 780 " pdb=" N ILE A 780 " pdb=" C ILE A 780 " pdb=" CB ILE A 780 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1817 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 669 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO A 670 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 669 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 670 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 524 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" CD GLU B 524 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU B 524 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 524 " 0.010 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 349 2.72 - 3.27: 11554 3.27 - 3.81: 19877 3.81 - 4.36: 24111 4.36 - 4.90: 42538 Nonbonded interactions: 98429 Sorted by model distance: nonbonded pdb=" NH2 ARG B1049 " pdb=" O PRO B1105 " model vdw 2.177 3.120 nonbonded pdb=" NH2 ARG A1049 " pdb=" O PRO A1105 " model vdw 2.177 3.120 nonbonded pdb=" O VAL B 838 " pdb=" NH1 ARG B1039 " model vdw 2.250 3.120 nonbonded pdb=" O VAL A 838 " pdb=" NH1 ARG A1039 " model vdw 2.251 3.120 nonbonded pdb=" OD2 ASP A 818 " pdb=" NH2 ARG A1039 " model vdw 2.254 3.120 ... (remaining 98424 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.960 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.002 0.082 12446 Z= 0.094 Angle : 0.411 5.482 16816 Z= 0.220 Chirality : 0.037 0.132 1820 Planarity : 0.004 0.081 2142 Dihedral : 16.682 89.271 4662 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.15 % Allowed : 18.02 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.23), residues: 1486 helix: 2.22 (0.20), residues: 704 sheet: -1.16 (0.34), residues: 230 loop : 0.11 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 912 TYR 0.012 0.001 TYR A 888 PHE 0.010 0.001 PHE A 649 TRP 0.007 0.001 TRP B1189 HIS 0.002 0.000 HIS B 883 Details of bonding type rmsd covalent geometry : bond 0.00227 (12446) covalent geometry : angle 0.41132 (16816) hydrogen bonds : bond 0.11760 ( 606) hydrogen bonds : angle 5.60179 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.463 Fit side-chains REVERT: A 856 TRP cc_start: 0.7409 (m100) cc_final: 0.7134 (m100) REVERT: B 503 LYS cc_start: 0.7053 (tppt) cc_final: 0.6495 (ttmm) REVERT: B 701 ASP cc_start: 0.8363 (t70) cc_final: 0.8125 (t0) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.1038 time to fit residues: 21.8966 Evaluate side-chains 133 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.176833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132249 restraints weight = 13145.460| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.00 r_work: 0.3278 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12446 Z= 0.203 Angle : 0.507 5.901 16816 Z= 0.267 Chirality : 0.041 0.143 1820 Planarity : 0.004 0.060 2142 Dihedral : 3.611 15.537 1662 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.06 % Allowed : 17.56 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.23), residues: 1486 helix: 2.08 (0.20), residues: 688 sheet: -0.80 (0.37), residues: 192 loop : -0.11 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1039 TYR 0.014 0.002 TYR B 888 PHE 0.013 0.002 PHE B1191 TRP 0.010 0.001 TRP B1189 HIS 0.005 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00502 (12446) covalent geometry : angle 0.50747 (16816) hydrogen bonds : bond 0.03896 ( 606) hydrogen bonds : angle 4.64015 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.326 Fit side-chains REVERT: A 682 VAL cc_start: 0.8372 (m) cc_final: 0.8123 (p) REVERT: B 521 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8464 (ttmm) REVERT: B 542 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7417 (pp) REVERT: B 682 VAL cc_start: 0.8560 (m) cc_final: 0.8301 (p) REVERT: B 878 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8176 (ptpp) outliers start: 27 outliers final: 15 residues processed: 158 average time/residue: 0.1032 time to fit residues: 23.2698 Evaluate side-chains 150 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.178611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135673 restraints weight = 13214.227| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.12 r_work: 0.3293 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12446 Z= 0.124 Angle : 0.433 5.501 16816 Z= 0.228 Chirality : 0.039 0.134 1820 Planarity : 0.004 0.050 2142 Dihedral : 3.458 14.283 1662 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.75 % Allowed : 16.95 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.23), residues: 1486 helix: 2.13 (0.20), residues: 694 sheet: -1.08 (0.36), residues: 212 loop : 0.09 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 912 TYR 0.016 0.001 TYR A 888 PHE 0.009 0.001 PHE A 710 TRP 0.010 0.001 TRP A1189 HIS 0.003 0.001 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00300 (12446) covalent geometry : angle 0.43310 (16816) hydrogen bonds : bond 0.03362 ( 606) hydrogen bonds : angle 4.40130 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 1156 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7524 (tp30) REVERT: B 542 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7717 (pp) REVERT: B 682 VAL cc_start: 0.8420 (m) cc_final: 0.8165 (p) REVERT: B 878 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8166 (ptpp) REVERT: B 962 GLU cc_start: 0.7927 (tt0) cc_final: 0.7727 (tt0) REVERT: B 1048 MET cc_start: 0.8850 (mtp) cc_final: 0.8498 (mtp) outliers start: 36 outliers final: 21 residues processed: 164 average time/residue: 0.0995 time to fit residues: 23.4572 Evaluate side-chains 153 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN A 892 HIS B 880 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132049 restraints weight = 13158.251| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.20 r_work: 0.3248 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12446 Z= 0.183 Angle : 0.483 5.367 16816 Z= 0.253 Chirality : 0.040 0.143 1820 Planarity : 0.004 0.044 2142 Dihedral : 3.667 15.181 1662 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.28 % Allowed : 17.10 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.23), residues: 1486 helix: 2.03 (0.20), residues: 682 sheet: -0.91 (0.37), residues: 192 loop : -0.24 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 912 TYR 0.015 0.001 TYR A 888 PHE 0.010 0.001 PHE B1191 TRP 0.010 0.001 TRP A1189 HIS 0.004 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00454 (12446) covalent geometry : angle 0.48272 (16816) hydrogen bonds : bond 0.03711 ( 606) hydrogen bonds : angle 4.43204 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.481 Fit side-chains REVERT: A 927 GLU cc_start: 0.7645 (tp30) cc_final: 0.7382 (mm-30) REVERT: A 1156 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7536 (tp30) REVERT: B 521 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8419 (ttmm) REVERT: B 682 VAL cc_start: 0.8349 (m) cc_final: 0.8090 (p) REVERT: B 701 ASP cc_start: 0.8445 (t70) cc_final: 0.8127 (t0) REVERT: B 878 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8189 (ptpp) REVERT: B 962 GLU cc_start: 0.7902 (tt0) cc_final: 0.7636 (tt0) REVERT: B 1048 MET cc_start: 0.8823 (mtp) cc_final: 0.8503 (mtp) REVERT: B 1156 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7498 (tt0) outliers start: 43 outliers final: 30 residues processed: 169 average time/residue: 0.0953 time to fit residues: 23.6919 Evaluate side-chains 162 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 18 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.177046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133771 restraints weight = 13199.558| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.17 r_work: 0.3280 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12446 Z= 0.129 Angle : 0.446 6.155 16816 Z= 0.233 Chirality : 0.039 0.137 1820 Planarity : 0.004 0.042 2142 Dihedral : 3.536 14.428 1662 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.05 % Allowed : 17.56 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.23), residues: 1486 helix: 2.12 (0.20), residues: 694 sheet: -0.93 (0.37), residues: 192 loop : -0.15 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 912 TYR 0.009 0.001 TYR B 946 PHE 0.010 0.001 PHE B 710 TRP 0.011 0.001 TRP B1189 HIS 0.003 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00317 (12446) covalent geometry : angle 0.44570 (16816) hydrogen bonds : bond 0.03308 ( 606) hydrogen bonds : angle 4.30776 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.367 Fit side-chains REVERT: A 441 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8167 (p) REVERT: A 892 HIS cc_start: 0.6887 (m-70) cc_final: 0.6634 (m170) REVERT: A 927 GLU cc_start: 0.7735 (tp30) cc_final: 0.7428 (mm-30) REVERT: A 1156 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: B 521 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8426 (ttmm) REVERT: B 682 VAL cc_start: 0.8306 (m) cc_final: 0.8068 (p) REVERT: B 878 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8218 (ptpp) REVERT: B 962 GLU cc_start: 0.8054 (tt0) cc_final: 0.7795 (tt0) REVERT: B 1048 MET cc_start: 0.8918 (mtp) cc_final: 0.8628 (mtp) REVERT: B 1156 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7571 (tt0) outliers start: 40 outliers final: 28 residues processed: 165 average time/residue: 0.0925 time to fit residues: 22.8533 Evaluate side-chains 158 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 147 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.0570 chunk 101 optimal weight: 0.8980 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.179218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135406 restraints weight = 13214.145| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.23 r_work: 0.3338 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12446 Z= 0.092 Angle : 0.415 6.278 16816 Z= 0.218 Chirality : 0.037 0.135 1820 Planarity : 0.003 0.040 2142 Dihedral : 3.354 13.481 1662 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.44 % Allowed : 18.17 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.23), residues: 1486 helix: 2.13 (0.20), residues: 706 sheet: -1.14 (0.36), residues: 212 loop : -0.00 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 912 TYR 0.011 0.001 TYR A 946 PHE 0.010 0.001 PHE B 710 TRP 0.010 0.001 TRP B1189 HIS 0.003 0.000 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00213 (12446) covalent geometry : angle 0.41542 (16816) hydrogen bonds : bond 0.02926 ( 606) hydrogen bonds : angle 4.14975 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 892 HIS cc_start: 0.6883 (m-70) cc_final: 0.6572 (m170) REVERT: A 1156 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: B 441 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.8110 (p) REVERT: B 521 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8380 (ttmm) REVERT: B 878 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8267 (ptpp) REVERT: B 927 GLU cc_start: 0.8015 (tp30) cc_final: 0.7720 (mm-30) REVERT: B 962 GLU cc_start: 0.8022 (tt0) cc_final: 0.7776 (tt0) REVERT: B 1048 MET cc_start: 0.8902 (mtp) cc_final: 0.8613 (mtp) REVERT: B 1156 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7559 (tt0) outliers start: 32 outliers final: 20 residues processed: 153 average time/residue: 0.0948 time to fit residues: 21.6490 Evaluate side-chains 156 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.178427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134837 restraints weight = 13077.882| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.42 r_work: 0.3344 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12446 Z= 0.109 Angle : 0.430 6.348 16816 Z= 0.224 Chirality : 0.038 0.138 1820 Planarity : 0.003 0.038 2142 Dihedral : 3.354 12.884 1662 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.67 % Allowed : 18.09 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.23), residues: 1486 helix: 2.12 (0.20), residues: 706 sheet: -1.12 (0.36), residues: 212 loop : -0.02 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 912 TYR 0.010 0.001 TYR A 946 PHE 0.010 0.001 PHE B 710 TRP 0.011 0.001 TRP B1189 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00265 (12446) covalent geometry : angle 0.42980 (16816) hydrogen bonds : bond 0.03020 ( 606) hydrogen bonds : angle 4.12078 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 441 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8094 (p) REVERT: A 736 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7322 (mtm180) REVERT: A 1156 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: B 441 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8108 (p) REVERT: B 521 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8524 (ttmm) REVERT: B 736 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7319 (mtm180) REVERT: B 878 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8220 (ptpp) REVERT: B 927 GLU cc_start: 0.7973 (tp30) cc_final: 0.7687 (mm-30) REVERT: B 962 GLU cc_start: 0.8010 (tt0) cc_final: 0.7761 (tt0) REVERT: B 1048 MET cc_start: 0.8901 (mtp) cc_final: 0.8622 (mtp) REVERT: B 1156 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7528 (tt0) outliers start: 35 outliers final: 26 residues processed: 159 average time/residue: 0.1082 time to fit residues: 24.7857 Evaluate side-chains 158 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 736 ARG Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 123 optimal weight: 0.1980 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.177637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133804 restraints weight = 13082.772| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.20 r_work: 0.3318 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12446 Z= 0.125 Angle : 0.441 5.705 16816 Z= 0.232 Chirality : 0.038 0.140 1820 Planarity : 0.003 0.037 2142 Dihedral : 3.403 13.333 1662 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.90 % Allowed : 17.71 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.23), residues: 1486 helix: 2.09 (0.20), residues: 706 sheet: -1.18 (0.35), residues: 218 loop : -0.04 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 912 TYR 0.009 0.001 TYR A 946 PHE 0.010 0.001 PHE B 710 TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00308 (12446) covalent geometry : angle 0.44096 (16816) hydrogen bonds : bond 0.03149 ( 606) hydrogen bonds : angle 4.15963 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 441 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 1156 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: B 441 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 521 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8522 (ttmm) REVERT: B 878 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8243 (ptpp) REVERT: B 891 LYS cc_start: 0.7944 (tptp) cc_final: 0.7732 (tptp) REVERT: B 927 GLU cc_start: 0.7940 (tp30) cc_final: 0.7658 (mm-30) REVERT: B 962 GLU cc_start: 0.8042 (tt0) cc_final: 0.7792 (tt0) REVERT: B 1048 MET cc_start: 0.8900 (mtp) cc_final: 0.8634 (mtp) REVERT: B 1156 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7529 (tt0) outliers start: 38 outliers final: 25 residues processed: 155 average time/residue: 0.1004 time to fit residues: 22.9868 Evaluate side-chains 155 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 64 optimal weight: 4.9990 chunk 111 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.178631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135108 restraints weight = 13136.275| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.19 r_work: 0.3329 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12446 Z= 0.106 Angle : 0.436 6.597 16816 Z= 0.226 Chirality : 0.038 0.135 1820 Planarity : 0.003 0.037 2142 Dihedral : 3.341 12.961 1662 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.67 % Allowed : 17.79 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.23), residues: 1486 helix: 2.14 (0.20), residues: 706 sheet: -1.17 (0.35), residues: 218 loop : 0.02 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 912 TYR 0.010 0.001 TYR A 946 PHE 0.010 0.001 PHE B 710 TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00255 (12446) covalent geometry : angle 0.43579 (16816) hydrogen bonds : bond 0.02987 ( 606) hydrogen bonds : angle 4.10802 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 441 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8158 (p) REVERT: A 736 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7335 (mtm180) REVERT: A 1156 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7527 (tp30) REVERT: B 441 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8145 (p) REVERT: B 521 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8529 (ttmm) REVERT: B 736 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7339 (mtm180) REVERT: B 878 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8239 (ptpp) REVERT: B 962 GLU cc_start: 0.8023 (tt0) cc_final: 0.7777 (tt0) REVERT: B 1048 MET cc_start: 0.8896 (mtp) cc_final: 0.8635 (mtp) REVERT: B 1156 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7531 (tt0) outliers start: 35 outliers final: 24 residues processed: 154 average time/residue: 0.1218 time to fit residues: 27.1568 Evaluate side-chains 153 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 736 ARG Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.178493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135022 restraints weight = 13128.239| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.16 r_work: 0.3323 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12446 Z= 0.108 Angle : 0.435 6.689 16816 Z= 0.229 Chirality : 0.038 0.137 1820 Planarity : 0.003 0.037 2142 Dihedral : 3.333 13.027 1662 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 18.24 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.23), residues: 1486 helix: 2.14 (0.20), residues: 706 sheet: -1.21 (0.35), residues: 218 loop : 0.04 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 912 TYR 0.010 0.001 TYR A 946 PHE 0.010 0.001 PHE B 710 TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00261 (12446) covalent geometry : angle 0.43538 (16816) hydrogen bonds : bond 0.02985 ( 606) hydrogen bonds : angle 4.09362 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 441 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 736 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7364 (mtm180) REVERT: A 1156 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7539 (tp30) REVERT: B 441 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8153 (p) REVERT: B 521 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8535 (ttmm) REVERT: B 878 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8244 (ptpp) REVERT: B 891 LYS cc_start: 0.7931 (tptp) cc_final: 0.7707 (tptp) REVERT: B 962 GLU cc_start: 0.8056 (tt0) cc_final: 0.7815 (tt0) REVERT: B 1048 MET cc_start: 0.8900 (mtp) cc_final: 0.8642 (mtp) REVERT: B 1156 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7534 (tt0) outliers start: 31 outliers final: 25 residues processed: 152 average time/residue: 0.1101 time to fit residues: 24.0402 Evaluate side-chains 155 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.0030 chunk 129 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.174507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133033 restraints weight = 12971.464| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.01 r_work: 0.3347 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12446 Z= 0.105 Angle : 0.432 6.707 16816 Z= 0.227 Chirality : 0.038 0.136 1820 Planarity : 0.003 0.037 2142 Dihedral : 3.309 12.849 1662 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.52 % Allowed : 18.17 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.23), residues: 1486 helix: 2.15 (0.20), residues: 706 sheet: -1.20 (0.35), residues: 218 loop : 0.05 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 912 TYR 0.010 0.001 TYR A 946 PHE 0.010 0.001 PHE B 710 TRP 0.010 0.001 TRP B1189 HIS 0.003 0.000 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00254 (12446) covalent geometry : angle 0.43218 (16816) hydrogen bonds : bond 0.02950 ( 606) hydrogen bonds : angle 4.08296 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2808.63 seconds wall clock time: 48 minutes 46.30 seconds (2926.30 seconds total)