Starting phenix.real_space_refine on Sat May 17 03:45:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2s_44113/05_2025/9b2s_44113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2s_44113/05_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_44113/05_2025/9b2s_44113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2s_44113/05_2025/9b2s_44113.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2s_44113/05_2025/9b2s_44113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2s_44113/05_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-5687/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: 9.35, per 1000 atoms: 0.60 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: 3.75 Conformation dependent library (CDL) restraints added in 1.3 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: 6.52 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: 7.27 Time building geometry restraints manager: 4.47 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 41.320 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.570 ------------------------------------------------------------------------------- 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 : 1.202 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 138 average time/residue: 0.4157 time to fit residues: 75.8357 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 : 1.523 ------------------------------------------------------------------------------- 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 = 0.113656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079333 restraints weight = 27982.300| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.80 r_work: 0.2911 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 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 0.06633 ( 892) hydrogen bonds : angle 3.26924 ( 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 : 1.268 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8157 (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: 0.8903 (t80) cc_final: 0.8454 (t80) REVERT: K 781 MET cc_start: 0.7273 (ptt) cc_final: 0.6845 (ptt) outliers start: 26 outliers final: 14 residues processed: 158 average time/residue: 0.3754 time to fit residues: 80.0336 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 : 1.236 ------------------------------------------------------------------------------- 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: 7.9990 chunk 15 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 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: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.113988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079846 restraints weight = 27852.872| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.77 r_work: 0.2919 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0964 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= 0.193 Angle : 0.542 7.025 23515 Z= 0.320 Chirality : 0.036 0.129 2667 Planarity : 0.004 0.038 1890 Dihedral : 29.003 176.320 4691 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.80 % Allowed : 19.57 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1122 helix: 2.59 (0.21), residues: 641 sheet: 1.35 (0.70), residues: 53 loop : -1.23 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 652 HIS 0.003 0.001 HIS K 651 PHE 0.014 0.001 PHE K 495 TYR 0.010 0.001 TYR D 37 ARG 0.003 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.06228 ( 892) hydrogen bonds : angle 3.03467 ( 2256) covalent geometry : bond 0.00427 (16421) covalent geometry : angle 0.54197 (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 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: E 59 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: K 747 TYR cc_start: 0.9076 (t80) cc_final: 0.8412 (t80) REVERT: K 781 MET cc_start: 0.7245 (ptt) cc_final: 0.6944 (ptt) outliers start: 27 outliers final: 17 residues processed: 158 average time/residue: 0.3476 time to fit residues: 75.0778 Evaluate side-chains 157 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 603 LEU 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: 10.0000 chunk 112 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.113031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078924 restraints weight = 27766.194| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.86 r_work: 0.2900 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16421 Z= 0.214 Angle : 0.556 7.953 23515 Z= 0.327 Chirality : 0.036 0.131 2667 Planarity : 0.004 0.039 1890 Dihedral : 29.046 175.752 4691 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.11 % Allowed : 19.77 % 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 (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: 2.60 (0.21), residues: 639 sheet: 1.43 (0.70), residues: 53 loop : -1.21 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 652 HIS 0.003 0.001 HIS K 647 PHE 0.011 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.002 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.06688 ( 892) hydrogen bonds : angle 3.05997 ( 2256) covalent geometry : bond 0.00481 (16421) covalent geometry : angle 0.55567 (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 169 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: E 59 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: E 131 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7737 (mtp85) REVERT: H 73 GLU cc_start: 0.9124 (tp30) cc_final: 0.8818 (tp30) REVERT: K 723 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6178 (mpt-90) outliers start: 30 outliers final: 21 residues processed: 159 average time/residue: 0.3586 time to fit residues: 77.4848 Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 74 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.113968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079827 restraints weight = 28068.947| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.75 r_work: 0.2922 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1069 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= 0.158 Angle : 0.544 9.946 23515 Z= 0.319 Chirality : 0.035 0.144 2667 Planarity : 0.004 0.039 1890 Dihedral : 29.020 175.982 4691 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 1.86 (0.26), residues: 1122 helix: 2.68 (0.21), residues: 639 sheet: 1.52 (0.72), residues: 53 loop : -1.16 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 652 HIS 0.005 0.001 HIS K 778 PHE 0.013 0.001 PHE K 495 TYR 0.013 0.001 TYR K 722 ARG 0.002 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.06125 ( 892) hydrogen bonds : angle 3.03265 ( 2256) covalent geometry : bond 0.00331 (16421) covalent geometry : angle 0.54415 (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 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: E 59 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: E 131 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7746 (mtp85) REVERT: H 73 GLU cc_start: 0.9126 (tp30) cc_final: 0.8788 (tp30) REVERT: K 723 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6030 (mpt-90) outliers start: 31 outliers final: 20 residues processed: 160 average time/residue: 0.3757 time to fit residues: 81.5242 Evaluate side-chains 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 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 119 THR Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 559 LEU 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 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: 0.9980 chunk 130 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.111648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077346 restraints weight = 27950.550| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.81 r_work: 0.2864 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16421 Z= 0.272 Angle : 0.592 9.723 23515 Z= 0.346 Chirality : 0.039 0.140 2667 Planarity : 0.004 0.039 1890 Dihedral : 29.121 174.072 4691 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.93 % Allowed : 19.57 % Favored : 76.50 % 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: 1.61 (0.26), residues: 1122 helix: 2.46 (0.21), residues: 645 sheet: 1.47 (0.71), residues: 53 loop : -1.31 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 652 HIS 0.004 0.001 HIS E 113 PHE 0.012 0.002 PHE B 61 TYR 0.012 0.001 TYR K 580 ARG 0.003 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.07556 ( 892) hydrogen bonds : angle 3.14758 ( 2256) covalent geometry : bond 0.00623 (16421) covalent geometry : angle 0.59233 (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: 38 poor density : 139 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8289 (pt0) REVERT: E 59 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: E 131 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7896 (mtp85) REVERT: K 722 TYR cc_start: 0.8536 (m-80) cc_final: 0.8299 (m-80) REVERT: K 723 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6309 (mpt-90) REVERT: K 781 MET cc_start: 0.7385 (ptt) cc_final: 0.6937 (ptt) outliers start: 38 outliers final: 28 residues processed: 166 average time/residue: 0.3598 time to fit residues: 81.2440 Evaluate side-chains 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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 H residue 119 THR 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 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: 9.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 = 0.112936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078822 restraints weight = 27942.973| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.84 r_work: 0.2890 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1083 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= 0.171 Angle : 0.568 11.166 23515 Z= 0.332 Chirality : 0.036 0.141 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.096 174.621 4691 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.31 % Allowed : 20.19 % Favored : 76.50 % 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: 2.52 (0.21), residues: 645 sheet: 1.53 (0.72), residues: 53 loop : -1.25 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 744 HIS 0.003 0.001 HIS K 746 PHE 0.013 0.001 PHE K 495 TYR 0.015 0.001 TYR K 688 ARG 0.004 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.06682 ( 892) hydrogen bonds : angle 3.11023 ( 2256) covalent geometry : bond 0.00364 (16421) covalent geometry : angle 0.56846 (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: 32 poor density : 141 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: E 59 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: K 721 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8198 (mm) REVERT: K 722 TYR cc_start: 0.8525 (m-80) cc_final: 0.8250 (m-80) REVERT: K 723 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6225 (mpt-90) REVERT: K 781 MET cc_start: 0.7350 (ptt) cc_final: 0.6942 (ptt) outliers start: 32 outliers final: 26 residues processed: 161 average time/residue: 0.3581 time to fit residues: 78.4083 Evaluate side-chains 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 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 G residue 110 ASN Chi-restraints excluded: chain H residue 28 LYS 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 650 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 103 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.112725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078536 restraints weight = 27815.143| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.81 r_work: 0.2895 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 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 : 0.005 0.040 16421 Z= 0.207 Angle : 0.562 11.108 23515 Z= 0.329 Chirality : 0.036 0.130 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.053 174.474 4691 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.83 % Allowed : 19.67 % Favored : 76.50 % 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: 1.70 (0.26), residues: 1122 helix: 2.53 (0.21), residues: 645 sheet: 1.51 (0.72), residues: 53 loop : -1.25 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 652 HIS 0.004 0.001 HIS K 647 PHE 0.014 0.001 PHE K 495 TYR 0.018 0.001 TYR K 667 ARG 0.002 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.06674 ( 892) hydrogen bonds : angle 3.05071 ( 2256) covalent geometry : bond 0.00465 (16421) covalent geometry : angle 0.56189 (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 178 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8957 (mt) REVERT: A 133 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: E 59 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: E 131 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7790 (mtp85) REVERT: K 721 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8234 (mm) REVERT: K 722 TYR cc_start: 0.8528 (m-80) cc_final: 0.8247 (m-80) REVERT: K 723 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6298 (mpt-90) REVERT: K 781 MET cc_start: 0.7316 (ptt) cc_final: 0.6947 (ptt) outliers start: 37 outliers final: 28 residues processed: 165 average time/residue: 0.3602 time to fit residues: 80.5823 Evaluate side-chains 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 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 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 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=1.50 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 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: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.113396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080000 restraints weight = 27875.562| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.59 r_work: 0.2894 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16421 Z= 0.171 Angle : 0.556 11.376 23515 Z= 0.325 Chirality : 0.035 0.127 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.041 174.639 4691 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: 1.76 (0.26), residues: 1122 helix: 2.56 (0.21), residues: 645 sheet: 1.66 (0.71), residues: 52 loop : -1.21 (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 0.013 0.001 PHE K 495 TYR 0.010 0.001 TYR D 37 ARG 0.002 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.06321 ( 892) hydrogen bonds : angle 3.03842 ( 2256) covalent geometry : bond 0.00368 (16421) covalent geometry : angle 0.55648 (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 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: E 59 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: K 721 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8201 (mm) REVERT: K 722 TYR cc_start: 0.8508 (m-80) cc_final: 0.8217 (m-80) REVERT: K 723 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6288 (mpt-90) REVERT: K 781 MET cc_start: 0.7310 (ptt) cc_final: 0.6936 (ptt) outliers start: 32 outliers final: 26 residues processed: 159 average time/residue: 0.3547 time to fit residues: 77.0529 Evaluate side-chains 166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 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 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 50 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079881 restraints weight = 28158.868| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.71 r_work: 0.2904 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16421 Z= 0.164 Angle : 0.553 11.910 23515 Z= 0.323 Chirality : 0.035 0.185 2667 Planarity : 0.004 0.039 1890 Dihedral : 29.019 174.813 4691 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.31 % Allowed : 19.77 % Favored : 76.92 % 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: 1.82 (0.26), residues: 1122 helix: 2.61 (0.21), residues: 645 sheet: 1.67 (0.72), residues: 52 loop : -1.18 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 652 HIS 0.005 0.001 HIS K 647 PHE 0.013 0.001 PHE K 495 TYR 0.013 0.001 TYR B 51 ARG 0.002 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.06129 ( 892) hydrogen bonds : angle 3.00746 ( 2256) covalent geometry : bond 0.00348 (16421) covalent geometry : angle 0.55312 (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 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8940 (mt) REVERT: A 63 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8294 (mmp80) REVERT: A 133 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: E 59 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: E 131 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7750 (mtp85) REVERT: K 722 TYR cc_start: 0.8501 (m-80) cc_final: 0.8196 (m-80) REVERT: K 723 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6231 (mpt-90) REVERT: K 781 MET cc_start: 0.7293 (ptt) cc_final: 0.6918 (ptt) outliers start: 32 outliers final: 25 residues processed: 157 average time/residue: 0.3607 time to fit residues: 76.5331 Evaluate side-chains 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ARG 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 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 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 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 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: 0.7980 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.110486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075697 restraints weight = 28264.978| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.57 r_work: 0.2806 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16421 Z= 0.241 Angle : 0.581 11.090 23515 Z= 0.340 Chirality : 0.038 0.135 2667 Planarity : 0.004 0.040 1890 Dihedral : 29.101 173.361 4691 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.21 % Allowed : 20.19 % 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: 1.69 (0.26), residues: 1122 helix: 2.50 (0.21), residues: 646 sheet: 1.65 (0.71), residues: 52 loop : -1.25 (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 0.001 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 0.07134 ( 892) hydrogen bonds : angle 3.08547 ( 2256) covalent geometry : bond 0.00548 (16421) covalent geometry : angle 0.58062 (23515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9383.60 seconds wall clock time: 162 minutes 15.86 seconds (9735.86 seconds total)