Starting phenix.real_space_refine on Fri Jun 13 16:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2s_44113/06_2025/9b2s_44113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2s_44113/06_2025/9b2s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2s_44113/06_2025/9b2s_44113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2s_44113/06_2025/9b2s_44113.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2s_44113/06_2025/9b2s_44113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2s_44113/06_2025/9b2s_44113.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.42, per 1000 atoms: 0.67 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: 3.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 7.12 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: 7.43 Time building geometry restraints manager: 4.26 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=" N VAL E 35 " pdb=" CA VAL E 35 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.18e-02 7.18e+03 9.17e+00 bond pdb=" N ARG E 26 " pdb=" CA ARG E 26 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.75e+00 bond pdb=" N THR E 22 " pdb=" CA THR E 22 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.54e+00 bond pdb=" N GLN E 19 " pdb=" CA GLN E 19 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.18e-02 7.18e+03 7.38e+00 bond pdb=" N THR E 32 " pdb=" CA THR E 32 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.22e+00 ... (remaining 16416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 22852 1.69 - 3.38: 614 3.38 - 5.08: 40 5.08 - 6.77: 6 6.77 - 8.46: 3 Bond angle restraints: 23515 Sorted by residual: angle pdb=" N ASP B 24 " pdb=" CA ASP B 24 " pdb=" C ASP B 24 " ideal model delta sigma weight residual 110.91 105.84 5.07 1.17e+00 7.31e-01 1.88e+01 angle pdb=" N THR E 22 " pdb=" CA THR E 22 " pdb=" C THR E 22 " ideal model delta sigma weight residual 114.16 108.67 5.49 1.48e+00 4.57e-01 1.38e+01 angle pdb=" C SER E 28 " pdb=" CA SER E 28 " pdb=" CB SER E 28 " ideal model delta sigma weight residual 115.89 111.41 4.48 1.32e+00 5.74e-01 1.15e+01 angle pdb=" CA ALA E 24 " pdb=" C ALA E 24 " pdb=" O ALA E 24 " ideal model delta sigma weight residual 122.41 118.34 4.07 1.21e+00 6.83e-01 1.13e+01 angle pdb=" CA LYS E 27 " pdb=" C LYS E 27 " pdb=" O LYS E 27 " ideal model delta sigma weight residual 121.51 117.96 3.55 1.12e+00 7.97e-01 1.00e+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: 1932 0.039 - 0.078: 590 0.078 - 0.117: 126 0.117 - 0.156: 17 0.156 - 0.195: 2 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=" CA VAL E 35 " pdb=" N VAL E 35 " pdb=" C VAL E 35 " pdb=" CB VAL E 35 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA PRO D 47 " pdb=" N PRO D 47 " pdb=" C PRO D 47 " pdb=" CB PRO D 47 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.45e-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: 5.190 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 43.030 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 : 0.005 0.066 16421 Z= 0.256 Angle : 0.618 8.461 23515 Z= 0.374 Chirality : 0.038 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (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 TRP 0.007 0.002 TRP K 652 HIS 0.007 0.001 HIS K 778 PHE 0.012 0.001 PHE K 777 TYR 0.014 0.002 TYR K 580 ARG 0.003 0.000 ARG K 648 Details of bonding type rmsd hydrogen bonds : bond 0.13064 ( 892) hydrogen bonds : angle 4.12469 ( 2256) covalent geometry : bond 0.00527 (16421) covalent geometry : angle 0.61800 (23515) *********************** 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 : 1.381 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 138 average time/residue: 0.4147 time to fit residues: 76.0236 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 : 1.427 ------------------------------------------------------------------------------- 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 117 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.113655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079336 restraints weight = 27982.502| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.80 r_work: 0.2912 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16421 Z= 0.196 Angle : 0.560 7.283 23515 Z= 0.330 Chirality : 0.036 0.128 2667 Planarity : 0.004 0.039 1890 Dihedral : 29.036 177.978 4691 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.69 % Allowed : 19.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1122 helix: 2.54 (0.21), residues: 638 sheet: 1.21 (0.70), residues: 53 loop : -1.18 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 652 HIS 0.003 0.001 HIS K 794 PHE 0.010 0.001 PHE B 61 TYR 0.017 0.001 TYR K 739 ARG 0.005 0.000 ARG E 2 Details of bonding type rmsd hydrogen bonds : bond 0.06634 ( 892) hydrogen bonds : angle 3.26928 ( 2256) covalent geometry : bond 0.00434 (16421) covalent geometry : angle 0.56004 (23515) *********************** 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 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: E 59 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: E 131 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: K 747 TYR cc_start: 0.8904 (t80) cc_final: 0.8453 (t80) REVERT: K 781 MET cc_start: 0.7270 (ptt) cc_final: 0.6843 (ptt) outliers start: 26 outliers final: 14 residues processed: 158 average time/residue: 0.3633 time to fit residues: 77.5943 Evaluate side-chains 155 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 44 GLN 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 H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 624 THR 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 82 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.114730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081348 restraints weight = 27888.881| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.58 r_work: 0.2929 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16421 Z= 0.176 Angle : 0.531 7.032 23515 Z= 0.314 Chirality : 0.035 0.127 2667 Planarity : 0.004 0.038 1890 Dihedral : 28.954 176.705 4691 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.69 % Allowed : 19.77 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1122 helix: 2.63 (0.21), residues: 642 sheet: 1.37 (0.70), residues: 53 loop : -1.19 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 652 HIS 0.005 0.001 HIS K 651 PHE 0.013 0.001 PHE K 495 TYR 0.009 0.001 TYR D 37 ARG 0.002 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05825 ( 892) hydrogen bonds : angle 3.00719 ( 2256) covalent geometry : bond 0.00387 (16421) covalent geometry : angle 0.53062 (23515) *********************** 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 166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: E 59 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: K 553 THR cc_start: 0.7358 (m) cc_final: 0.7147 (m) REVERT: K 747 TYR cc_start: 0.9081 (t80) cc_final: 0.8391 (t80) REVERT: K 781 MET cc_start: 0.7233 (ptt) cc_final: 0.6927 (ptt) outliers start: 26 outliers final: 16 residues processed: 157 average time/residue: 0.3558 time to fit residues: 76.5305 Evaluate side-chains 156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN 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 748 LEU Chi-restraints excluded: chain K residue 753 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 99 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.115412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081214 restraints weight = 27826.169| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.78 r_work: 0.2967 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16421 Z= 0.151 Angle : 0.524 8.188 23515 Z= 0.309 Chirality : 0.034 0.126 2667 Planarity : 0.003 0.038 1890 Dihedral : 28.937 177.151 4691 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.69 % Allowed : 20.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.26), residues: 1122 helix: 2.73 (0.21), residues: 641 sheet: 1.48 (0.72), residues: 53 loop : -1.13 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 652 HIS 0.004 0.001 HIS K 651 PHE 0.009 0.001 PHE K 495 TYR 0.009 0.001 TYR K 580 ARG 0.001 0.000 ARG E 8 Details of bonding type rmsd hydrogen bonds : bond 0.05447 ( 892) hydrogen bonds : angle 2.96256 ( 2256) covalent geometry : bond 0.00316 (16421) covalent geometry : angle 0.52382 (23515) *********************** 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: 26 poor density : 135 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: E 59 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: E 131 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: K 723 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5868 (mpt-90) outliers start: 26 outliers final: 15 residues processed: 152 average time/residue: 0.3634 time to fit residues: 74.6526 Evaluate side-chains 152 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 76 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 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 710 LEU Chi-restraints excluded: chain K residue 723 ARG Chi-restraints excluded: chain K residue 748 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.114890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080306 restraints weight = 28212.615| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.84 r_work: 0.2959 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16421 Z= 0.170 Angle : 0.521 8.830 23515 Z= 0.309 Chirality : 0.034 0.126 2667 Planarity : 0.004 0.038 1890 Dihedral : 28.938 175.910 4691 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.90 % Allowed : 20.08 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.26), residues: 1122 helix: 2.76 (0.21), residues: 642 sheet: 1.64 (0.72), residues: 52 loop : -1.12 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 652 HIS 0.004 0.001 HIS K 651 PHE 0.013 0.001 PHE K 777 TYR 0.012 0.001 TYR K 722 ARG 0.002 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 892) hydrogen bonds : angle 2.92468 ( 2256) covalent geometry : bond 0.00371 (16421) covalent geometry : angle 0.52140 (23515) *********************** 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 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: E 59 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: E 131 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8604 (mtp85) REVERT: K 722 TYR cc_start: 0.8591 (m-80) cc_final: 0.8311 (m-80) REVERT: K 723 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6211 (mpt-90) outliers start: 28 outliers final: 18 residues processed: 158 average time/residue: 0.3714 time to fit residues: 79.5449 Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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 603 LEU 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 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 33 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 78 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.112974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.078759 restraints weight = 27951.862| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.81 r_work: 0.2891 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16421 Z= 0.218 Angle : 0.559 10.171 23515 Z= 0.329 Chirality : 0.037 0.133 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.046 173.974 4691 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.31 % Allowed : 20.08 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.26), residues: 1122 helix: 2.60 (0.21), residues: 645 sheet: 1.66 (0.71), residues: 52 loop : -1.22 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 744 HIS 0.003 0.001 HIS K 647 PHE 0.011 0.001 PHE K 495 TYR 0.011 0.001 TYR D 37 ARG 0.003 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.06859 ( 892) hydrogen bonds : angle 3.04092 ( 2256) covalent geometry : bond 0.00489 (16421) covalent geometry : angle 0.55915 (23515) *********************** 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 177 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: C 73 ASN cc_start: 0.8292 (t160) cc_final: 0.8074 (t0) REVERT: E 59 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: E 131 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7827 (mtp85) REVERT: H 73 GLU cc_start: 0.9124 (tp30) cc_final: 0.8851 (tp30) REVERT: K 722 TYR cc_start: 0.8574 (m-80) cc_final: 0.8253 (m-80) REVERT: K 723 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6103 (mpt-90) REVERT: K 781 MET cc_start: 0.7334 (ptt) cc_final: 0.6906 (ptt) outliers start: 32 outliers final: 21 residues processed: 167 average time/residue: 0.3849 time to fit residues: 87.5605 Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 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 H residue 53 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 601 ILE 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 81 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.113339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079085 restraints weight = 27945.562| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.76 r_work: 0.2908 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16421 Z= 0.182 Angle : 0.555 10.710 23515 Z= 0.325 Chirality : 0.035 0.127 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.035 174.205 4691 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.11 % Allowed : 20.08 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.26), residues: 1122 helix: 2.62 (0.21), residues: 645 sheet: 1.70 (0.72), residues: 52 loop : -1.22 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 652 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.001 PHE K 495 TYR 0.013 0.001 TYR K 688 ARG 0.003 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.06473 ( 892) hydrogen bonds : angle 3.02972 ( 2256) covalent geometry : bond 0.00396 (16421) covalent geometry : angle 0.55506 (23515) *********************** 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 173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: E 59 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: E 131 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7734 (mtp85) REVERT: H 73 GLU cc_start: 0.9118 (tp30) cc_final: 0.8802 (tp30) REVERT: K 722 TYR cc_start: 0.8549 (m-80) cc_final: 0.8248 (m-80) REVERT: K 723 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6059 (mpt-90) REVERT: K 781 MET cc_start: 0.7370 (ptt) cc_final: 0.6971 (ptt) outliers start: 30 outliers final: 23 residues processed: 163 average time/residue: 0.3572 time to fit residues: 79.4790 Evaluate side-chains 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 H residue 53 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 502 ILE Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 601 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 103 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.111328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076912 restraints weight = 28251.484| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.64 r_work: 0.2825 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16421 Z= 0.214 Angle : 0.557 11.413 23515 Z= 0.327 Chirality : 0.036 0.131 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.017 174.578 4691 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.21 % Allowed : 20.08 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1122 helix: 2.58 (0.21), residues: 645 sheet: 1.67 (0.72), residues: 52 loop : -1.23 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 652 HIS 0.003 0.001 HIS E 113 PHE 0.012 0.001 PHE K 495 TYR 0.010 0.001 TYR D 37 ARG 0.003 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.06581 ( 892) hydrogen bonds : angle 3.00825 ( 2256) covalent geometry : bond 0.00480 (16421) covalent geometry : angle 0.55728 (23515) *********************** 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 174 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: E 59 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: E 131 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7739 (mtp85) REVERT: H 73 GLU cc_start: 0.9139 (tp30) cc_final: 0.8832 (tp30) REVERT: K 721 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8237 (mm) REVERT: K 722 TYR cc_start: 0.8575 (m-80) cc_final: 0.8235 (m-80) REVERT: K 723 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6162 (mpt-90) REVERT: K 781 MET cc_start: 0.7329 (ptt) cc_final: 0.6915 (ptt) outliers start: 31 outliers final: 24 residues processed: 163 average time/residue: 0.4438 time to fit residues: 98.9951 Evaluate side-chains 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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 553 THR Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 601 ILE 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 721 ILE 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 31 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.077559 restraints weight = 28213.655| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.63 r_work: 0.2845 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 16421 Z= 0.161 Angle : 0.548 12.197 23515 Z= 0.321 Chirality : 0.035 0.283 2667 Planarity : 0.004 0.040 1890 Dihedral : 28.999 174.763 4691 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.42 % Allowed : 20.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.26), residues: 1122 helix: 2.64 (0.21), residues: 645 sheet: 1.63 (0.72), residues: 52 loop : -1.20 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 744 HIS 0.003 0.001 HIS B 75 PHE 0.017 0.001 PHE K 495 TYR 0.011 0.001 TYR B 51 ARG 0.002 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.06034 ( 892) hydrogen bonds : angle 2.97527 ( 2256) covalent geometry : bond 0.00349 (16421) covalent geometry : angle 0.54793 (23515) *********************** 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 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8955 (mt) REVERT: A 133 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: B 52 GLU cc_start: 0.8334 (mp0) cc_final: 0.8133 (mm-30) REVERT: E 59 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8484 (pm20) REVERT: E 131 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7699 (mtp85) REVERT: H 73 GLU cc_start: 0.9138 (tp30) cc_final: 0.8832 (tp30) REVERT: K 721 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8226 (mm) REVERT: K 722 TYR cc_start: 0.8541 (m-80) cc_final: 0.8206 (m-80) REVERT: K 723 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6077 (mpt-90) REVERT: K 781 MET cc_start: 0.7316 (ptt) cc_final: 0.6895 (ptt) outliers start: 33 outliers final: 24 residues processed: 163 average time/residue: 0.3667 time to fit residues: 81.2225 Evaluate side-chains 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER 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 73 ASN Chi-restraints excluded: chain C residue 76 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 502 ILE Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 601 ILE 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 721 ILE 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 50 optimal weight: 0.0020 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.112871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078358 restraints weight = 28517.424| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.60 r_work: 0.2866 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16421 Z= 0.152 Angle : 0.538 12.593 23515 Z= 0.315 Chirality : 0.034 0.232 2667 Planarity : 0.004 0.039 1890 Dihedral : 28.964 175.096 4691 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.00 % Allowed : 20.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 1122 helix: 2.70 (0.21), residues: 645 sheet: 1.65 (0.73), residues: 52 loop : -1.16 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 652 HIS 0.003 0.001 HIS B 75 PHE 0.015 0.001 PHE K 495 TYR 0.010 0.001 TYR K 722 ARG 0.007 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05749 ( 892) hydrogen bonds : angle 2.95308 ( 2256) covalent geometry : bond 0.00321 (16421) covalent geometry : angle 0.53805 (23515) ********************** 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 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8937 (mt) REVERT: A 133 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: E 59 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: E 131 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7711 (mtp85) REVERT: K 721 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8236 (mm) REVERT: K 722 TYR cc_start: 0.8521 (m-80) cc_final: 0.8204 (m-80) REVERT: K 723 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6014 (mpt-90) REVERT: K 781 MET cc_start: 0.7289 (ptt) cc_final: 0.6915 (ptt) outliers start: 29 outliers final: 23 residues processed: 161 average time/residue: 0.3592 time to fit residues: 78.6715 Evaluate side-chains 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER 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 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 H residue 53 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 502 ILE Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 601 ILE 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 721 ILE 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 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.110237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.075410 restraints weight = 28235.566| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.56 r_work: 0.2796 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16421 Z= 0.268 Angle : 0.596 11.873 23515 Z= 0.347 Chirality : 0.039 0.185 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.099 174.621 4691 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.52 % Allowed : 20.39 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.26), residues: 1122 helix: 2.50 (0.21), residues: 646 sheet: 1.57 (0.71), residues: 52 loop : -1.27 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 652 HIS 0.003 0.001 HIS H 46 PHE 0.012 0.002 PHE B 61 TYR 0.011 0.002 TYR D 37 ARG 0.003 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.07398 ( 892) hydrogen bonds : angle 3.11788 ( 2256) covalent geometry : bond 0.00612 (16421) covalent geometry : angle 0.59571 (23515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10800.27 seconds wall clock time: 188 minutes 15.03 seconds (11295.03 seconds total)