Starting phenix.real_space_refine on Fri Jul 3 17:10:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2s_44113/07_2026/9b2s_44113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2s_44113/07_2026/9b2s_44113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b2s_44113/07_2026/9b2s_44113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2s_44113/07_2026/9b2s_44113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b2s_44113/07_2026/9b2s_44113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2s_44113/07_2026/9b2s_44113.map" } resolution = 3.01 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= 0.017 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: 5 Type Number sf(0) Gaussians P 314 5.49 5 S 27 5.16 5 C 8771 2.51 5 N 2883 2.21 5 O 3502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15497 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1074 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "K" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2636 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain: "I" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3196 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "J" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3241 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Time building chain proxies: 2.64, per 1000 atoms: 0.17 Number of scatterers: 15497 At special positions: 0 Unit cell: (81.48, 169.75, 137.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 314 15.00 O 3502 8.00 N 2883 7.00 C 8771 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: 1.16 Conformation dependent library (CDL) restraints added in 439.8 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 59.3% alpha, 6.8% beta 145 base pairs and 287 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.700A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.814A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.682A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.131A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.708A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 103 through 121 Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.625A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.621A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.672A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.706A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.666A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.253A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.570A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.519A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.503A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.739A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.559A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 121 Processing helix chain 'K' and resid 475 through 479 Processing helix chain 'K' and resid 480 through 486 Processing helix chain 'K' and resid 532 through 545 Processing helix chain 'K' and resid 546 through 548 No H-bonds generated for 'chain 'K' and resid 546 through 548' Processing helix chain 'K' and resid 570 through 584 Processing helix chain 'K' and resid 621 through 644 Processing helix chain 'K' and resid 707 through 712 removed outlier: 3.969A pdb=" N LEU K 710 " --> pdb=" O ASP K 707 " (cutoff:3.500A) Processing helix chain 'K' and resid 716 through 730 removed outlier: 3.529A pdb=" N ASP K 720 " --> pdb=" O ASP K 716 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR K 722 " --> pdb=" O GLN K 718 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG K 723 " --> pdb=" O PHE K 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 738 through 755 removed outlier: 3.722A pdb=" N VAL K 742 " --> pdb=" O PRO K 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 764 through 781 Processing helix chain 'K' and resid 782 through 784 No H-bonds generated for 'chain 'K' and resid 782 through 784' Processing helix chain 'K' and resid 786 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.957A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.296A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.793A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.229A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.528A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 473 through 474 removed outlier: 5.785A pdb=" N VAL K 473 " --> pdb=" O GLN K 566 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU K 559 " --> pdb=" O GLU K 606 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU K 606 " --> pdb=" O LEU K 559 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER K 561 " --> pdb=" O GLU K 604 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU K 599 " --> pdb=" O ILE K 515 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY K 496 " --> pdb=" O GLU K 492 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU K 492 " --> pdb=" O GLY K 496 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL K 498 " --> pdb=" O ILE K 490 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 520 through 521 Processing sheet with id=AB3, first strand: chain 'K' and resid 610 through 611 Processing sheet with id=AB4, first strand: chain 'K' and resid 664 through 669 Processing sheet with id=AB5, first strand: chain 'K' and resid 693 through 695 514 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 378 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 287 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2899 1.33 - 1.45: 5151 1.45 - 1.57: 7701 1.57 - 1.69: 626 1.69 - 1.81: 44 Bond restraints: 16421 Sorted by residual: bond pdb=" C3' DT J 67 " pdb=" C2' DT J 67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG J 63 " pdb=" C2' DG J 63 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C1' DT I -47 " pdb=" N1 DT I -47 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.76e+00 ... (remaining 16416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 22219 1.69 - 3.38: 1241 3.38 - 5.08: 46 5.08 - 6.77: 6 6.77 - 8.46: 3 Bond angle restraints: 23515 Sorted by residual: angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" O4' DA I -69 " pdb=" C4' DA I -69 " pdb=" C3' DA I -69 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT I -65 " pdb=" C4 DT I -65 " pdb=" O4 DT I -65 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT I 34 " pdb=" C4 DT I 34 " pdb=" O4 DT I 34 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 53 " pdb=" C4 DT I 53 " pdb=" O4 DT I 53 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 ... (remaining 23510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 7476 35.32 - 70.65: 1592 70.65 - 105.97: 11 105.97 - 141.29: 0 141.29 - 176.62: 4 Dihedral angle restraints: 9083 sinusoidal: 5777 harmonic: 3306 Sorted by residual: dihedral pdb=" CG ARG E 2 " pdb=" CD ARG E 2 " pdb=" NE ARG E 2 " pdb=" CZ ARG E 2 " ideal model delta sinusoidal sigma weight residual 90.00 0.19 89.81 2 1.50e+01 4.44e-03 2.13e+01 dihedral pdb=" CA HIS K 647 " pdb=" C HIS K 647 " pdb=" N ARG K 648 " pdb=" CA ARG K 648 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C4' DT I -65 " pdb=" C3' DT I -65 " pdb=" O3' DT I -65 " pdb=" P DC I -64 " ideal model delta sinusoidal sigma weight residual 220.00 43.38 176.62 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 9080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1682 0.039 - 0.078: 694 0.078 - 0.117: 247 0.117 - 0.156: 40 0.156 - 0.195: 4 Chirality restraints: 2667 Sorted by residual: chirality pdb=" CA GLN E 5 " pdb=" N GLN E 5 " pdb=" C GLN E 5 " pdb=" CB GLN E 5 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" C3' DT I -65 " pdb=" C4' DT I -65 " pdb=" O3' DT I -65 " pdb=" C2' DT I -65 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 2664 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C ASP B 24 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP B 24 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN B 25 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 24 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" CG ASP B 24 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP B 24 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 24 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.023 2.00e-02 2.50e+03 9.98e-03 2.74e+00 pdb=" N9 DA I -35 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 485 2.69 - 3.24: 12834 3.24 - 3.79: 25654 3.79 - 4.35: 34720 4.35 - 4.90: 50573 Nonbonded interactions: 124266 Sorted by model distance: nonbonded pdb=" CB ARG E 2 " pdb=" NH1 ARG E 2 " model vdw 2.134 3.520 nonbonded pdb=" OG1 THR K 528 " pdb=" OE1 GLU K 531 " model vdw 2.156 3.040 nonbonded pdb=" NZ LYS K 659 " pdb=" OP1 DC J 55 " model vdw 2.221 3.120 nonbonded pdb=" N GLU B 52 " pdb=" OE1 GLU B 52 " model vdw 2.237 3.120 nonbonded pdb=" O SER K 621 " pdb=" OG1 THR K 624 " model vdw 2.239 3.040 ... (remaining 124261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) selection = chain 'H' } 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: 4.700 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 : 0.007 0.066 16421 Z= 0.572 Angle : 0.757 8.461 23515 Z= 0.644 Chirality : 0.047 0.195 2667 Planarity : 0.004 0.038 1890 Dihedral : 26.765 176.619 6947 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.52 % Allowed : 22.15 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.45 (0.26), residues: 1122 helix: 2.35 (0.21), residues: 629 sheet: 1.04 (0.68), residues: 54 loop : -1.19 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 648 TYR 0.014 0.002 TYR K 580 PHE 0.012 0.001 PHE K 777 TRP 0.007 0.002 TRP K 652 HIS 0.007 0.001 HIS K 778 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.57 (16421) covalent geometry : angle 0.75682 / 0.64 (23515) hydrogen bonds : bond 0.13064 / 8.75 ( 892) hydrogen bonds : angle 4.12469 / 2.95 ( 2256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.364 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 138 average time/residue: 0.1824 time to fit residues: 33.9104 Evaluate side-chains 135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 27 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 5 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079747 restraints weight = 27919.881| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.71 r_work: 0.2936 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16421 Z= 0.164 Angle : 0.622 7.488 23515 Z= 0.365 Chirality : 0.045 0.281 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.258 179.353 4691 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.28 % Allowed : 19.88 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.64 (0.26), residues: 1122 helix: 2.51 (0.21), residues: 641 sheet: 1.17 (0.70), residues: 53 loop : -1.26 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 26 TYR 0.021 0.001 TYR K 739 PHE 0.010 0.001 PHE K 719 TRP 0.007 0.001 TRP K 652 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (16421) covalent geometry : angle 0.62216 / 0.36 (23515) hydrogen bonds : bond 0.06953 / 4.77 ( 892) hydrogen bonds : angle 3.38507 / 2.42 ( 2256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: E 59 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: E 131 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7714 (mtp85) REVERT: K 553 THR cc_start: 0.7420 (m) cc_final: 0.7203 (m) REVERT: K 747 TYR cc_start: 0.8830 (t80) cc_final: 0.8475 (t80) REVERT: K 781 MET cc_start: 0.7190 (ptt) cc_final: 0.6638 (ptt) outliers start: 22 outliers final: 10 residues processed: 152 average time/residue: 0.1834 time to fit residues: 37.4108 Evaluate side-chains 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 748 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.113307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078753 restraints weight = 27996.001| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.71 r_work: 0.2907 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16421 Z= 0.186 Angle : 0.608 7.170 23515 Z= 0.355 Chirality : 0.045 0.284 2667 Planarity : 0.004 0.042 1890 Dihedral : 29.439 178.242 4691 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.11 % Allowed : 19.46 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.69 (0.26), residues: 1122 helix: 2.58 (0.21), residues: 638 sheet: 1.24 (0.69), residues: 53 loop : -1.26 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.016 0.001 TYR K 739 PHE 0.013 0.001 PHE K 495 TRP 0.007 0.001 TRP K 652 HIS 0.004 0.001 HIS K 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (16421) covalent geometry : angle 0.60793 / 0.36 (23515) hydrogen bonds : bond 0.07229 / 4.95 ( 892) hydrogen bonds : angle 3.25307 / 2.33 ( 2256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: C 73 ASN cc_start: 0.8149 (t160) cc_final: 0.7910 (t0) REVERT: E 59 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: E 131 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7657 (mtp85) REVERT: K 553 THR cc_start: 0.7469 (m) cc_final: 0.7243 (m) REVERT: K 747 TYR cc_start: 0.8958 (t80) cc_final: 0.8455 (t80) REVERT: K 781 MET cc_start: 0.7323 (ptt) cc_final: 0.6924 (ptt) outliers start: 30 outliers final: 18 residues processed: 161 average time/residue: 0.1598 time to fit residues: 35.3413 Evaluate side-chains 156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 688 TYR Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 748 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 104 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080212 restraints weight = 28092.904| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.78 r_work: 0.2940 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 16421 Z= 0.145 Angle : 0.596 9.823 23515 Z= 0.346 Chirality : 0.044 0.280 2667 Planarity : 0.004 0.043 1890 Dihedral : 29.401 178.771 4691 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.48 % Allowed : 20.29 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1122 helix: 2.67 (0.21), residues: 638 sheet: 1.29 (0.70), residues: 53 loop : -1.18 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 27 TYR 0.019 0.001 TYR K 739 PHE 0.013 0.001 PHE K 495 TRP 0.004 0.001 TRP K 652 HIS 0.004 0.001 HIS K 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.15 (16421) covalent geometry : angle 0.59593 / 0.35 (23515) hydrogen bonds : bond 0.06438 / 4.42 ( 892) hydrogen bonds : angle 3.19597 / 2.28 ( 2256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8150 (pt0) REVERT: E 59 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8362 (pm20) REVERT: K 553 THR cc_start: 0.7434 (m) cc_final: 0.7210 (m) REVERT: K 781 MET cc_start: 0.7244 (ptt) cc_final: 0.6873 (ptt) outliers start: 24 outliers final: 18 residues processed: 155 average time/residue: 0.1670 time to fit residues: 35.5222 Evaluate side-chains 154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 688 TYR Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 753 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.114794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081144 restraints weight = 28219.199| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.86 r_work: 0.2929 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16421 Z= 0.152 Angle : 0.573 10.873 23515 Z= 0.335 Chirality : 0.042 0.282 2667 Planarity : 0.004 0.041 1890 Dihedral : 29.429 177.972 4691 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.21 % Allowed : 19.57 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1122 helix: 2.75 (0.21), residues: 639 sheet: 1.41 (0.71), residues: 53 loop : -1.12 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 2 TYR 0.018 0.001 TYR K 667 PHE 0.015 0.001 PHE K 495 TRP 0.006 0.001 TRP K 652 HIS 0.004 0.001 HIS K 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (16421) covalent geometry : angle 0.57279 / 0.33 (23515) hydrogen bonds : bond 0.06177 / 4.23 ( 892) hydrogen bonds : angle 3.08188 / 2.20 ( 2256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: E 59 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: E 131 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8571 (mtp85) REVERT: K 553 THR cc_start: 0.7452 (m) cc_final: 0.7232 (m) REVERT: K 722 TYR cc_start: 0.8547 (m-80) cc_final: 0.8263 (m-80) REVERT: K 723 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6069 (mpt-90) REVERT: K 781 MET cc_start: 0.7233 (ptt) cc_final: 0.6937 (ptt) outliers start: 31 outliers final: 20 residues processed: 158 average time/residue: 0.1718 time to fit residues: 37.1770 Evaluate side-chains 156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 688 TYR Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 723 ARG Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 753 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077638 restraints weight = 27867.689| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.80 r_work: 0.2873 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16421 Z= 0.233 Angle : 0.646 8.175 23515 Z= 0.367 Chirality : 0.048 0.283 2667 Planarity : 0.004 0.043 1890 Dihedral : 29.572 175.423 4691 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.73 % Allowed : 19.15 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.67 (0.26), residues: 1122 helix: 2.52 (0.21), residues: 640 sheet: 1.44 (0.70), residues: 53 loop : -1.24 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.012 0.002 TYR K 580 PHE 0.012 0.002 PHE K 495 TRP 0.010 0.002 TRP K 652 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (16421) covalent geometry : angle 0.64629 / 0.37 (23515) hydrogen bonds : bond 0.07986 / 5.49 ( 892) hydrogen bonds : angle 3.24978 / 2.33 ( 2256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: C 73 ASN cc_start: 0.8247 (t0) cc_final: 0.8039 (t0) REVERT: E 59 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8453 (pm20) REVERT: E 131 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7745 (mtp85) REVERT: K 722 TYR cc_start: 0.8551 (m-80) cc_final: 0.8274 (m-80) REVERT: K 723 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6048 (mpt-90) REVERT: K 781 MET cc_start: 0.7422 (ptt) cc_final: 0.7022 (ptt) outliers start: 36 outliers final: 25 residues processed: 163 average time/residue: 0.1688 time to fit residues: 37.9357 Evaluate side-chains 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 723 ARG Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 753 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 123 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.113584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079569 restraints weight = 27644.094| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.75 r_work: 0.2916 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 16421 Z= 0.150 Angle : 0.620 11.840 23515 Z= 0.353 Chirality : 0.045 0.276 2667 Planarity : 0.004 0.041 1890 Dihedral : 29.507 176.049 4691 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.38 % Allowed : 21.22 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.72 (0.26), residues: 1122 helix: 2.55 (0.21), residues: 645 sheet: 1.49 (0.71), residues: 53 loop : -1.25 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 27 TYR 0.025 0.001 TYR K 688 PHE 0.012 0.001 PHE K 495 TRP 0.005 0.001 TRP K 744 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (16421) covalent geometry : angle 0.61971 / 0.35 (23515) hydrogen bonds : bond 0.06831 / 4.70 ( 892) hydrogen bonds : angle 3.21063 / 2.29 ( 2256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: E 59 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: K 722 TYR cc_start: 0.8556 (m-80) cc_final: 0.8254 (m-80) REVERT: K 723 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.5948 (mpt-90) REVERT: K 781 MET cc_start: 0.7350 (ptt) cc_final: 0.6956 (ptt) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.1674 time to fit residues: 35.2160 Evaluate side-chains 156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 723 ARG Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 753 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079558 restraints weight = 28001.267| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.76 r_work: 0.2908 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16421 Z= 0.153 Angle : 0.596 10.400 23515 Z= 0.342 Chirality : 0.044 0.280 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.515 176.630 4691 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.80 % Allowed : 21.01 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.81 (0.26), residues: 1122 helix: 2.62 (0.21), residues: 645 sheet: 1.49 (0.71), residues: 53 loop : -1.21 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.011 0.001 TYR K 688 PHE 0.014 0.001 PHE K 495 TRP 0.006 0.001 TRP K 652 HIS 0.003 0.001 HIS K 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (16421) covalent geometry : angle 0.59571 / 0.34 (23515) hydrogen bonds : bond 0.06783 / 4.66 ( 892) hydrogen bonds : angle 3.12990 / 2.24 ( 2256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: E 59 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8415 (pm20) REVERT: K 722 TYR cc_start: 0.8565 (m-80) cc_final: 0.8262 (m-80) REVERT: K 723 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.6111 (mpt-90) REVERT: K 781 MET cc_start: 0.7366 (ptt) cc_final: 0.6967 (ptt) outliers start: 27 outliers final: 20 residues processed: 155 average time/residue: 0.1631 time to fit residues: 34.7611 Evaluate side-chains 158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 723 ARG Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 753 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 113 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.113714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079620 restraints weight = 27888.744| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.76 r_work: 0.2919 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16421 Z= 0.154 Angle : 0.594 11.335 23515 Z= 0.341 Chirality : 0.044 0.280 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.503 176.349 4691 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.80 % Allowed : 21.01 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.81 (0.26), residues: 1122 helix: 2.62 (0.21), residues: 645 sheet: 1.52 (0.71), residues: 53 loop : -1.20 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 723 TYR 0.014 0.001 TYR K 739 PHE 0.015 0.001 PHE K 495 TRP 0.006 0.001 TRP K 652 HIS 0.004 0.001 HIS K 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (16421) covalent geometry : angle 0.59445 / 0.34 (23515) hydrogen bonds : bond 0.06671 / 4.58 ( 892) hydrogen bonds : angle 3.11122 / 2.22 ( 2256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: C 73 ASN cc_start: 0.7987 (t160) cc_final: 0.7779 (t0) REVERT: E 59 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: K 722 TYR cc_start: 0.8571 (m-80) cc_final: 0.8260 (m-80) REVERT: K 723 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6109 (mpt-90) REVERT: K 781 MET cc_start: 0.7354 (ptt) cc_final: 0.6973 (ptt) outliers start: 27 outliers final: 22 residues processed: 156 average time/residue: 0.1672 time to fit residues: 35.9245 Evaluate side-chains 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 502 ILE Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 723 ARG Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 753 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 88 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 64 optimal weight: 0.0060 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 0.0010 overall best weight: 1.1006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.113916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079711 restraints weight = 28004.509| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.74 r_work: 0.2934 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16421 Z= 0.155 Angle : 0.586 11.336 23515 Z= 0.337 Chirality : 0.043 0.279 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.501 176.140 4691 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.69 % Allowed : 20.91 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.87 (0.26), residues: 1122 helix: 2.67 (0.21), residues: 645 sheet: 1.50 (0.71), residues: 53 loop : -1.17 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 27 TYR 0.011 0.001 TYR K 739 PHE 0.014 0.001 PHE K 495 TRP 0.007 0.001 TRP K 652 HIS 0.005 0.001 HIS K 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (16421) covalent geometry : angle 0.58604 / 0.34 (23515) hydrogen bonds : bond 0.06486 / 4.45 ( 892) hydrogen bonds : angle 3.06943 / 2.19 ( 2256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: E 59 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: E 131 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7694 (mtp85) REVERT: K 722 TYR cc_start: 0.8544 (m-80) cc_final: 0.8250 (m-80) REVERT: K 723 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6113 (mpt-90) REVERT: K 781 MET cc_start: 0.7344 (ptt) cc_final: 0.6965 (ptt) outliers start: 26 outliers final: 22 residues processed: 157 average time/residue: 0.1650 time to fit residues: 35.6794 Evaluate side-chains 162 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 500 GLN Chi-restraints excluded: chain K residue 502 ILE Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 723 ARG Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 753 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 99 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078569 restraints weight = 27669.620| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.76 r_work: 0.2886 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16421 Z= 0.204 Angle : 0.621 11.043 23515 Z= 0.353 Chirality : 0.046 0.278 2667 Planarity : 0.004 0.041 1890 Dihedral : 29.571 174.516 4691 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.69 % Allowed : 20.91 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.72 (0.26), residues: 1122 helix: 2.55 (0.21), residues: 646 sheet: 1.51 (0.71), residues: 53 loop : -1.26 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 27 TYR 0.011 0.001 TYR D 37 PHE 0.012 0.001 PHE K 495 TRP 0.009 0.001 TRP K 652 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (16421) covalent geometry : angle 0.62133 / 0.35 (23515) hydrogen bonds : bond 0.07360 / 5.05 ( 892) hydrogen bonds : angle 3.14869 / 2.25 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.33 seconds wall clock time: 81 minutes 3.93 seconds (4863.93 seconds total)